MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Acta Crystallographica Section D' source. Thu, 09 Feb 2012 13:38:23 +0100 http://www.medworm.com/index.php?rid=5603659&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fme0456 (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5603659 Tue, 17 Jan 2012 05:00:00 +0100 5603659 http://www.medworm.com/index.php?rid=5603658&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5245 In this study, CotA laccase has been used as a model system to assess the role of Asp116 in the reduction process of dioxygen to water. The crystal structures of three distinct mutants, D116E, D116N and D116A, produced by site-saturation mutagenesis have been determined. In addition, theoretical calculations have provided further support for a role of this residue in the protonation events. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5603658 Tue, 17 Jan 2012 05:00:00 +0100 5603658 http://www.medworm.com/index.php?rid=5603657&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5240 In Bacillus subtilis, the arabinose repressor AraR negatively controls the expression of genes in the metabolic pathway of arabinose-containing polysaccharides. The protein is composed of two domains of different phylogenetic origin and function: an N-terminal DNA-binding domain belonging to the GntR family and a C-terminal effector-binding domain that shows similarity to members of the GalR/LacI family. The crystal structure of the C-terminal effector-binding domain of AraR in complex with the effector l-arabinose has been determined at 2.2 Å resolution. The l-arabinose binding affinity was characterized by isothermal titration calorimetry and differential scanning fluorimetry; the Kd value was 8.4 ± 0.4 µM. The effect of l-arabinose on the protein oligomeric state was investigate... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5603657 Tue, 17 Jan 2012 05:00:00 +0100 5603657 http://www.medworm.com/index.php?rid=5603656&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5241 Global radiation damage to 19 thaumatin crystals has been measured using dose rates from 3 to 680 kGy s−1. At room temperature damage per unit dose appears to be roughly independent of dose rate, suggesting that the timescales for important damage processes are less than ∼1 s. However, at T = 260 K approximately half of the global damage manifested at dose rates of ∼10 kGy s−1 can be outrun by collecting data at 680 kGy s−1. Appreciable sample-to-sample variability in global radiation sensitivity at fixed dose rate is observed. This variability cannot be accounted for by errors in dose calculation, crystal slippage or the size of the data sets in the assay. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5603656 Tue, 17 Jan 2012 05:00:00 +0100 5603656 http://www.medworm.com/index.php?rid=5592670&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdw5005 Octahaem cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens (TvNiR), like the previously characterized pentahaem nitrite reductases (NrfAs), catalyzes the six-electron reductions of nitrite to ammonia and of sulfite to sulfide. The active site of both TvNiR and NrfAs is formed by the lysine-coordinated haem and His, Tyr and Arg residues. The distinguishing structural feature of TvNiR is the presence of a covalent bond between the CE2 atom of the catalytic Tyr303 and the S atom of Cys305, which might be responsible for the higher nitrite reductase activity of TvNiR compared with NrfAs. In the present study, a new modified form of the enzyme (TvNiRb) that contains an additional covalent bond between Tyr303 CE1 and Gln360 CG is reported. Structures of TvNiRb in complexe... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5592670 Fri, 13 Jan 2012 05:00:00 +0100 5592670 http://www.medworm.com/index.php?rid=5592669&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdw5007 Post-translational modifications involving ubiquitin regulate a wide range of biological processes including protein degradation, responses to DNA damage and immune signalling. Ubiquitin polymerizes into chains which may contain eight different linkage types; the ubiquitin C-terminal glycine can link to one of the seven lysine residues or the N-terminal amino group of methionine in the distal ubiquitin molecule. The latter head-to-tail linkage type, referred to as a linear ubiquitin chain, is involved in NF-κB activation through specific interactions with NF-κB essential modulator (NEMO). Here, a crystal structure of linear diubiquitin at a resolution of 2.2 Å is reported. Although the two ubiquitin moieties do not interact with each other directly, the overall structure adopts a comp... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5592669 Fri, 13 Jan 2012 05:00:00 +0100 5592669 http://www.medworm.com/index.php?rid=5592668&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fcb5004 Kif7, a member of the kinesin 4 superfamily, is implicated in a variety of diseases including Joubert, hydrolethalus and acrocallosal syndromes. It is also involved in primary cilium formation and the Hedgehog signalling pathway and may play a role in cancer. Its activity is crucial for embryonic development. Kif7 and Kif27, a closely related kinesin in the same subfamily, are orthologues of the Drosophila melanogaster kinesin-like protein Costal-2 (Cos2). In vertebrates, they work together to fulfil the role of the single Cos2 gene in Drosophila. Here, the high-resolution structure of the human Kif7 motor domain is reported and is compared with that of conventional kinesin, the founding member of the kinesin superfamily. These data are a first step towards structural characterization o... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5592668 Fri, 13 Jan 2012 05:00:00 +0100 5592668 http://www.medworm.com/index.php?rid=5592667&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmh5051 Evectin-2 is a recycling endosomal protein involved in retrograde transport. Its primary sequence contains an N-terminal pleckstrin homology (PH) domain and a C-terminal hydrophobic region. The PH domain of evectin-2 can specifically bind phosphatidylserine, which is enriched in recycling endosomes, and plays an essential role in retrograde transport from recycling endosomes to the trans-Golgi network. The structure of human evectin-2 PH domain in complex with O-phospho-l-serine has recently been reported and demonstrates how the head group of phosphatidylserine is recognized. However, it was not possible to elucidate from the structure why evectin-2 cannot bind phosphatidic acid or phosphatidylethanolamine, which share a common moiety with phosphatidylserine. Here, the crystal structure a... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5592667 Fri, 13 Jan 2012 05:00:00 +0100 5592667 http://www.medworm.com/index.php?rid=5568539&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fxb5042 The outer membrane protein complex (BAM complex) plays an important role in outer membrane protein (OMP) assembly in Escherichia coli. The BAM complex includes the integral β-barrel protein BamA as well as four lipoproteins: BamB, BamC, BamD and BamE. One of these lipoproteins, BamD, is essential for the survival of Escherichia coli. The structure of BamD at 2.6 Å resolution shows that this lipoprotein is composed of ten α-helices that form five tetratricopeptide-repeat (TPR) motifs. The arrangement of the BamD motifs is similar to that in the periplasmic part of BamA. One of the ten α-helices, α10, which has been shown to be important for the assembly of the BAM complex, is located in the very C-terminal region of BamD. A deep groove between TPR domains 4 and 5 is also observed. ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5568539 Sat, 07 Jan 2012 00:43:34 +0100 5568539 http://www.medworm.com/index.php?rid=5568543&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmh5053 A number of pathogens, including the causative agents of tuberculosis and malaria, synthesize the essential isoprenoid precursor isopentenyl diphosphate via the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway rather than the classical mevalonate pathway that is found in humans. As part of a structure-based drug-discovery program against tuberculosis, DXR, the enzyme that carries out the second step in the MEP pathway, has been investigated. This enzyme is the target for the antibiotic fosmidomycin and its active acetyl derivative FR-900098. The structure of DXR from Mycobacterium tuberculosis in complex with FR-900098, manganese and the NADPH cofactor has been solved and refined. This is a new crystal form that diffracts to a higher resolution than any other DXR complex reported to date.... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5568543 Fri, 06 Jan 2012 05:00:00 +0100 5568543 http://www.medworm.com/index.php?rid=5568542&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fkw5037 The first crystal structure of a member of peptaibol antibiotic subfamily 4, trichovirin I-4A (14 residues), has been determined by direct methods and refined at atomic resolution. The monoclinic unit cell has two molecules in the asymmetric unit. Both molecules assume a 310 right-handed helical conformation and are significantly bent. The molecules pack loosely along the crystallographic twofold axis, forming two large tunnels between symmetry-related molecules in which no ordered solvent could be located. Carbonyl O atoms which are not involved in intramolecular hydrogen bonding participate in close van der Waals interactions with apolar groups. The necessary amphipathicity for biological activity of peptaibols is not realised in the crystal structure. Hence, a structural change of trich... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5568542 Fri, 06 Jan 2012 05:00:00 +0100 5568542 http://www.medworm.com/index.php?rid=5568541&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5239 The crystal structure of an RNA/DNA hybrid dodecamer, r(5′-uaaaagaaaagg):d(5′-CCTTTTCTTTTA), which contains three-quarters of the polypurine tract (PPT) sequence of the HIV RNA genome is reported. The hybrid structure was determined at 1.6 Å resolution and was found to have the A-form conformation. However, the presence of alternate conformations along the RNA template strand indicated increased flexibility of the PPT sequence. Two segments (at nucleotides 1–2 and 6–8) of the RNA chain have two conformations exhibiting differences in torsion and pseudorotation angles. For conformation I(1–2, 6–8), 25% of the RNA sugars have the C2′-exo pucker and the rest have the expected C3′-endo pucker. The II1–2 and II6–8 conformations of the RNA strand have one sugar with the ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5568541 Fri, 06 Jan 2012 05:00:00 +0100 5568541 http://www.medworm.com/index.php?rid=5568540&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmn5007 Rhizobial NodZ α1,6-fucosyltransferase (α1,6-FucT) catalyzes the transfer of the fucose (Fuc) moiety from guanosine 5′-diphosphate-β-l-fucose to the reducing end of the chitin oligosaccharide core during Nod-factor (NF) biosynthesis. NF is a key signalling molecule required for successful symbiosis with a legume host for atmospheric nitrogen fixation. To date, only two α1,6-FucT structures have been determined, both without any donor or acceptor molecule that could highlight the structural background of the catalytic mechanism. Here, the first crystal structures of α1,6-FucT in complex with its substrate GDP-Fuc and with GDP, which is a byproduct of the enzymatic reaction, are presented. The crystal of the complex with GDP-Fuc was obtained through soaking of native NodZ crystals ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5568540 Fri, 06 Jan 2012 05:00:00 +0100 5568540 http://www.medworm.com/index.php?rid=5512080&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Frr5004 α-Helices are peculiar atomic arrangements characterizing protein structures. Their occurrence can be used within crystallographic methods as minimal a priori information to drive the phasing process towards solution. Recently, brute-force methods have been developed which search for all possible positions of α-helices in the crystal cell by molecular replacement and explore all of them systematically. Knowing the α-helix orientations in advance would be a great advantage for this kind of approach. For this purpose, a fully automatic procedure to find α-helix orientations within the Patterson map has been developed. The method is based on Fourier techniques specifically addressed to the identification of helical shapes and operating on Patterson maps described in spherical coordinates.... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5512080 Sat, 17 Dec 2011 06:56:51 +0100 5512080 http://www.medworm.com/index.php?rid=5512089&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fpf0088 (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5512089 Wed, 14 Dec 2011 05:00:00 +0100 5512089 http://www.medworm.com/index.php?rid=5512088&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5192 Staphylococcus aureus is an opportunistic Gram-positive bacterium which causes a wide variety of diseases ranging from minor skin infections to potentially fatal conditions such as pneumonia, meningitis and septicaemia. The pathogen is a leading cause of nosocomial acquired infections, a problem that is exacerbated by the existence of methicillin- and glycopeptide antibiotic-resistant strains which can be challenging to treat. Alanine racemase (Alr) is a pyridoxal-5′-phosphate-dependent enzyme which catalyzes reversible racemization between enantiomers of alanine. As d-alanine is an essential component of the bacterial cell-wall peptidoglycan, inhibition of Alr is lethal to prokaryotes. Additionally, while ubiquitous amongst bacteria, this enzyme is absent in humans and most eukaryotes... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5512088 Fri, 09 Dec 2011 05:00:00 +0100 5512088 http://www.medworm.com/index.php?rid=5512087&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fwd5164 Both crystallization and cryoprotection are often bottlenecks for high-resolution X-ray structure determination of macromolecules. Methylamine osmolytes are known stabilizers of protein structure. One such osmolyte, trimethylamine N-oxide (TMAO), has seen occasional use as an additive to improve macromolecular crystal quality and has recently been shown to be an effective cryoprotective agent for low-temperature data collection. Here, TMAO and the related osmolytes sarcosine and betaine are investigated as primary precipitating agents for protein crystal growth. Crystallization experiments were undertaken with 14 proteins. Using TMAO, seven proteins crystallized in a total of 13 crystal forms, including a new tetragonal crystal form of trypsin. The crystals diffracted well, and eight of th... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5512087 Fri, 09 Dec 2011 05:00:00 +0100 5512087 http://www.medworm.com/index.php?rid=5512086&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgx5197 In this study, a phasing strategy is developed for the scenario in which a crystal is grown from a mixture in which anomalous scattering atoms have been incorporated into only one enantiomeric form of the protein molecule in an otherwise racemic mixture. The structure of a protein crystallized in such a quasi-racemic form has been determined in previous work [Pentelute et al. (2008), J. Am. Chem. Soc. 130, 9695–9701] using the multiwavelength anomalous dispersion (MAD) method. Here, it is shown that although the phases from such a crystal are not strictly centric, their approximate centricity provides a powerful way to break the phase ambiguity that ordinarily arises when using the single-wavelength anomalous dispersion (SAD) method. It is shown that good phases and electron-density map... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5512086 Fri, 09 Dec 2011 05:00:00 +0100 5512086 http://www.medworm.com/index.php?rid=5512085&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmv5050 The region spanning residues 95–146 of the rotavirus nonstructural protein NSP4 from the asymptomatic human strain ST3 has been purified and crystallized and diffraction data have been collected to a resolution of 2.6 Å. Several attempts to solve the structure by the molecular-replacement method using the available tetrameric structures of this domain were unsuccessful despite a sequence identity of 73% to the already known structures. A more systematic approach with a dimer as the search model led to an unexpected pentameric structure using the program Phaser. The various steps involved in arriving at this molecular-replacement solution, which unravelled a case of subtle variation between different oligomeric states unknown at the time of solving the structure, are presented in this ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5512085 Fri, 09 Dec 2011 05:00:00 +0100 5512085 http://www.medworm.com/index.php?rid=5512084&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fwd5161 The data-collection parameters used in a macromolecular diffraction experiment have a strong impact on data quality. A careful choice of parameters leads to better data and can make the difference between success and failure in phasing attempts, and will also result in a more accurate atomic model. The selection of parameters has to account for the application of the data in various phasing methods or high-resolution refinement. Furthermore, experimental factors such as crystal characteristics, available experiment time and the properties of the X-ray source and detector have to be considered. For many years, CCD detectors have been the prevalent type of detectors used in macromolecular crystallography. Recently, hybrid pixel X-ray detectors that operate in single-photon-counting mode hav... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5512084 Fri, 09 Dec 2011 05:00:00 +0100 5512084 http://www.medworm.com/index.php?rid=5512083&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5184 In this report, it is shown that a rapid data-collection strategy can be a valuable alternative to longer data-collection times in appropriate cases. Comparison of perdeuterated rubredoxin structures refined against neutron data sets collected over hours and up to 5 d shows that rapid neutron data collection in just 14 h is sufficient to provide the positions of 269 D atoms without ambiguity. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5512083 Fri, 09 Dec 2011 05:00:00 +0100 5512083 http://www.medworm.com/index.php?rid=5512082&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgm5019 Bach2 is a transcriptional repressor that is expressed during specific stages of B-cell development and in neuronal cells. It plays a critical role in modulating class-switch recombination during the differentiation of mature B cells to antibody-secreting plasma cells and it is also an important regulator of apoptotic responses to oxidative stress. Bach2 has been implicated both as an oncogene and as a tumour suppressor in human malignancy. The interaction of Bach2 with its target genes is mediated via its basic leucine-zipper region, whereas the N-terminal POZ domain recruits transcriptional co-repressors and class II histone deacetylases. Here, the crystal structure of the human Bach2 POZ domain is reported at 2.1 Å resolution. The Bach2 POZ-domain dimer resembles the POZ-domain dim... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5512082 Fri, 09 Dec 2011 05:00:00 +0100 5512082 http://www.medworm.com/index.php?rid=5512081&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fwd5167 β-Secretase (β-site amyloid precursor protein-cleaving enzyme 1; BACE1) is a transmembrane aspartic protease that cleaves the β-amyloid precursor protein en route to generation of the amyloid β-peptide (Aβ) that is believed to be responsible for the Alzheimer's disease amyloid cascade. It is thus a prime target for the development of inhibitors which may serve as drugs in the treatment and/or prevention of Alzheimer's disease. In the following determination of the crystal structures of both apo and complexed BACE1, structural analysis of all crystal structures of BACE1 deposited in the PDB and molecular dynamics (MD) simulations of monomeric and `dimeric' BACE1 were used to study conformational changes in the active-site region of the enzyme. It was observed that a flap able to cover... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5512081 Fri, 09 Dec 2011 05:00:00 +0100 5512081 http://www.medworm.com/index.php?rid=5453897&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Frr5003 Cyclic diguanosine monophosphate (c-di-GMP) is a key signalling molecule involved in regulating many important biological functions in bacteria. The synthesis of c-di-GMP is catalyzed by the GGDEF-domain-containing diguanylate cyclase (DGC), the activity of which is regulated by the binding of product at the allosteric inhibitory (I) site. However, a significant number of GGDEF domains lack the RxxD motif characteristic of the allosteric I site. Here, the structure of XCC4471GGDEF, the GGDEF domain of a DGC from Xanthomonas campestris, in complex with c-di-GMP has been solved. Unexpectedly, the structure of the complex revealed a GGDEF-domain dimer cross-linked by two molecules of c-di-GMP at the strongly conserved active sites. In the complex (c-di-GMP)2 adopts a novel partially interca... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5453897 Tue, 29 Nov 2011 07:18:29 +0100 5453897 http://www.medworm.com/index.php?rid=5453902&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgx9191 A correction is made to a citation in the article by Suzuki et al. (2011) [Acta Cryst. D67, 894–901]. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5453902 Fri, 18 Nov 2011 05:00:00 +0100 5453902 http://www.medworm.com/index.php?rid=5453901&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5190 Many different proteins utilize the chemical energy provided by the cofactor adenosine triphosphate (ATP) for their proper function. A number of structures in the Protein Data Bank (PDB) contain adenosine 5′-(β,γ-imido)triphosphate (AMPPNP), a nonhydrolysable analog of ATP in which the bridging O atom between the two terminal phosphate groups is substituted by the imido function. Under mild conditions imides do not have acidic properties and thus the imide nitrogen should be protonated. However, an analysis of protein structures containing AMPPNP reveals that the imide group is deprotonated in certain complexes if the negative charges of the phosphate moieties in AMPPNP are in part neutralized by coordinating divalent metals or a guanidinium group of an arginine. (Source: Acta Crystall... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5453901 Fri, 18 Nov 2011 05:00:00 +0100 5453901 http://www.medworm.com/index.php?rid=5453900&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmn5005 Lip is a membrane-bound lipoprotein and a core component of the type VI secretion system found in Gram-negative bacteria. The structure of a Lip construct (residues 29–176) from Serratia marcescens (SmLip) has been determined at 1.92 Å resolution. Experimental phases were derived using a single-wavelength anomalous dispersion approach on a sample cocrystallized with iodide. The membrane localization of the native protein was confirmed. The structure is that of the globular domain lacking only the lipoprotein signal peptide and the lipidated N-terminus of the mature protein. The protein fold is dominated by an eight-stranded β-sandwich and identifies SmLip as a new member of the transthyretin family of proteins. Transthyretin and the only other member of the family fold, 5-hydroxy... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5453900 Fri, 18 Nov 2011 05:00:00 +0100 5453900 http://www.medworm.com/index.php?rid=5453899&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmv5049 The three-dimensional structure of indole-3-glycerol phosphate synthase (IGPS) from the thermophilic bacterium Thermus thermophilus HB8 (TtIGPS) has been determined at 1.8 Å resolution. The structure adopts a typical (β/α)8-barrel fold with an additional N-terminal extension of 46 residues. A detailed comparison of the crystal structure of TtIGPS with available structures of IGPS from the archaeon Sulfolobus solfataricus (SsIGPS) and the bacteria Thermotoga maritima (TmIGPS) and Escherichia coli (EcIGPS) has been performed. Although the overall folds of the proteins are the same, there are differences in amino-acid composition, structural rigidity, ionic features and stability clusters which may account for the high thermostability of the hyperthermophilic (SsIGPS and TmIGPS) and the... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5453899 Fri, 18 Nov 2011 05:00:00 +0100 5453899 http://www.medworm.com/index.php?rid=5453898&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdw5003 Human fructose-1,6-bisphosphatase is an allosteric enzyme that is regulated by different ligands. There are only two known isozymes in human tissues: the liver isozyme (the key enzyme of gluconeogenesis), which is regulated by fructose 2,6-bisphosphate, and its muscle counterpart (participating in glycogen synthesis), which is regulated by calcium ions. AMP, which is an allosteric inhibitor of both isozymes, inhibits the muscle isozyme with an I0.5 that is 35–100 times lower than for the liver isozyme and the reason for this difference remains obscure. In studies aiming at an explanation of the main differences in the regulation of the two isozymes, it has been shown that only one residue, in position 69, regulates the sensitivity towards calcium ions. As a consequence of this finding, ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5453898 Fri, 18 Nov 2011 05:00:00 +0100 5453898 http://www.medworm.com/index.php?rid=5396476&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5187 Bacterial flagella are driven by an ion influx through the peptidoglycan (PG)-tethered MotA/MotB stator. Stator precomplexes assemble in the membrane and remain inactive until they incorporate into the motor, upon which MotA/MotB changes conformation. The nature of this change and the mechanism of inhibition of the PG-binding and ion-conducting activities of the precomplexes are unknown. Here, the structural analysis of a series of N-terminally truncated MotB fragments is presented, the mechanism of inhibition by the linker is identified and the structural basis for the formation of the PG-binding-competent open-channel MotA/MotB conformation via a mechanism that entails linker unfolding and rotational displacement of MotB transmembrane helices is uncovered. (Source: Acta Crystallographic... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5396476 Fri, 11 Nov 2011 07:29:34 +0100 5396476 http://www.medworm.com/index.php?rid=5396481&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fme0464 The affiliation of one of the authors of Abdulmalik et al. (2011) [Acta Cryst. D67, 920–928] is corrected. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5396481 Sat, 05 Nov 2011 04:00:00 +0100 5396481 http://www.medworm.com/index.php?rid=5396480&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmh5048 β-Propellers are widely utilized in nature as recognition modules. The well conserved β-propeller fold exhibits a high degree of functional diversity, which is probably accomplished through variations in the surface properties of the proteins. Little is known about the interactions between β-propeller proteins and nucleic acids. In the present study, it has been found that the bacterial β-propeller protein YncE binds to DNA. Crystal structures of YncE in the free form and complexed with DNA revealed that the surface region of YncE corresponding to the `canonical' substrate-binding site forms essential contacts with DNA. A single DNA base within a single-stranded DNA region is trapped in the hydrophobic pocket located within the central channel of the β-propeller protein. These data pr... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5396480 Sat, 05 Nov 2011 04:00:00 +0100 5396480 http://www.medworm.com/index.php?rid=5396479&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5242 Human transthyretin (TTR) is a homotetrameric protein that is responsible for the formation of amyloid in patients with familiar amyloidotic polyneuropathy (FAP), familiar amyloidotic cardiomyopathy (FAC) and senile systemic amyloidosis (SSA). Amyloid fibrils are characterized by a cross-β structure. However, details of how TTR monomers are organized to form such an assembly remain unknown. The effect of Zn2+ in increasing TTR L55P amyloidogenecity has been reported. Crystals of the TTR L55P–Zn2+ complex were grown under conditions similar to those leading to higher amyloidogenic potential of the variant protein and the three-dimensional structure of the complex was determined by X-ray crystallography. Two different tetrahedral Zn2+-binding sites were identified: one cross-links two te... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5396479 Sat, 05 Nov 2011 04:00:00 +0100 5396479 http://www.medworm.com/index.php?rid=5396478&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdw5006 Ribosomal protein L1 consists of two domains connected by two oppositely directed fragments of the polypeptide chain in a hinge-resembling fashion. The domain arrangement determines the overall shape of the protein, corresponding to an open or a closed conformation. Ribosomal L1 proteins from archaea demonstrate the open conformation in both isolated and RNA-bound forms. RNA-free ribosomal L1 proteins from bacteria display the closed conformation, whereas in complex with RNA these proteins exist in an open conformation similar to their archaeal counterparts. Analysis of all available L1 amino-acid sequences shows that in comparison to the archaeal proteins, the bacterial proteins possess an extra residue in one of the two interdomain fragments which could be responsible for their closed c... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5396478 Sat, 05 Nov 2011 04:00:00 +0100 5396478 http://www.medworm.com/index.php?rid=5396477&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5201 Tuberculosis (TB) is a major infectious disease that accounts for over 1.7 million deaths every year. Mycobacterium tuberculosis, the causative agent of tuberculosis, enters the human host by the inhalation of infectious aerosols. Additionally, one third of the world's population is likely to be infected with latent TB. The incidence of TB is on the rise owing in part to the emergence of multidrug-resistant strains. As a result, there is a growing need to focus on novel M. tuberculosis enzyme targets. M. tuberculosis triosephosphate isomerase (MtTPI) is an essential enzyme for gluconeogenetic pathways, making it a potential target for future therapeutics. In order to determine its structure, the X-ray crystal structure of MtTPI has been determined, as well as that of MtTPI bound with a re... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5396477 Sat, 05 Nov 2011 04:00:00 +0100 5396477 http://www.medworm.com/index.php?rid=5330227&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Flv5014 Mason–Pfizer monkey virus (M-PMV), a D-type retrovirus assembling in the cytoplasm, causes simian acquired immunodeficiency syndrome (SAIDS) in rhesus monkeys. Its pepsin-like aspartic protease (retropepsin) is an integral part of the expressed retroviral polyproteins. As in all retroviral life cycles, release and dimerization of the protease (PR) is strictly required for polyprotein processing and virion maturation. Biophysical and NMR studies have indicated that in the absence of substrates or inhibitors M-PMV PR should fold into a stable monomer, but the crystal structure of this protein could not be solved by molecular replacement despite countless attempts. Ultimately, a solution was obtained in mr-rosetta using a model constructed by players of the online protein-folding game Foldi... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5330227 Wed, 19 Oct 2011 17:29:13 +0100 5330227 http://www.medworm.com/index.php?rid=5330237&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Frr5006 Suv3 is a helicase that is involved in efficient turnover and surveillance of RNA in eukaryotes. In vitro studies show that human Suv3 (hSuv3) in complex with human polynucleotide phosphorylase has RNA degradosome activity. The enzyme is mainly localized in mitochondria, but small fractions are found in cell nuclei. Here, two X-ray crystallographic structures of human Suv3 in complex with AMPPNP, a nonhydrolysable analog of ATP, and with a short five-nucleotide strand of RNA are presented at resolutions of 2.08 and 2.9 Å, respectively. The structure of the enzyme is very similar in the two complexes and consists of four domains. Two RecA-like domains form the tandem typical of all helicases from the SF2 superfamily which together with the C-terminal all-helical domain makes a ring struc... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5330237 Wed, 19 Oct 2011 04:00:00 +0100 5330237 http://www.medworm.com/index.php?rid=5330236&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgx5190 The methodology of protein crystallography provides a number of potential bottlenecks. Here, an approach to successful structure solution of a difficult heterodimeric complex of two human proteins, paraspeckle component 1 (PSPC1) and non-POU domain-containing octamer-binding protein (NONO), that are involved in gene regulation and the structural integrity of nuclear bodies termed paraspeckles is described. With the aid of bioinformatic predictions and systematic screening of a panel of constructs, bottlenecks of protein solubility, crystallization, crystal quality and crystallographic pseudosymmetry were overcome in order to produce crystals that ultimately revealed the structure. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5330236 Wed, 19 Oct 2011 04:00:00 +0100 5330236 http://www.medworm.com/index.php?rid=5330235&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5199 The acquisition of ferrous iron in prokaryotes is achieved by the G-protein-coupled membrane protein FeoB. This protein possesses a large C-terminal membrane-spanning domain preceded by two soluble cytoplasmic domains that are together termed `NFeoB'. The first of these soluble domains is a GTPase domain (G-domain), which is then followed by an entirely α-helical domain. GTP hydrolysis by the G-domain is essential for iron uptake by FeoB, and various NFeoB mutant proteins from Streptococcus thermophilus have been constructed. These mutations investigate the role of conserved amino acids from the protein's critical Switch regions. Five crystal structures of these mutant proteins have been determined. The structures of E66A and E67A mutant proteins were solved in complex with nonhydrolyzabl... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5330235 Wed, 19 Oct 2011 04:00:00 +0100 5330235 http://www.medworm.com/index.php?rid=5330234&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fwd5162 It is demonstrated that the crystallographic models of macromolecules may appear to diverge upon extended refinement against experimental data. Two regimes are identified for this phenomenon. Firstly, at higher resolution the apparent instability of the resulting models is shown to originate from the relatively small fraction of disordered atoms present in the initial model. Secondly, at lower resolution additional refinement instability may arise from insufficiently strong geometry restraints. The convergence of crystallographic refinement is proposed as one of the possible criteria in selecting a specific refinement strategy and in model validation. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5330234 Wed, 19 Oct 2011 04:00:00 +0100 5330234 http://www.medworm.com/index.php?rid=5330233&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5236 In the past, weighting between the sum of chemical and data-based targets in macromolecular crystallographic refinement was based on comparing the gradients or Hessian diagonal terms of the two potential functions. Here, limitations of this scheme are demonstrated, especially in the context of a maximum-likelihood target that is inherently weighted by the model and data errors. In fact, the congruence between the maximum-likelihood target and a chemical potential based on polarizable atomic multipole electrostatics evaluated with Ewald summation has opened the door to a transferable static weight. An optimal static weight is derived from first principles and is demonstrated to be transferable across a broad range of data resolutions in the context of a recent implementation of X-ray cryst... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5330233 Wed, 19 Oct 2011 04:00:00 +0100 5330233 http://www.medworm.com/index.php?rid=5330232&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgx5193 The nucleoside kinase (NK) from the mesophilic Gram-negative bacterium Burkholderia thailandensis (BthNK) is a member of the phosphofructokinase B (Pfk-B) family and catalyzes the Mg2+- and ATP-dependent phosphorylation of a broad range of nucleosides such as inosine (INO), adenosine (ADO) and mizoribine (MZR). BthNK is currently used in clinical practice to measure serum MZR levels. Here, crystal structures of BthNK in a ligand-free form and in complexes with INO, INO–ADP, MZR–ADP and AMP–Mg2+–AMP are described. The typical homodimeric architecture of Pfk-B enzymes was detected in three distinct conformational states: an asymmetric dimer with one subunit in an open conformation and the other in a closed conformation (the ligand-free form), a closed conformation (the binary comple... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5330232 Wed, 19 Oct 2011 04:00:00 +0100 5330232 http://www.medworm.com/index.php?rid=5330231&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5237 The microneme protein SML-2 is a member of a small family of galactose-specific lectins that play a role during host-cell invasion by the apicomplexan parasite Sarcocystis muris. The structures of apo SML-2 and the 1-thio-β-d-galactose–SML-2 complex were determined at 1.95 and 2.1 Å resolution, respectively, by sulfur-SAD phasing. Highly elongated dimers are formed by PAN-domain tandems in the protomer, bearing the galactose-binding cavities at the distal apple-like domains. The detailed structure of the binding site in SML-2 explains the high specificity of galactose-endgroup binding and the broader specificity of the related Toxoplasma gondii protein TgMIC4 towards galactose and glucose. A large buried surface of highly hydrophobic character and 24 intersubunit hydrogen bonds stab... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5330231 Wed, 19 Oct 2011 04:00:00 +0100 5330231 http://www.medworm.com/index.php?rid=5330230&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Frr5005 Glucokinase (GK) catalyses the formation of glucose 6-phosphate from glucose and ATP. A specific feature of GK amongst hexokinases is that it can cycle between active and inactive conformations as a function of glucose concentration, resulting in a unique positive kinetic cooperativity with glucose, which turns GK into a unique key sensor of glucose metabolism, notably in the pancreas. GK is a target of antidiabetic drugs aimed at the activation of GK activity, leading to insulin secretion. Here, the first structures of a GK–glucose complex without activator, of GK–glucose–AMP-PNP and of GK–glucose–AMP-PNP with a bound activator are reported. All these structures are extremely similar, thus demonstrating that binding of GK activators does not result in conformational changes of t... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5330230 Wed, 19 Oct 2011 04:00:00 +0100 5330230 http://www.medworm.com/index.php?rid=5330229&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fea5150 Vanillin has previously been studied clinically as an antisickling agent to treat sickle-cell disease. In vitro investigations with pyridyl derivatives of vanillin, including INN-312 and INN-298, showed as much as a 90-fold increase in antisickling activity compared with vanillin. The compounds preferentially bind to and modify sickle hemoglobin (Hb S) to increase the affinity of Hb for oxygen. INN-312 also led to a considerable increase in the solubility of deoxygenated Hb S under completely deoxygenated conditions. Crystallographic studies of normal human Hb with INN-312 and INN-298 showed that the compounds form Schiff-base adducts with the N-terminus of the α-subunits to constrain the liganded (or relaxed-state) Hb conformation relative to the unliganded (or tense-state) Hb conforma... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5330229 Wed, 19 Oct 2011 04:00:00 +0100 5330229 http://www.medworm.com/index.php?rid=5330228&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbw5398 In this study, the thermal stability of 657 samples was estimated using a simplified Thermofluor assay. These samples were also subjected to automated vapour-diffusion crystallization screening under a constant protocol. Analysis of the data shows that samples with an apparent melting temperature (Tm) of 318 K or higher crystallized in 49% of cases, while the crystallization success rate decreased rapidly for samples with lower Tm. Only 23% of samples with a Tm below 316 K produced crystals. Based on this analysis, a simple method for estimation of the crystallization likelihood of biological samples is proposed. This method is easy, rapid and consumes very small amounts of sample. The results of this assay can be used to determine optimal incubation temperatures for crystallization e... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5330228 Tue, 18 Oct 2011 04:00:00 +0100 5330228 http://www.medworm.com/index.php?rid=5233082&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fyt5036 O-Acetylhomoserine sulfhydrylase (OAHS) is a pyridoxal 5′-phosphate (PLP) dependent sulfide-utilizing enzyme in the l-cysteine and l-methionine biosynthetic pathways of various enteric bacteria and fungi. OAHS catalyzes the conversion of O-acetylhomoserine to homocysteine using sulfide in a process known as direct sulfhydrylation. However, the source of the sulfur has not been identified and no structures of OAHS have been reported in the literature. Here, the crystal structure of Wolinella succinogenes OAHS (MetY) determined at 2.2 Å resolution is reported. MetY crystallized in space group C2 with two monomers in the asymmetric unit. Size-exclusion chromatography, dynamic light scattering and crystal packing indicate that the biological unit is a tetramer in solution. This is furth... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5233082 Mon, 19 Sep 2011 21:08:30 +0100 5233082 http://www.medworm.com/index.php?rid=5233090&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgm5017 In this study, it is demonstrated that when some crystals of macromolecules are mounted in the complete absence of surrounding liquid no crystalline ice is formed and the diffraction resolution, merging R factors and mosaic spread values are comparable to those of crystals cryocooled in the presence of a cryoprotectant. This potentially removes one of the most onerous manual steps in the structure-solution pipeline and could alleviate some of the foreseen difficulties in the automation of crystal mounting. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5233090 Thu, 08 Sep 2011 04:00:00 +0100 5233090 http://www.medworm.com/index.php?rid=5233089&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgx5191 Chlamydomonas reinhardtii α-type carbonic anhydrase (Cr-αCA1) is a dimeric enzyme that catalyses the interconversion of carbon dioxide and carbonic acid. The precursor form of Cr-αCA1 undergoes post-translational cleavage and N-glycosylation. Comparison of the genomic sequences of precursor Cr-αCA1 and other αCAs shows that Cr-αCA1 contains a different N-terminal sequence and two insertion sequences. A 35-residue peptide in one of the insertion sequences is deleted from the precursor during maturation. The crystal structure of the mature form of Cr-αCA1 has been determined at 1.88 Å resolution. Each subunit is cleaved into the long and short peptides, but they are linked together by a disulfide bond. The two subunits are linked by a disulfide bond. N-Glycosylations occur at three... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5233089 Thu, 08 Sep 2011 04:00:00 +0100 5233089 http://www.medworm.com/index.php?rid=5233088&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5169 Recent studies have defined a data-collection protocol and a metric that provide a robust measure of global radiation damage to protein crystals. Using this protocol and metric, 19 small-molecule compounds (introduced either by cocrystallization or soaking) were evaluated for their ability to protect lysozyme crystals from radiation damage. The compounds were selected based upon their ability to interact with radiolytic products (e.g. hydrated electrons, hydrogen, hydroxyl and perhydroxyl radicals) and/or their efficacy in protecting biological molecules from radiation damage in dilute aqueous solutions. At room temperature, 12 compounds had no effect and six had a sensitizing effect on global damage. Only one compound, sodium nitrate, appeared to extend crystal lifetimes, but not in all p... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5233088 Thu, 08 Sep 2011 04:00:00 +0100 5233088 http://www.medworm.com/index.php?rid=5233087&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fea5147 In order to understand the structure–activity profile observed for a series of substituted dibenz[b,f]azepine antifolates, the crystal structure of the binary complex of human dihydrofolate reductase (hDHFR) with the potent and selective inhibitor 2,4-diamino-6-{2′-O-(3-carboxypropyl)oxydibenz[b,f]-azepin-5-yl}methylpteridine (PT684) was determined to 1.8 Å resolution. These data revealed that the carboxylate side chain of PT684 occupies two alternate positions, neither of which interacts with the conserved Arg70 in the active-site pocket, which in turn hydrogen bonds to water. These observations are in contrast to those reported for the ternary complex of mouse DHFR (mDHFR) with NADPH [Cody et al. (2008), Acta Cryst. D64, 977–984], in which the 3-carboxypropyl side chain of PT68... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5233087 Thu, 08 Sep 2011 04:00:00 +0100 5233087 http://www.medworm.com/index.php?rid=5233086&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5192 The apo structure of N5-carboxyaminoimidazole ribonucleotide synthase (PurK) from Bacillus anthracis (baPurK) with Mg2+ in the active site is reported at 1.96 Å resolution. PurK is an enzyme in the purine-biosynthetic pathway, unique to prokaryotes, that converts 5-aminoimidazole ribonucleotide to N5-carboxyaminoimidazole ribonucleotide and has been suggested as a potential antimicrobial drug target. Two interesting features of baPurK are a flexible B-loop (residues 149/150–157) that is in close contact with the active site and the binding of Mg2+ to the active site without additional ligands. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5233086 Thu, 08 Sep 2011 04:00:00 +0100 5233086 http://www.medworm.com/index.php?rid=5233085&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5177 Isocitrate dehydrogenase catalyzes the first oxidative and decarboxylation steps in the citric acid cycle. It also lies at a crucial bifurcation point between CO2-generating steps in the cycle and carbon-conserving steps in the glyoxylate bypass. Hence, the enzyme is a focus of regulation. The bacterial enzyme is typically dependent on the coenzyme nicotinamide adenine dinucleotide phosphate. The monomeric enzyme from Corynebacterium glutamicum is highly specific towards this coenzyme and the substrate isocitrate while retaining a high overall efficiency. Here, a 1.9 Å resolution crystal structure of the enzyme in complex with its coenzyme and the cofactor Mg2+ is reported. Coenzyme specificity is mediated by interactions with the negatively charged 2′-phosphate group, which is surr... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5233085 Thu, 08 Sep 2011 04:00:00 +0100 5233085 http://www.medworm.com/index.php?rid=5233084&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5181 Human glioma pathogenesis-related protein 1 (GLIPR1) is a membrane protein that is highly upregulated in brain cancers but is barely detectable in normal brain tissue. GLIPR1 is composed of a signal peptide that directs its secretion, a conserved cysteine-rich CAP (cysteine-rich secretory proteins, antigen 5 and pathogenesis-related 1 proteins) domain and a transmembrane domain. GLIPR1 is currently being investigated as a candidate for prostate cancer gene therapy and for glioblastoma targeted therapy. Crystal structures of a truncated soluble domain of the human GLIPR1 protein (sGLIPR1) solved by molecular replacement using a truncated polyalanine search model of the CAP domain of stecrisp, a snake-venom cysteine-rich secretory protein (CRISP), are presented. The correct molecular-replace... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5233084 Thu, 08 Sep 2011 04:00:00 +0100 5233084 http://www.medworm.com/index.php?rid=5233083&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmh5044 Two-photon excited ultraviolet fluorescence (TPE-UVF) microscopy is explored for sensitive protein-crystal detection as a complement to second-order nonlinear optical imaging of chiral crystals (SONICC). Like conventional ultraviolet fluorescence (UVF), TPE-UVF generates image contrast based on the intrinsic fluorescence of aromatic residues, generally producing higher fluorescence emission within crystals than the mother liquor by nature of the higher local protein concentration. However, TPE-UVF has several advantages over conventional UVF, including (i) insensitivity to optical scattering, allowing imaging in turbid matrices, (ii) direct compatibility with conventional optical plates and windows by using visible light for excitation, (iii) elimination of potentially damaging out-of-pla... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5233083 Thu, 08 Sep 2011 04:00:00 +0100 5233083 http://www.medworm.com/index.php?rid=5116885&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5231 X-ray crystallography is now a recognized technique for ligand screening, especially for fragment-based drug design. However, protein crystal handling is still tedious and limits further automation. An alternative method for the solution of crystal structures of proteins in complex with small ligands is proposed. Crystallization drops are directly exposed to an X-ray beam after cocrystallization or soaking with the desired ligands. The use of dedicated plates in connection with an optimal parametrization of the G-rob robot allows efficient data collection. Three proteins currently under study in our laboratory for ligand screening by X-ray crystallography were used as validation test cases. The protein crystals belonged to different space groups, including a challenging monoclinic case. T... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5116885 Thu, 11 Aug 2011 16:47:23 +0100 5116885 http://www.medworm.com/index.php?rid=5116894&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgx5187 RiVax is a recombinant protein that is currently under clinical development as part of a human vaccine to protect against ricin poisoning. RiVax includes ricin A-chain (RTA) residues 1–267 with two intentional amino-acid substitutions, V76M and Y80A, aimed at reducing toxicity. Here, the crystal structure of RiVax was solved to 2.1 Å resolution and it was shown that it is superposable with that of the ricin toxin A-chain from Ricinus communis with a root-mean-square deviation of 0.6 Å over 258 Cα atoms. The RiVax structure is also compared with the recently determined structure of another potential ricin-vaccine immunogen, RTA 1–33/44–198 R48C/T77C. Finally, the locations and solvent-exposure of two toxin-neutralizing B-cell epitopes were examined and it was found that these ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5116894 Mon, 08 Aug 2011 23:00:00 +0100 5116894 http://www.medworm.com/index.php?rid=5116893&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmh5042 Tropomyosin (TM) is an elongated two-chain protein that binds along actin filaments. Important binding sites are localized in the N-terminus of tropomyosin. The structure of the N-terminus of the long muscle α-TM has been solved by both NMR and X-ray crystallography. Only the NMR structure of the N-terminus of the short nonmuscle α-TM is available. Here, the crystal structure of the N-terminus of the short nonmuscle α-TM (αTm1bZip) at a resolution of 0.98 Å is reported, which was solved from crystals belonging to space group P31 with unit-cell parameters a = b = 33.00, c = 52.03 Å, α = β = 90, γ = 120°. The first five N-terminal residues are flexible and residues 6–35 form an α-helical coiled coil. The overall fold and the secondary structure of the crystal structure of α... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5116893 Mon, 08 Aug 2011 23:00:00 +0100 5116893 http://www.medworm.com/index.php?rid=5116892&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fwd5158 Atomic resolution crystallographic studies of streptavidin and its biotin complex have been carried out at 1.03 and 0.95 Å, respectively. The wild-type protein crystallized with a tetramer in the asymmetric unit, while the crystals of the biotin complex contained two subunits in the asymmetric unit. Comparison of the six subunits shows the various ways in which the protein accommodates ligand binding and different crystal-packing environments. Conformational variation is found in each of the polypeptide loops connecting the eight strands in the β-sandwich subunit, but the largest differences are found in the flexible binding loop (residues 45–52). In three of the unliganded subunits the loop is in an `open' conformation, while in the two subunits binding biotin, as well as in one of ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5116892 Mon, 08 Aug 2011 23:00:00 +0100 5116892 http://www.medworm.com/index.php?rid=5116891&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fwd5155 Ab initio phasing is one of the remaining challenges in protein crystallography. Recent progress in computational structure prediction has enabled the generation of de novo models with high enough accuracy to solve the phase problem ab initio. This `ab initio phasing with de novo models' method first generates a huge number of de novo models and then selects some lowest energy models to solve the phase problem using molecular replacement. The amount of CPU time required is huge even for small proteins and this has limited the utility of this method. Here, an approach is described that significantly reduces the computing time required to perform ab initio phasing with de novo models. Instead of performing molecular replacement after the completion of all models, molecular replacement is ini... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5116891 Mon, 08 Aug 2011 23:00:00 +0100 5116891 http://www.medworm.com/index.php?rid=5116890&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5228 Can radiation damage to protein crystals be `outrun' by collecting a structural data set before damage is manifested? Recent experiments using ultra-intense pulses from a free-electron laser show that the answer is yes. Here, evidence is presented that significant reductions in global damage at temperatures above 200 K may be possible using conventional X-ray sources and current or soon-to-be available detectors. Specifically, `dark progression' (an increase in damage with time after the X-rays have been turned off) was observed at temperatures between 180 and 240 K and on timescales from 200 to 1200 s. This allowed estimation of the temperature-dependent timescale for damage. The rate of dark progression is consistent with an Arrhenius law with an activation energy of 14 kJ molâ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5116890 Mon, 08 Aug 2011 23:00:00 +0100 5116890 http://www.medworm.com/index.php?rid=5116889&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5176 In a recently characterized thiamin-salvage pathway, thiamin-degradation products are hydrolyzed by thiaminase II, yielding 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP). This compound is an intermediate in thiamin biosynthesis that, once phosphorylated by an HMP kinase, can be used to synthesize thiamin monophosphate. Here, the crystal structure of Saccharomyces cerevisiae THI20, a trifunctional enzyme containing an N-terminal HMP kinase/HMP-P kinase (ThiD-like) domain and a C-terminal thiaminase II (TenA-like) domain, is presented. Comparison to structures of the monofunctional enzymes reveals that while the ThiD-like dimer observed in THI20 resembles other ThiD structures, the TenA-like domain, which is tetrameric in all previously reported structures, forms a dimer. Similarly, the ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5116889 Mon, 08 Aug 2011 23:00:00 +0100 5116889 http://www.medworm.com/index.php?rid=5116888&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgx5185 Previous studies of complexes of Mycobacterium tuberculosis PanK (MtPanK) with nucleotide diphosphates and nonhydrolysable analogues of nucleoside triphosphates in the presence or the absence of pantothenate established that the enzyme has dual specificity for ATP and GTP, revealed the unusual movement of ligands during enzyme action and provided information on the effect of pantothenate on the location and conformation of the nucleotides at the beginning and the end of enzyme action. The X-ray analyses of the binary complexes of MtPanK with pantothenate, pantothenol and N-nonylpantothenamide reported here demonstrate that in the absence of nucleotide these ligands occupy, with a somewhat open conformation, a location similar to that occupied by phosphopantothenate in the `end' complexes, ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5116888 Mon, 08 Aug 2011 23:00:00 +0100 5116888 http://www.medworm.com/index.php?rid=5116887&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgx5184 In this study, crystal structures of human PDK4 complexed with either AMPPNP, ADP or the inhibitor M77976 were determined. ADP-bound PDK4 has a slightly wider active-site cleft and a more disordered ATP lid compared with AMPPNP-bound PDK4, although both forms of PDK4 assume open conformations with a wider active-site cleft than that in the closed conformation of the previously reported ADP-bound PDK2 structure. M77976 binds to the ATP-binding pocket of PDK4 and causes local conformational changes with complete disordering of the ATP lid. M77976 binding also leads to a large domain rearrangement that further expands the active-site cleft of PDK4 compared with the ADP- and AMPPNP-bound forms. Biochemical analyses revealed that M77976 inhibits PDK4 with increased potency compared with the pr... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5116887 Mon, 08 Aug 2011 23:00:00 +0100 5116887 http://www.medworm.com/index.php?rid=5116886&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmv5046 The crystallization and structural characterization of bovine liver catalase (BLC) has been intensively studied for decades. Forms I and II of BLC have previously been fully characterized using single-crystal X-ray diffraction. Form III has previously been analyzed by electron microscopy, but owing to the thinness of this crystal form an X-ray crystal structure had not been determined. Here, the crystal structure of form III of BLC is presented in space group P212121, with unit-cell parameters a = 68.7, b = 173.7, c = 186.3 Å. The asymmetric unit is composed of the biological tetramer, which is packed in a tetrahedron motif with three other BLC tetramers. This higher resolution structure has allowed an assessment of the previously published electron-microscopy studies. (Source: Acta Cry... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5116886 Mon, 08 Aug 2011 23:00:00 +0100 5116886 http://www.medworm.com/index.php?rid=5017628&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhm5097 The stereospecific oxidative degradation of uric acid to (S)-allantoin has recently been demonstrated to proceed via two unstable intermediates and requires three separate enzymatic reactions. The second step of this reaction, the conversion of 5-hydroxyisourate (HIU) to 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline, is catalyzed by HIU hydrolase (HIUH). The high-resolution crystal structure of HIUH from the opportunistic pathogen Klebsiella pneumoniae (KpHIUH) has been determined. KpHIUH is a homotetrameric protein that, based on sequence and structural similarity, belongs to the transthyretin-related protein family. In addition, the steady-state kinetic parameters for this enzyme and four active-site mutants have been measured. These data provide valuable insight into the functional ro... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5017628 Tue, 12 Jul 2011 20:00:08 +0100 5017628 http://www.medworm.com/index.php?rid=5017637&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fyt9032 A correction is made to a figure in the article by Porta et al. [(2011). Acta Cryst. D67, 628–638]. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5017637 Mon, 11 Jul 2011 23:00:00 +0100 5017637 http://www.medworm.com/index.php?rid=5017636&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmh5043 Fully oxidized cytochrome c oxidase (CcO) under enzymatic turnover is capable of pumping protons, while fully oxidized CcO as isolated is not able to do so upon one-electron reduction. The functional difference is expected to be a consequence of structural differences: [Fe3+–OH−] under enzymatic turnover versus [Fe3+–O22−–Cu2+] for the as-isolated CcO. However, the electron density for O22− is equally assignable to Cl−. An anomalous dispersion analysis was performed in order to conclusively demonstrate the absence of Cl− between the Fe3+ and Cu2+. Thus, the peroxide moiety receives electron equivalents from cytochrome c without affecting the oxidation states of the metal sites. The metal-site reduction is coupled to the proton pump. (Source: Acta Crystallographica Section ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5017636 Mon, 11 Jul 2011 23:00:00 +0100 5017636 http://www.medworm.com/index.php?rid=5017635&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5232 It is often discussed, mainly in connection with the rather high macromolecular R factors, that the treatment of bulk solvent in macromolecular refinement may lack the detail needed for modelling the solvent environment of molecules as complex as proteins and nucleic acids. This line of thought directly leads to the hypothesis that improvements in the modelling of the bulk solvent may substantially improve the agreement between the experimental data and the crystallographic models. Here, part of this hypothesis is being tested through the construction, via molecular-dynamics simulations, of a highly detailed, physics-based, structure-specific and crystallographic data-agnostic model of the bulk solvent of a known crystal structure. The water-distribution map obtained from the simulation i... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5017635 Mon, 11 Jul 2011 23:00:00 +0100 5017635 http://www.medworm.com/index.php?rid=5017634&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5224 Currently, about two thirds of all new macromolecular structures are determined by molecular replacement. In general the method works reliably, but it reaches its limits when the search model differs too much from the target structure in terms of coordinate deviations or completeness. Since anomalously scattering substructures are better conserved than the overall structure, these substructures and the corresponding anomalous intensity differences can be utilized to enhance the performance of molecular-replacement approaches. It is demonstrated that the combined and concomitant use of structure-factor amplitudes and anomalous differences constitutes a promising approach to push the limits of molecular replacement and to make more structures amenable to structure solution by this technique... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5017634 Mon, 11 Jul 2011 23:00:00 +0100 5017634 http://www.medworm.com/index.php?rid=5017633&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fyt5034 Assemblies with helical symmetry can be conveniently formulated in many distinct ways. Here, a new convention is presented which unifies the two most commonly used helical systems for generating helical assemblies from asymmetric units determined by X-ray fibre diffraction and EM imaging. A helical assembly is viewed as being composed of identical repetitive units in a one- or two-dimensional lattice, named 1-D and 2-D helical systems, respectively. The unification suggests that a new helical description with only four parameters [n1, n2, twist, rise], which is called the augmented 1-D helical system, can generate the complete set of helical arrangements, including coverage of helical discontinuities (seams). A unified four-parameter characterization implies similar parameters for similar ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5017633 Mon, 11 Jul 2011 23:00:00 +0100 5017633 http://www.medworm.com/index.php?rid=5017632&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fea5142 With the rapid rise of methicillin-resistant Staphylococcus aureus infections, new strategies against S. aureus are urgently needed. De novo purine biosynthesis is a promising yet unexploited target, insofar as abundant evidence has shown that bacteria with compromised purine biosynthesis are attenuated. Fundamental differences exist within the process by which humans and bacteria convert 5-aminoimidazole ribonucleotide (AIR) to 4-carboxy-5-aminoimidazole ribonucleotide (CAIR). In bacteria, this transformation occurs through a two-step conversion catalyzed by PurK and PurE; in humans, it is mediated by a one-step conversion catalyzed by class II PurE. Thus, these bacterial enzymes are potential targets for selective antibiotic development. Here, the first comprehensive structural and bio... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5017632 Mon, 11 Jul 2011 23:00:00 +0100 5017632 http://www.medworm.com/index.php?rid=5017631&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5233 To utilize a new conformation-dependent backbone-geometry library (CDL) in protein refinements at atomic resolution, a script was written that creates a restraint file for the SHELXL refinement program. It was found that the use of this library allows models to be created that have a substantially better fit to main-chain bond angles and lengths without degrading their fit to the X-ray data even at resolutions near 1 Å. For models at much higher resolution (∼0.7 Å), the refined model for parts adopting single well occupied positions is largely independent of the restraints used, but these structures still showed much smaller r.m.s.d. residuals when assessed with the CDL. Examination of the refinement tests across a wide resolution range from 2.4 to 0.65 Å revealed consistent b... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5017631 Mon, 11 Jul 2011 23:00:00 +0100 5017631 http://www.medworm.com/index.php?rid=5017630&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5173 In this study, the crystal structure of heterologously expressed peroxisomal catalase from the thermotolerant yeast Hansenula polymorpha has been determined at 2.9 Å resolution. H. polymorpha catalase is a typical peroxisomal catalase; it is tetrameric and is highly similar to catalases from other organisms. However, its hydrogen peroxide-degrading activity is higher than those of a number of other catalases for which structural data are available. Structural superimpositions indicate that the nature of the major channel, the path for hydrogen peroxide to the active site, varies from those seen in other catalase structures, an observation that may account for the high activity of H. polymorpha catalase. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5017630 Mon, 11 Jul 2011 23:00:00 +0100 5017630 http://www.medworm.com/index.php?rid=5017629&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5229 In most organisms, efficient d-galactose utilization requires the highly conserved Leloir pathway that converts d-galactose to d-glucose 1-phosphate. However, in some bacterial and fungal species alternative routes of d-galactose assimilation have been identified. In the so-called De Ley–Doudoroff pathway, d-galactose is metabolized into pyruvate and d-glyceraldehyde 3-phosphate in five consecutive reactions carried out by specific enzymes. The penultimate step in this pathway involves the phosphorylation of 2-oxo-3-deoxygalactonate to 2-oxo-3-deoxygalactonate 6-phosphate catalyzed by 2-oxo-3-deoxygalactonate kinase, with ATP serving as a phosphoryl-group donor. Here, a crystal structure of 2-oxo-3-deoxygalactonate kinase from Klebsiella pneumoniae determined at 2.1 Å resolution is re... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=5017629 Mon, 11 Jul 2011 23:00:00 +0100 5017629 http://www.medworm.com/index.php?rid=4931909&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fwd5154 The soluble 155 kDa glycoprotein factor H (FH) protects host tissue from damage by the human complement system. It accelerates decay of the alternative-pathway C3 convertase, C3bBb, and is a cofactor for factor I-mediated cleavage of the opsonin C3b. Numerous mutations and single-nucleotide polymorphisms (SNPs) occur in the gene encoding FH and the resulting missense mutations and truncation products result in altered functionality that predisposes to the development of the serious renal condition atypical haemolytic uraemic syndrome (aHUS). Other polymorphisms are linked to membranoproliferative glomerulonephritis and macular degeneration. The two C-terminal modules of FH (FH19-20) harbour numerous aHUS-associated mutations that disrupt the ability of factor H to protect host cells from ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4931909 Thu, 16 Jun 2011 19:39:16 +0100 4931909 http://www.medworm.com/index.php?rid=4931913&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fyt5032 Recent challenges in biological X-ray crystallography include the processing of modulated diffraction data. A modulated crystal has lost its three-dimensional translational symmetry but retains long-range order that can be restored by refining a periodic modulation function. The presence of a crystal modulation is indicated by an X-ray diffraction pattern with periodic main reflections flanked by off-lattice satellite reflections. While the periodic main reflections can easily be indexed using three reciprocal-lattice vectors a*, b*, c*, the satellite reflections have a non-integral relationship to the main lattice and require a q vector for indexing. While methods for the processing of diffraction intensities from modulated small-molecule crystals are well developed, they have not been a... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4931913 Wed, 15 Jun 2011 23:00:00 +0100 4931913 http://www.medworm.com/index.php?rid=4931911&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fea5138 The potential in macromolecular crystallography for using multiple crystals to collect X-ray diffraction data simultaneously from assemblies of up to seven crystals is explored. The basic features of the algorithms used to extract data and their practical implementation are described. The procedure could be useful both in relation to diffraction data obtained from intergrown crystals and to alleviate the problem of rapid diffraction decay arising from the effects of radiation damage. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4931911 Wed, 15 Jun 2011 23:00:00 +0100 4931911 http://www.medworm.com/index.php?rid=4931912&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5185 Entamoeba histolytica enolase (EhENO) reversibly interconverts 2-phosphoglyceric acid (2-PGA) and phosphoenolpyruvic acid (PEP). The crystal structure of the homodimeric EhENO is presented at a resolution of 1.9 Å. In the crystal structure EhENO presents as an asymmetric dimer with one active site in the open conformation and the other active site in the closed conformation. Interestingly, both active sites contain a copurified 2-PGA molecule. While the 2-PGA molecule in the closed active site closely resembles the conformation known from other enolase–2-PGA complexes, the conformation in the open active site is different. Here, 2-PGA is shifted approximately 1.6 Å away from metal ion I, most likely representing a precatalytic situation. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4931912 Mon, 13 Jun 2011 23:00:00 +0100 4931912 http://www.medworm.com/index.php?rid=4931910&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fea5135 Histidine triad nucleotide-binding protein 1 (HINT1) represents the most ancient and widespread branch in the histidine-triad protein superfamily. HINT1 plays an important role in various biological processes and has been found in many species. Here, the first complete structure of the rabbit HINT1–adenosine complex is reported at 1.10 Å resolution, which is one of the highest resolutions obtained for a HINT1 structure. The final structure has an Rcryst of 14.25% (Rfree = 16.77%) and the model exhibits good stereochemical qualities. A detailed analysis of the atomic resolution data allowed an update of the details of the protein structure in comparison to previously published data. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4931910 Mon, 13 Jun 2011 23:00:00 +0100 4931910 http://www.medworm.com/index.php?rid=4931916&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fea5141 The crystal structures of acyl carrier protein synthase (AcpS) from Mycobacterium tuberculosis (Mtb) and Corynebacterium ammoniagenes determined at pH 5.3 and pH 6.5, respectively, are reported. Comparison of the Mtb apo-AcpS structure with the recently reported structure of the Mtb AcpS–ADP complex revealed that AcpS adopts two different conformations: the orthorhombic and trigonal space-group structures show structural differences in the α2 helix and in the conformation of the α3–α4 connecting loop, which is in a closed conformation. The apo-AcpS structure shows electron density for the entire model and was obtained at lower pH values (4.4–6.0). In contrast, at a higher pH value (6.5) AcpS undergoes significant conformational changes, resulting in disordered regions that show no... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4931916 Fri, 10 Jun 2011 23:00:00 +0100 4931916 http://www.medworm.com/index.php?rid=4931915&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbw5396 X-ray transparent crystallization plates based upon a novel drop-pinning technology provide a flexible, simple and inexpensive approach to protein crystallization and screening. The plates consist of open cells sealed top and bottom by thin optically, UV and X-ray transparent films. The plates do not need wells or depressions to contain liquids. Instead, protein drops and reservoir solution are held in place by rings with micrometre dimensions that are patterned onto the bottom film. These rings strongly pin the liquid contact lines, thereby improving drop shape and position uniformity, and thus crystallization reproducibility, and simplifying automated image analysis of drop contents. The same rings effectively pin solutions containing salts, proteins, cryoprotectants, oils, alcohols and ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4931915 Fri, 10 Jun 2011 23:00:00 +0100 4931915 http://www.medworm.com/index.php?rid=4931914&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5230 Isothiazolidinone (IZD) heterocycles can act as effective components of protein tyrosine phosphatase (PTP) inhibitors by simultaneously replicating the binding interactions of both a phosphoryl group and a highly conserved water molecule, as exemplified by the structures of several PTP1B–inhibitor complexes. In the first unambiguous demonstration of IZD interactions with a PTP other than PTP1B, it is shown by X-ray crystallography that the IZD motif binds within the catalytic site of the Yersinia pestis PTP YopH by similarly displacing a highly conserved water molecule. It is also shown that IZD-based bidentate ligands can inhibit YopH in a nonpromiscuous fashion at low micromolar concentrations. Hence, the IZD moiety may represent a useful starting point for the development of YopH in... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4931914 Fri, 10 Jun 2011 23:00:00 +0100 4931914 http://www.medworm.com/index.php?rid=4839436&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5171 Two errors in sugar stereochemistry in the structure of ristocetin A have been corrected and the structure has been re-refined. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4839436 Wed, 18 May 2011 23:00:00 +0100 4839436 http://www.medworm.com/index.php?rid=4839435&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Ftm5035 The hydration of the coenzyme cob(II)alamin has been studied using high-resolution monochromatic neutron crystallographic data collected at room temperature to a resolution of 0.92 Å on the original D19 diffractometer with a prototype 4° × 64° detector at the high-flux reactor neutron source run by the Institute Laue–Langevin. The resulting structure provides hydrogen-bonding parameters for the hydration of biomacromolecules to unprecedented accuracy. These experimental parameters will be used to define more accurate force fields for biomacromolecular structure refinement. The presence of a hydrophobic bowl motif surrounded by flexible side chains with terminal functional groups may be significant for the efficient scavenging of ligands. The feasibility of extending the resolution... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4839435 Wed, 18 May 2011 23:00:00 +0100 4839435 http://www.medworm.com/index.php?rid=4839434&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmv5043 The nucleosome is the fundamental repeating unit of chromatin, via which genomic DNA is packaged into the nucleus in eukaryotes. In the nucleosome, two copies of each core histone, H2A, H2B, H3 and H4, form a histone octamer which wraps 146 base pairs of DNA around itself. All of the core histones except for histone H4 have nonallelic isoforms called histone variants. In humans, eight histone H3 variants, H3.1, H3.2, H3.3, H3T, H3.5, H3.X, H3.Y and CENP-A, have been reported to date. Previous studies have suggested that histone H3 variants possess distinct functions in the formation of specific chromosome regions and/or in the regulation of transcription and replication. H3.1, H3.2 and H3.3 are the most abundant H3 variants. Here, crystal structures of human nucleosomes containing either H... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4839434 Mon, 16 May 2011 23:00:00 +0100 4839434 http://www.medworm.com/index.php?rid=4839433&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmv5044 The constraints imposed on structure-factor phases by noncrystallographic symmetry (NCS) allow phase improvement, phase extension to higher resolution and hence ab initio phase determination. The more numerous the NCS redundancy and the greater the volume used for solvent flattening, the greater the power for phase determination. In a case analyzed here the icosahedral NCS phasing appeared to have broken down, although later successful phase extension was possible when the envelope around the NCS region was tightened. The phases from the failed phase-determination attempt fell into four classes, all of which satisfied the NCS constraints. These four classes corresponded to the correct solution, opposite enantiomorph, Babinet inversion and opposite enantiomorph with Babinet inversion. These... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4839433 Mon, 16 May 2011 23:00:00 +0100 4839433 http://www.medworm.com/index.php?rid=4839432&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fyt5033 The modular multifunctional protein large T antigen (T-ag) from simian virus 40 orchestrates many of the events needed for replication of the viral double-stranded DNA genome. This protein assembles into single and double hexamers on specific DNA sequences located at the origin of replication. This complicated process begins when the origin-binding domain of large T antigen (T-ag ODB) binds the GAGGC sequences in the central region (site II) of the viral origin of replication. While many of the functions of purified T-ag OBD can be studied in isolation, it is primarily monomeric in solution and cannot assemble into hexamers. To overcome this limitation, the possibility of engineering intermolecular disulfide bonds in the origin-binding domain which could oligomerize in solution was invest... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4839432 Mon, 16 May 2011 23:00:00 +0100 4839432 http://www.medworm.com/index.php?rid=4839431&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5183 Steroid hormone receptors are key components of mammalian stress and sex hormone systems. Many of them rely on the Hsp90 chaperone system for full function and are further fine-tuned by Hsp90-associated peptidyl–prolyl isomerases such as FK506-binding proteins 51 and 52. FK506-binding protein 51 (FKBP51) has been shown to reduce glucocorticoid receptor signalling and has been genetically associated with human stress resilience and with numerous psychiatric disorders. The peptidyl–prolyl isomerase domain of FKBP51 contains a high-affinity binding site for the natural products FK506 and rapamycin and has further been shown to convey most of the inhibitory activity on the glucocorticoid receptor. FKBP51 has therefore become a prime new target for the treatment of stress-related affective ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4839431 Mon, 16 May 2011 23:00:00 +0100 4839431 http://www.medworm.com/index.php?rid=4839430&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmn5004 The flexible flaps and the 80s loops (Pro79–Ile84) of HIV-1 protease are crucial in inhibitor binding. Previously, it was reported that the crystal structure of multidrug-resistant 769 (MDR769) HIV-1 protease shows a wide-open conformation of the flaps owing to conformational rigidity acquired by the accumulation of mutations. In the current study, the effect of mutations on the conformation of the 80s loop of MDR769 HIV-1 protease variants is reported. Alternate conformations of Pro81 (proline switch) with a root-mean-square deviation of 3–4.8 Å in the Cα atoms of the I10V mutant and a side chain with a `flipped-out' conformation in the A82F mutant cause distortion in the S1/S1′ binding pockets that affects inhibitor binding. The A82S and A82T mutants show local changes in the ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4839430 Mon, 16 May 2011 23:00:00 +0100 4839430 http://www.medworm.com/index.php?rid=4839429&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgx5180 MitoNEET is the only identified Fe–S protein localized to the outer mitochondrial membrane and a 1.5 Å resolution X-ray analysis has revealed a unique structure [Paddock et al. (2007), Proc. Natl Acad. Sci. USA, 104, 14342–14347]. The 2Fe–2S cluster is bound with a 3Cys–1His coordination which defines a new class of 2Fe–2S proteins. The hallmark feature of this class is the single noncysteine ligand His87, which when replaced by Cys decreases the redox potential (Em) by ∼300 mV and increases the stability of the cluster by around sixfold. Unexpectedly, the pH dependence of the lifetime of the 2Fe–2S cluster remains the same as in the wild-type protein. Here, the crystal structure of H87C mitoNEET was determined to 1.7 Å resolution (R factor = 18%) to investigate the ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4839429 Mon, 16 May 2011 23:00:00 +0100 4839429 http://www.medworm.com/index.php?rid=4811811&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5182 Proliferating cellular nuclear antigen (PCNA) is a toroidal-shaped protein that is involved in cell-cycle control, DNA replication and DNA repair. Parasitic protozoa are early-diverged eukaryotes that are responsible for neglected diseases. In this work, a PCNA from a parasitic protozoon was identified, cloned and biochemically characterized and its crystal structure was determined. Structural and biochemical studies demonstrate that PCNA from Entamoeba histolytica assembles as a homotrimer that is able to interact with and stimulate the activity of a PCNA-interacting peptide-motif protein from E. histolytica, EhDNAligI. The data indicate a conservation of the biochemical mechanisms of PCNA-mediated interactions between metazoa, yeast and parasitic protozoa. (Source: Acta Crystallographic... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4811811 Thu, 12 May 2011 04:35:48 +0100 4811811 http://www.medworm.com/index.php?rid=4811814&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5180 A chimeric feline immunodeficiency virus (FIV) protease (PR) has been engineered that supports infectivity but confers sensitivity to the human immunodeficiency virus (HIV) PR inhibitors darunavir (DRV) and lopinavir (LPV). The 6s-98S PR has five replacements mimicking homologous residues in HIV PR and a sixth which mutated from Pro to Ser during selection. Crystal structures of the 6s-98S FIV PR chimera with DRV and LPV bound have been determined at 1.7 and 1.8 Å resolution, respectively. The structures reveal the role of a flexible 90s loop and residue 98 in supporting Gag processing and infectivity and the roles of residue 37 in the active site and residues 55, 57 and 59 in the flap in conferring the ability to specifically recognize HIV PR drugs. Specifically, Ile37Val preserves ter... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4811814 Wed, 11 May 2011 23:00:00 +0100 4811814 http://www.medworm.com/index.php?rid=4811813&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5225 The X-CHIP (X-ray Crystallization High-throughput Integrated Platform) is a novel microchip that has been developed to combine multiple steps of the crystallographic pipeline from crystallization to diffraction data collection on a single device to streamline the entire process. The system has been designed for crystallization condition screening, visual crystal inspection, initial X-ray screening and data collection in a high-throughput fashion. X-ray diffraction data acquisition can be performed directly on-the-chip at room temperature using an in situ approach. The capabilities of the chip eliminate the necessity for manual crystal handling and cryoprotection of crystal samples, while allowing data collection from multiple crystals in the same drop. This technology would be especially b... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4811813 Wed, 11 May 2011 23:00:00 +0100 4811813 http://www.medworm.com/index.php?rid=4811812&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fwd5149 The potent cellulose-binding modules of cellulosomal scaffoldin subunits belong to the greater family of carbohydrate-binding modules (CBMs). They have generally been classified as belonging to family 3a on the basis of sequence similarity. They form nine-stranded β-sandwich structures with jelly-roll topology. The members of this family possess on their surface a planar array of aromatic amino-acid residues (known as the linear strip) that form stacking interactions with the glucose rings of cellulose chains and have a conserved Ca2+-binding site. Intriguingly, the CBM3 from scaffoldin A (ScaA) of Bacteroides cellulosolvens exhibits alterations in sequence that make it more similar to the CBMs of free cellulolytic enzymes, which are classified into CBM family 3b. X-ray structural analysi... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4811812 Wed, 11 May 2011 23:00:00 +0100 4811812 http://www.medworm.com/index.php?rid=4718882&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fpf0083 (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4718882 Fri, 15 Apr 2011 23:00:00 +0100 4718882 http://www.medworm.com/index.php?rid=4718881&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmh5040 Monomeric haemoglobin component V (Hb V) from the larva of the midge Propsilocerus akamusi shows high Cl− affinity under high salt concentrations at acidic pH. In order to understand the structural changes that depend on Cl− binding, crystal structures of Hb V were determined under acidic high-salt conditions and the structural changes arising from different haem-bound ligands were simulated. Crystal structures of Hb V under acidic high-salt conditions indicated that the side chain of ArgE10 on the distal face of the haem contributes to stabilizing haem-bound Cl−. The conformation of the Arg side chain in the Cl−-bound form was almost identical to that in ligated Hb V at neutral pH but not to that in met Hb V under acidic salt-free conditions. Furthermore, preliminary molecular-dy... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4718881 Fri, 15 Apr 2011 23:00:00 +0100 4718881 http://www.medworm.com/index.php?rid=4718880&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5226 There are over 100 genes in the human genome that encode protein tyrosine phosphatases (PTPs) and approximately 60 of these are classified as dual-specificity phosphatases (DUSPs). Although many dual-specificity phosphatases are still not well characterized, novel functions have been discovered for some of them that have led to new insights into a variety of biological processes and the molecular basis for certain diseases. Indeed, as the functions of DUSPs continue to be elucidated, a growing number of them are emerging as potential therapeutic targets for diseases such as cancer, diabetes and inflammatory disorders. Here, the overexpression, purification and structure determination of DUSP27 at 2.38 Å resolution are presented. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4718880 Fri, 15 Apr 2011 23:00:00 +0100 4718880 http://www.medworm.com/index.php?rid=4708592&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5167 AMP-activated protein kinase (AMPK) is a serine/threonine kinase that functions as a sensor to maintain energy balance at both the cellular and the whole-body levels and is therefore a potential target for drug design against metabolic syndrome, obesity and type 2 diabetes. Here, the crystal structure of the phosphorylated-state mimic T172D mutant kinase domain from the human AMPK α2 subunit is reported in the apo form and in complex with a selective inhibitor, compound C. The AMPK α2 kinase domain exhibits a typical bilobal kinase fold and exists as a monomer in the crystal. Like the wild-type apo form, the T172D mutant apo form adopts the autoinhibited structure of the `DFG-out' conformation, with the Phe residue of the DFG motif anchored within the putative ATP-binding pocket. Compoun... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4708592 Wed, 13 Apr 2011 23:00:00 +0100 4708592 http://www.medworm.com/index.php?rid=4708591&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmv5039 Ligand-induced conformational changes in proteins are of immense functional relevance. It is a major challenge to elucidate the network of amino acids that are responsible for the percolation of ligand-induced conformational changes to distal regions in the protein from a global perspective. Functionally important subtle conformational changes (at the level of side-chain noncovalent interactions) upon ligand binding or as a result of environmental variations are also elusive in conventional studies such as those using root-mean-square deviations (r.m.s.d.s). In this article, the network representation of protein structures and their analyses provides an efficient tool to capture these variations (both drastic and subtle) in atomistic detail in a global milieu. A generalized graph theoretic... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4708591 Wed, 13 Apr 2011 23:00:00 +0100 4708591 http://www.medworm.com/index.php?rid=4703366&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhm5096 The X-ray crystal structure of sheep liver sorbitol dehydrogenase (slSDH) has been determined using the crystal structure of human sorbitol dehydrogenase (hSDH) as a molecular-replacement model. slSDH crystallized in space group I222 with one monomer in the asymmetric unit. A conserved tetramer that superposes well with that seen in hSDH (despite belonging to a different space group) and obeying the 222 crystal symmetry is seen in slSDH. An acetate molecule is bound in the active site, coordinating to the active-site zinc through a water molecule. Glycerol, a substrate of slSDH, also occupies the substrate-binding pocket together with the acetate designed by nature to fit large polyol substrates. The substrate-binding pocket is seen to be in close proximity to the tetramer interface, which... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4703366 Tue, 12 Apr 2011 23:00:00 +0100 4703366 http://www.medworm.com/index.php?rid=4703365&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fxb5027 The structure of the human major histocompatability (MHC) class I molecule HLA-A*0301 (HLA-A3) in complex with a nonameric peptide (KLIETYFSK) has been determined by X-ray crystallography to 2.7 Å resolution. HLA-A3 is a predisposing allele for multiple sclerosis (MS), an autoimmune disease of the central nervous system. The KLIETYFSK peptide is a naturally processed epitope of proteolipid protein, a myelin protein and candidate target for immune-mediated myelin destruction in MS. Comparison of the structure of HLA-A3 with that of HLA-A2, an MHC class I molecule which is protective against MS, indicates that both MHC class I molecules present very similar faces for T-cell receptor recognition whilst differing in the specificity of their peptide-binding grooves. These characteristics may... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4703365 Tue, 12 Apr 2011 23:00:00 +0100 4703365 http://www.medworm.com/index.php?rid=4703364&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Flv5012 Arabinanase Abnx from Penicillium chrysogenum 31B, which belongs to the GH93 family, releases arabinobiose from the nonreducing terminus of α-1,5-l-arabinan, which is distributed in the primary cell walls of higher plants. Crystal structures of Abnx and of its complex with arabinobiose were determined at the high resolutions of 1.14 Å to an Rwork of 10.7% (Rfree = 12.8%) and 1.04 Å to an Rwork of 10.4% (Rfree = 12.5%). Abnx has a six-bladed β-propeller fold with a typical ring-closure mode called `Velcro', in which the last four-stranded β-sheet is completed by the incorporation of a strand from the N-terminus. Catalytic residues which act as a nucleophile and an acid/base were proposed from the structures and confirmed by site-directed mutagenesis. The substrate-binding groove i... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4703364 Tue, 12 Apr 2011 23:00:00 +0100 4703364 http://www.medworm.com/index.php?rid=4703363&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmh5041 The endoplasmic reticulum (ER) unfolded protein response (UPR) is comprised of several intracellular signaling pathways that alleviate ER stress. The ER-localized transmembrane kinase PERK is one of three major ER stress transducers. Oligomerization of PERK's N-terminal ER luminal domain by ER stress promotes PERK trans-autophosphorylation of the C-terminal cytoplasmic kinase domain at multiple residues including Thr980 on the kinase activation loop. Activated PERK phosphorylates Ser51 of the α-subunit of translation initiation factor 2 (eIF2α), which inhibits initiation of protein synthesis and reduces the load of unfolded proteins entering the ER. The crystal structure of PERK's kinase domain has been determined to 2.8 Å resolution. The structure resembles the back-to-back dimer obs... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4703363 Tue, 12 Apr 2011 23:00:00 +0100 4703363 http://www.medworm.com/index.php?rid=4703362&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fkw5027 This study presents the crystal structure of Greyhound hemoglobin (GrHb) determined to 1.9 Å resolution. GrHb was found to crystallize with an α1β1 dimer in the asymmetric unit and belongs to the R2 state. Oxygen-affinity measurements combined with the fact that GrHb crystallizes in the R2 state despite the high-salt conditions used for crystallization strongly indicate that GrHb can serve as a model high-oxygen-affinity hemoglobin (Hb) for higher mammals, especially humans. Structural analysis of GrHb and its comparison with the R2-state of human Hb revealed several regions that can potentially contribute to the high oxygen affinity of GrHb and serve to rationalize the additional stability of the R2-state of GrHb. A previously well studied hydrophobic cluster of bar-headed goose Hb n... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4703362 Tue, 12 Apr 2011 23:00:00 +0100 4703362 http://www.medworm.com/index.php?rid=4692385&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmv5041 A number of pathogens, including the causative agents of tuberculosis and malaria, synthesize isopentenyl diphosphate via the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway rather than the classical mevalonate pathway found in humans. As part of a structure-based drug-discovery program against tuberculosis, IspD, the enzyme that carries out the third step in the MEP pathway, was targeted. Constructs of both the Mycobacterium smegmatis and the Mycobacterium tuberculosis enzymes that were suitable for structural and inhibitor-screening studies were engineered. Two crystal structures of the M. smegmatis enzyme were produced, one in complex with CTP and the other in complex with CMP. In addition, the M. tuberculosis enzyme was crystallized in complex with CTP. Here, the structure determina... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4692385 Thu, 07 Apr 2011 23:00:00 +0100 4692385 http://www.medworm.com/index.php?rid=4682648&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbw5391 The Pi sampling method is derived from the incomplete factorial approach to macromolecular crystallization screen design. The resulting `Pi screens' have a modular distribution of a given set of up to 36 stock solutions. Maximally diverse conditions can be produced by taking into account the properties of the chemicals used in the formulation and the concentrations of the corresponding solutions. The Pi sampling method has been implemented in a web-based application that generates screen formulations and recipes. It is particularly adapted to screens consisting of 96 different conditions. The flexibility and efficiency of Pi sampling is demonstrated by the crystallization of soluble proteins and of an integral membrane-protein sample. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4682648 Thu, 07 Apr 2011 14:56:10 +0100 4682648 http://www.medworm.com/index.php?rid=4682649&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5223 Major proteins secreted by the infective larval stage hookworms upon host entry include Ancylostoma secreted proteins (ASPs), which are characterized by one or two CAP (cysteine-rich secretory protein/antigen 5/pathogenesis related-1) domains. The CAP domain has been reported in diverse phylogenetically unrelated proteins, but has no confirmed function. The first structure of a two-CAP-domain protein, Na-ASP-1, from the major human hookworm parasite Necator americanus was refined to a resolution limit of 2.2 Å. The structure was solved by molecular replacement (MR) using Na-ASP-2, a one-CAP-domain ASP, as the search model. The correct MR solution could only be obtained by truncating the polyalanine model of Na-ASP-2 and removing several loops. The structure reveals two CAP domains linke... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4682649 Wed, 06 Apr 2011 23:00:00 +0100 4682649 http://www.medworm.com/index.php?rid=4610122&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fme0445 (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4610122 Sat, 19 Mar 2011 01:32:37 +0100 4610122 http://www.medworm.com/index.php?rid=4610139&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fba5165 CCP4mg is a molecular-graphics program that is designed to give rapid access to both straightforward and complex static and dynamic representations of macromolecular structures. It has recently been updated with a new interface that provides more sophisticated atom-selection options and a wizard to facilitate the generation of complex scenes. These scenes may contain a mixture of coordinate-derived and abstract graphical objects, including text objects, arbitrary vectors, geometric objects and imported images, which can enhance a picture and eliminate the need for subsequent editing. Scene descriptions can be saved to file and transferred to other molecules. Here, the substantially enhanced version 2 of the program, with a new underlying GUI toolkit, is described. A built-in rendering modu... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4610139 Fri, 18 Mar 2011 00:00:00 +0100 4610139 http://www.medworm.com/index.php?rid=4610138&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fba5153 This paper presents a discussion of existing methods for the analysis of macromolecular interactions and complexes in crystal packing. Typical situations and conditions where wrong answers may be obtained in the course of ordinary procedures are presented and discussed. The more general question of what the relationship is between natural (in-solvent) and crystallized assemblies is discussed and researched. A computational analysis suggests that weak interactions with Kd ≥ 100 µM have a considerable chance of being lost during the course of crystallization. In such instances, crystal packing misrepresents macromolecular complexes and interactions. For as many as 20% of protein dimers in the PDB the likelihood of misrepresentation is estimated to be higher than 50%. Given that weak mac... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4610138 Fri, 18 Mar 2011 00:00:00 +0100 4610138 http://www.medworm.com/index.php?rid=4610137&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fba5156 The Joint Center for Structural Genomics (JCSG), one of four large-scale structure-determination centers funded by the US Protein Structure Initiative (PSI) through the National Institute for General Medical Sciences, has been operating an automated distributed structure-solution pipeline, Xsolve, for well over half a decade. During PSI-2, Xsolve solved, traced and partially refined 90% of the JCSG's nearly 770 MAD/SAD structures at an average resolution of about 2 Å without human intervention. Xsolve executes many well established publicly available crystallography software programs in parallel on a commodity Linux cluster, resulting in multiple traces for any given target. Additional software programs have been developed and integrated into Xsolve to further minimize human effort in... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4610137 Fri, 18 Mar 2011 00:00:00 +0100 4610137 http://www.medworm.com/index.php?rid=4610136&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fba5152 This paper describes various components of the macromolecular crystallographic refinement program REFMAC5, which is distributed as part of the CCP4 suite. REFMAC5 utilizes different likelihood functions depending on the diffraction data employed (amplitudes or intensities), the presence of twinning and the availability of SAD/SIRAS experimental diffraction data. To ensure chemical and structural integrity of the refined model, REFMAC5 offers several classes of restraints and choices of model parameterization. Reliable models at resolutions at least as low as 4 Å can be achieved thanks to low-resolution refinement tools such as secondary-structure restraints, restraints to known homologous structures, automatic global and local NCS restraints, `jelly-body' restraints and the use of nove... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4610136 Fri, 18 Mar 2011 00:00:00 +0100 4610136 http://www.medworm.com/index.php?rid=4610135&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fba5154 Density modification often suffers from an overestimation of phase quality, as seen by escalated figures of merit. A new cross-validation-based method to address this estimation bias by applying a bias-correction parameter `β' to maximum-likelihood phase-combination functions is proposed. In tests on over 100 single-wavelength anomalous diffraction data sets, the method is shown to produce much more reliable figures of merit and improved electron-density maps. Furthermore, significantly better results are obtained in automated model building iterated with phased refinement using the more accurate phase probability parameters from density modification. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4610135 Fri, 18 Mar 2011 00:00:00 +0100 4610135 http://www.medworm.com/index.php?rid=4610133&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fba5157 For its first release in 2004, CRANK was shown to effectively detect and phase anomalous scatterers from single-wavelength anomalous diffraction data. Since then, CRANK has been significantly improved and many more structures can be built automatically with single- or multiple-wavelength anomalous diffraction or single isomorphous replacement with anomalous scattering data. Here, the new algorithms that have been developed that have led to these substantial improvements are discussed and CRANK's performance on over 100 real data sets is shown. The latest version of CRANK is freely available for download at http://www.bfsc.leidenuniv.nl/software/crank/ and from CCP4 (http://www.ccp4.ac.uk/). (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4610133 Fri, 18 Mar 2011 00:00:00 +0100 4610133 http://www.medworm.com/index.php?rid=4610132&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fba5155 The Protein Data Bank in Europe (PDBe) is the European partner in the Worldwide PDB and as such handles depositions of X-ray, NMR and EM data and structure models. PDBe also provides advanced bioinformatics services based on data from the PDB and related resources. Some of the challenges facing the PDB and its guardians are discussed, as well as some of the areas on which PDBe activities will focus in the future (advanced services, ligands, integration, validation and experimental data). Finally, some recent developments at PDBe are described. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4610132 Fri, 18 Mar 2011 00:00:00 +0100 4610132 http://www.medworm.com/index.php?rid=4610131&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fba5167 Molecular replacement is one of the key methods used to solve the problem of determining the phases of structure factors in protein structure solution from X-ray image diffraction data. Its success rate has been steadily improving with the development of improved software methods and the increasing number of structures available in the PDB for use as search models. Despite this, in cases where there is low sequence identity between the target-structure sequence and that of its set of possible homologues it can be a difficult and time-consuming chore to isolate and prepare the best search model for molecular replacement. MrBUMP and BALBES are two recent developments from CCP4 that have been designed to automate and speed up the process of determining and preparing the best search models and... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4610131 Fri, 18 Mar 2011 00:00:00 +0100 4610131 http://www.medworm.com/index.php?rid=4610130&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fba5163 In molecular replacement, the quality of models can be improved by transferring information contained in sequence alignment to the template structure. A family of algorithms has been developed that make use of the sequence-similarity score calculated from residue-substitution scores smoothed over nearby residues to delete or downweight parts of the model that are unreliable. These algorithms have been implemented in the program Sculptor, together with well established methods that are in common use for model improvement. An analysis of the new algorithms has been performed by studying the effect of algorithm parameters on the quality of models. Benchmarking against existing techniques shows that models from Sculptor compare favourably, especially if the alignment is unreliable. Carrying ou... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4610130 Fri, 18 Mar 2011 00:00:00 +0100 4610130 http://www.medworm.com/index.php?rid=4610129&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fba5166 A typical diffraction experiment will generate many images and data sets from different crystals in a very short time. This creates a challenge for the high-throughput operation of modern synchrotron beamlines as well as for the subsequent data processing. Novice users in particular may feel overwhelmed by the tables, plots and numbers that the different data-processing programs and software packages present to them. Here, some of the more common problems that a user has to deal with when processing a set of images that will finally make up a processed data set are shown, concentrating on difficulties that may often show up during the first steps along the path of turning the experiment (i.e. data collection) into a model (i.e. interpreted electron density). Difficulties such as unexpect... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4610129 Fri, 18 Mar 2011 00:00:00 +0100 4610129 http://www.medworm.com/index.php?rid=4610128&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fba5158 This paper presents an overview of how to run the CCP4 programs for data reduction (SCALA, POINTLESS and CTRUNCATE) through the CCP4 graphical interface ccp4i and points out some issues that need to be considered, together with a few examples. It covers determination of the point-group symmetry of the diffraction data (the Laue group), which is required for the subsequent scaling step, examination of systematic absences, which in many cases will allow inference of the space group, putting multiple data sets on a common indexing system when there are alternatives, the scaling step itself, which produces a large set of data-quality indicators, estimation of |F| from intensity and finally examination of intensity statistics to detect crystal pathologies such as twinning. An appendix outline... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4610128 Fri, 18 Mar 2011 00:00:00 +0100 4610128 http://www.medworm.com/index.php?rid=4610127&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fba5160 iMOSFLM is a graphical user interface to the diffraction data-integration program MOSFLM. It is designed to simplify data processing by dividing the process into a series of steps, which are normally carried out sequentially. Each step has its own display pane, allowing control over parameters that influence that step and providing graphical feedback to the user. Suitable values for integration parameters are set automatically, but additional menus provide a detailed level of control for experienced users. The image display and the interfaces to the different tasks (indexing, strategy calculation, cell refinement, integration and history) are described. The most important parameters for each step and the best way of assessing success or failure are discussed. (Source: Acta Crystallographic... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4610127 Fri, 18 Mar 2011 00:00:00 +0100 4610127 http://www.medworm.com/index.php?rid=4610126&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fba5168 The measurement of X-ray diffraction data from macromolecular crystals for the purpose of structure determination is the convergence of two processes: the preparation of diffraction-quality crystal samples on the one hand and the construction and optimization of an X-ray beamline and end station on the other. Like sample preparation, a macromolecular crystallography beamline is geared to obtaining the best possible diffraction measurements from crystals provided by the synchrotron user. This paper describes the thoughts behind an experiment that fully exploits both the sample and the beamline and how these map into everyday decisions that users can and should make when visiting a beamline with their most precious crystals. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4610126 Fri, 18 Mar 2011 00:00:00 +0100 4610126 http://www.medworm.com/index.php?rid=4610125&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fba5164 The techniques used in protein production and structural biology have been developing rapidly, but techniques for recording the laboratory information produced have not kept pace. One approach is the development of laboratory information-management systems (LIMS), which typically use a relational database schema to model and store results from a laboratory workflow. The underlying philosophy and implementation of the Protein Information Management System (PiMS), a LIMS development specifically targeted at the flexible and unpredictable workflows of protein-production research laboratories of all scales, is described. PiMS is a web-based Java application that uses either Postgres or Oracle as the underlying relational database-management system. PiMS is available under a free licence to al... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4610125 Fri, 18 Mar 2011 00:00:00 +0100 4610125 http://www.medworm.com/index.php?rid=4610124&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fba5162 Macromolecular crystallography relies on the availability and quality of single crystals; these are typically obtained through extensive screening, which has a very low intrinsic success rate. Crystallization is not a completely stochastic process and many proteins do not succumb to crystallization because of specific microscopic features of their molecular surfaces. It follows that rational surface engineering through site-directed mutagenesis should allow a systematic and significant improvement in crystallization success rates. Here, one such established strategy, surface-entropy reduction (SER), is discussed, including its successes, limitations and possible future developments. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4610124 Fri, 18 Mar 2011 00:00:00 +0100 4610124 http://www.medworm.com/index.php?rid=4610123&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5219 The CCP4 (Collaborative Computational Project, Number 4) software suite is a collection of programs and associated data and software libraries which can be used for macromolecular structure determination by X-ray crystallography. The suite is designed to be flexible, allowing users a number of methods of achieving their aims. The programs are from a wide variety of sources but are connected by a common infrastructure provided by standard file formats, data objects and graphical interfaces. Structure solution by macromolecular crystallography is becoming increasingly automated and the CCP4 suite includes several automation pipelines. After giving a brief description of the evolution of CCP4 over the last 30 years, an overview of the current suite is given. While detailed descriptions are ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4610123 Fri, 18 Mar 2011 00:00:00 +0100 4610123 http://www.medworm.com/index.php?rid=4610134&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fba5159 Phaser is a program that implements likelihood-based methods to solve macromolecular crystal structures, currently by molecular replacement or single-wavelength anomalous diffraction (SAD). SAD phasing is based on a likelihood target derived from the joint probability distribution of observed and calculated pairs of Friedel-related structure factors. This target combines information from the total structure factor (primarily non-anomalous scattering) and the difference between the Friedel mates (anomalous scattering). Phasing starts from a substructure, which is usually but not necessarily a set of anomalous scatterers. The substructure can also be a protein model, such as one obtained by molecular replacement. Additional atoms are found using a log-likelihood gradient map, which shows the... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4610134 Sat, 05 Mar 2011 00:00:00 +0100 4610134 http://www.medworm.com/index.php?rid=4476857&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhm5086 Endonuclease IV (EndoIV) is an endonuclease that acts at apurinic/apyrimidinic (AP) sites and is classified as either long-type or short-type. The crystal structures of representative types of EndoIV from Geobacillus kaustophilus and Thermus thermophilus HB8 were determined using X-ray crystallography. G. kaustophilus EndoIV (the long type) had a higher affinity for double-stranded DNA containing an AP-site analogue than T. thermophilus EndoIV (the short type). Structural analysis of the two different EndoIVs suggested that a C-terminal DNA-recognition loop that is only present in the long type contributes to its high affinity for AP sites. A mutation analysis showed that Lys267 in the C-terminal DNA-recognition loop plays an important role in DNA binding. (Source: Acta Crystallographica S... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4476857 Tue, 15 Feb 2011 09:32:43 +0100 4476857 http://www.medworm.com/index.php?rid=4476866&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5215 P2, the major capsid protein of bacteriophage PM2, adopts the double β-barrel fold characteristic of the PRD1–adenoviral lineage. The 2.5 Å resolution X-ray data obtained by analysis of the two major lattices of a multiple crystal of P2 were phased by molecular replacement, using as a search model structure factors to 7.6 Å resolution obtained from electron density cut from the map of the entire PM2 virion. Phase extension to 2.5 Å resolution used solely sixfold cycling averaging and solvent flattening. This represents an atypical example of an oligomeric protein for which the structure has been determined at high resolution by bootstrapping from low-resolution initial phases. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4476866 Tue, 15 Feb 2011 00:00:00 +0100 4476866 http://www.medworm.com/index.php?rid=4476865&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmv5040 A mutant of Erythrina corallodendron lectin was generated with the aim of enhancing its affinity for N-acetylgalactosamine. A tyrosine residue close to the binding site of the lectin was mutated to a glycine in order to facilitate stronger interactions between the acetamido group of the sugar and the lectin which were prevented by the side chain of the tyrosine in the wild-type lectin. The crystal structures of this Y106G mutant lectin in complex with galactose and N-acetylgalactosamine have been determined. A structural rationale has been provided for the differences in the relative binding affinities of the wild-type and mutant lectins towards the two sugars based on the structures. A hydrogen bond between the O6 atom of the sugars and the variable loop of the carbohydrate-binding site o... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4476865 Tue, 15 Feb 2011 00:00:00 +0100 4476865 http://www.medworm.com/index.php?rid=4476864&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhm5095 The crystal structure of the sortase AcSrtC-1 from the oral microorganism Actinomyces oris has been determined to 2.4 Å resolution. AcSrtC-1 is a cysteine transpeptidase that is responsible for the formation of fimbriae by the polymerization of a shaft protein. Similar to other pili-associated sortases, the AcSrtC-1 active site is protected by a flexible lid. The asymmetric unit contains five AcSrtC-1 molecules and their catalytic Cys–His–Arg triads are trapped in two different conformations. It is also shown that the thermostability of the enzyme is increased by the presence of calcium. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4476864 Tue, 15 Feb 2011 00:00:00 +0100 4476864 http://www.medworm.com/index.php?rid=4476863&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5222 Galectin-4, a member of the tandem-repeat subfamily of galectins, participates in cell-membrane interactions and plays an important role in cell adhesion and modulation of immunity and malignity. The oligosaccharide specificity of the mouse galectin-4 carbohydrate-recognition domains (CRDs) has been reported previously. In this work, the structure and binding properties of the N-terminal domain CRD1 were further investigated and the crystal structure of CRD1 in complex with lactose was determined at 2.1 Å resolution. The lactose-binding affinity was characterized by fluorescence measurements and two lactose-binding sites were identified: a high-affinity site with a Kd value in the micromolar range (Kd1 = 600 ± 70 µM) and a low-affinity site with Kd2 = 28 ± 10 mM. (Source: Acta Cr... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4476863 Tue, 15 Feb 2011 00:00:00 +0100 4476863 http://www.medworm.com/index.php?rid=4476862&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fyt5031 The X-ray structure determination at 2.4 Å resolution of the putative orsellinic acid C3 O-methyltransferase (CalO1) involved in calicheamicin biosynthesis is reported. Comparison of CalO1 with a homology model of the functionally related calicheamicin orsellinic acid C2 O-methyltransferase (CalO6) implicates several residues that are likely to contribute to the regiospecificity of alkylation. Consistent with the proposed requirement of an acyl-carrier-protein-bound substrate, this structural study also reveals structural determinants within CalO1 that are anticipated to accommodate an association with an acyl carrier protein. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4476862 Tue, 15 Feb 2011 00:00:00 +0100 4476862 http://www.medworm.com/index.php?rid=4476861&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fyt5029 SH3 domains are small protein modules that mediate the assembly of specific protein complexes, typically via binding to proline-rich sequences in their respective binding partners. Most of the α-spectrin SH3-domain (Spc-SH3) structures determined to date using X-ray diffraction have been solved from crystals belonging to the orthorhombic space group P212121 with a needle-like morphology. All of these orthorhombic crystals exhibited a rapid growth rate. In addition to this crystal form, the R21D mutant of Spc-SH3 crystallizes in a new crystal form in the presence of sodium formate at pH values higher than 6. This new crystal form grows at a slower rate and belongs to the hexagonal space group P6522, with unit-cell parameters a = b = 42.9, c = 127.5 Å. When both polymorphs of the R21D... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4476861 Tue, 15 Feb 2011 00:00:00 +0100 4476861 http://www.medworm.com/index.php?rid=4476860&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5220 The trio of macromolecular crystallography beamlines constructed by the General Medicine and Cancer Institutes Collaborative Access Team (GM/CA-CAT) in Sector 23 of the Advanced Photon Source (APS) have been in growing demand owing to their outstanding beam quality and capacity to measure data from crystals of only a few micrometres in size. To take full advantage of the state-of-the-art mechanical and optical design of these beamlines, a significant effort has been devoted to designing fast, convenient, intuitive and robust beamline controls that could easily accommodate new beamline developments. The GM/CA-CAT beamline controls are based on the power of EPICS for distributed hardware control, the rich Java graphical user interface of Eclipse RCP and the task-oriented philosophy as well ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4476860 Tue, 15 Feb 2011 00:00:00 +0100 4476860 http://www.medworm.com/index.php?rid=4476859&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgx5181 dUTPases are housekeeping enzymes which catalyse the hydrolysis of dUTP to dUMP in an ion-dependent manner. Bacillus subtilis has both a genomic and an SPβ prophage homotrimeric dUTPase. Here, structure determination of the prophage apoenzyme and of its complexes with dUDP and dUpNHpp–Mg2+ is described at 1.75, 1.9 and 2.55 Å resolution, respectively. The C-terminal extension, which carries the conserved motif V, is disordered in all three structures. Unlike all other trimeric dUTPases for which structures are available, with the exception of the Bacillus genomic enzyme, the aromatic residue covering the uridine and acting as the Phe-lid is close to motif III in the sequence rather than in motif V. This is in spite of the presence of an aromatic amino acid at the usual Phe-lid positi... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4476859 Tue, 15 Feb 2011 00:00:00 +0100 4476859 http://www.medworm.com/index.php?rid=4476858&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5178 A crystallographic fragment screen was carried out to identify starting points for the development of inhibitors of protein kinase Pim-1, a potential target for tumour therapy. All fragment hits identified via soaking in this study turned out to bind to the unusually hydrophobic pocket at the hinge region. The most potent fragments, two cinnamic acid derivatives (with a best IC50 of 130 µM), additionally form a well defined hydrogen bond. The balance between hydrophobic and polar interactions makes these molecules good starting points for further optimization. Pim-2 inhibitors from a recently reported high-throughput screening campaign also feature a cinnamic acid moiety. Two of these Pim-2 inhibitors were synthesized, their potencies against Pim-1 were determined and their cocrystal st... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4476858 Tue, 15 Feb 2011 00:00:00 +0100 4476858 http://www.medworm.com/index.php?rid=4352514&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5166 In this work, the crystal structure of the β-trypsin–bovine pancreatic trypsin inhibitor (BPTI) complex was refined and the D and H atoms in the complex were identified using data from both 1.6 Å resolution X-ray diffraction and 2.15 Å resolution neutron diffraction. After crystallization in an H2O solution, the sample crystal was soaked in a D2O solution for about two weeks. The protonation states of the catalytic triad (Asp102, His57 and Ser195) were observed. These results confirmed that the nucleophilic reactivity of the hydroxyl group of Ser195 was increased by forming a hydrogen bond with His57. According to structural analysis, the trypsin–BPTI interfaces located at the scissile peptide and the active sites were inaccessible to solvent water, and the amide H atoms of P2â€... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4352514 Sat, 15 Jan 2011 00:00:00 +0100 4352514 http://www.medworm.com/index.php?rid=4352513&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fxb5025 Riboflavin biosynthesis is an essential pathway in bacteria, in contrast to animals, which obtain riboflavin from their diet. Therefore, the enzymes involved in the riboflavin-biosynthesis pathway are potential targets for the development of antibacterial drugs. Lumazine synthase, an enzyme that is involved in the penultimate step of riboflavin biosynthesis, catalyzes the formation of 6,7-dimethyl-8-ribityllumazine from 3,4-dihydroxy-2-butanone 4-phosphate and 5-amino-6-ribitylamino-2,4-(1H,3H)-pyrimidinedione. Lumazine synthase from Salmonella typhimurium (sLS) has been cloned, overexpressed, purified and was crystallized in three forms, each with different crystal packing. The crystal structure of sLS in the monoclinic space group P21 has been determined with 60 subunits per asymmetric ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4352513 Sat, 15 Jan 2011 00:00:00 +0100 4352513 http://www.medworm.com/index.php?rid=4352512&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5162 Pseudomonas aeruginosa utilizes the type II secretion machinery to transport virulence factors through the outer membrane into the extracellular space. Five proteins in the type II secretion system share sequence homology with pilin subunits of type IV pili and are called the pseudopilins. The major pseudopilin XcpTG assembles into an intraperiplasmic pilus and is thought to act in a piston-like manner to push substrates through an outer membrane secretin. The other four minor pseudopilins, XcpUH, XcpVI, XcpWJ and XcpXK, play less well defined roles in pseudopilus formation. It was recently discovered that these four minor pseudopilins form a quaternary complex that is presumed to initiate the formation of the pseudopilus and to localize to its tip. Here, the structure of XcpWJ was refined... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4352512 Sat, 15 Jan 2011 00:00:00 +0100 4352512 http://www.medworm.com/index.php?rid=4352511&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhm5093 E-ISA247 (voclosporin) is a cyclosporin A analogue that is in late-stage clinical development for the treatment of autoimmune diseases and the prevention of organ graft rejection. The X-ray crystal structures of E-ISA247 and its stereoisomer Z-ISA247 bound to cyclophilin A have been determined and their binding affinities were measured to be 15 and 61 nM, respectively, by fluorescence spectroscopy. The higher affinity of E-ISA247 can be explained by superior van der Waals contacts between its unique side chain and cyclophilin A. Comparison with the known ternary structure including calcineurin suggests that the higher immunosuppressive efficacy of E-ISA247 relative to cyclosporin A could be a consequence of structural changes in calcineurin induced by the modified E-ISA247 side chain. (S... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4352511 Sat, 15 Jan 2011 00:00:00 +0100 4352511 http://www.medworm.com/index.php?rid=4324692&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5161 In this study, the crystal structure of the effector-binding domain (EBD) of RovM, the first LTTR protein described as being involved in virulence regulation, was determined at a resolution of 2.4 Å. Size-exclusion chromatography and comparison with structures of full-length LTTRs show that RovM is most likely to adopt a tetrameric arrangement with two distant DNA-binding domains (DBDs), causing the DNA to bend around it. Additionally, a cavity was detected in RovM which could bind small inducer molecules. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4324692 Sat, 08 Jan 2011 18:26:05 +0100 4324692 http://www.medworm.com/index.php?rid=4324696&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5177 PAD4 is a peptidylarginine deiminase that catalyzes citrullination, a type of post-translational modification. In this reaction, arginine residues in proteins are converted to citrulline. PAD4 promotes the deimination of arginine residues in histones and may regulate transcription in the context of the chromatin. Single-nucleotide polymorphisms (SNP) in the gene encoding PAD4 identified it as one of the genes associated with susceptibility to rheumatoid arthritis. The PAD4 SNP involve three amino-acid substitutions: Ser55 to Gly, Ala82 to Val and Ala112 to Gly. Autoantibodies for improperly citrullinated proteins have been found in rheumatoid arthritis patients, suggesting that the PAD4SNP mRNA is more stable than the conventional PAD4 mRNA and/or the PAD4SNP protein possesses a higher cit... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4324696 Sat, 08 Jan 2011 00:00:00 +0100 4324696 http://www.medworm.com/index.php?rid=4324695&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5165 The Thermus thermophilus protein TTHA0988 is a protein of unknown function which represents a fusion of two proteins found almost ubiquitously across the bacterial kingdom. These two proteins perform a role regulating sporulation in Bacillus subtilis, where they are known as KipI and KipA. kipI and kipA genes are usually found immediately adjacent to each other and are often fused to produce a single polypeptide, as is the case with TTHA0988. Here, three crystal forms are reported of TTHA0988, the first structure to be solved from the family of `KipI–KipA fusion' proteins. Comparison of the three forms reveals structural flexibility which can be described as a hinge motion between the `KipI' and `KipA' components. TTHA0988 is annotated in various databases as a putative allophanate hy... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4324695 Sat, 08 Jan 2011 00:00:00 +0100 4324695 http://www.medworm.com/index.php?rid=4324694&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fyt5030 A sequence around the start codon of the mRNA of human thymidylate synthase (TS) folds into a secondary-structure motif in which the initiation site is sequestered in a metastable hairpin. Binding of the protein to its own mRNA at the hairpin prevents the production of TS through a translation-repression feedback mechanism. Stabilization of the mRNA hairpin by other ligands has been proposed as a strategy to reduce TS levels in anticancer therapy. Rapidly proliferating cells require high TS activity to maintain the production of thymidine as a building block for DNA synthesis. The crystal structure of a model oligonucleotide (TS1) that represents the TS-binding site of the mRNA has been determined. While fluorescence studies showed that the TS1 RNA preferentially adopts a hairpin structure... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4324694 Sat, 08 Jan 2011 00:00:00 +0100 4324694 http://www.medworm.com/index.php?rid=4324693&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5164 Propanediol metabolism in Citrobacter freundii occurs within a metabolosome, a subcellular proteinaceous bacterial microcompartment. The propanediol-utilization (Pdu) microcompartment shell is constructed from thousands of hexagonal-shaped protein complexes made from seven different types of protein subunit. Here, the structure of the bacterial microcompartment protein PduT, which has a tandem structural repeat within the subunit and forms trimers with pseudo-hexagonal symmetry, is reported. This trimeric assembly forms a flat approximately hexagonally shaped disc with a central pore that is suitable for a 4Fe–4S cluster. The essentially cubic shaped 4Fe–4S cluster conforms to the threefold symmetry of the trimer with one free iron, the role of which could be to supply electrons to an... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4324693 Sat, 08 Jan 2011 00:00:00 +0100 4324693 http://www.medworm.com/index.php?rid=4263969&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhm5091 Structural data are reported for five antifolates, namely 2,4-diamino-6-[5′-(5-carboxypentyloxy)-2′-methoxybenzyl]-5-methylpyrido[2,3-d]pyrimidine, (1), and the 5′-[3-(ethoxycarbonyl)propoxy]-, (2), 5′-[3-(ethoxycarbonyl)butoxy]-, (3), 5′-[3-(ethoxycarbonyl)pentyloxy]-, (4), and 5′-benzyloxy-, (5), derivatives, which are potent and selective for Pneumocystis carinii dihydrofolate reductase (pcDHFR). Crystal structures are reported for their ternary complexes with NADPH and pcDHFR refined to between 1.4 and 2.0 Å resolution and for that of 3 with human DHFR (hDHFR) to 1.8 Å resolution. These data reveal that the carboxylate of the ω-carboxyalkoxy side chain of 1, the most potent inhibitor in this series, forms ionic interactions with the conserved Arg75 in the substrate-b... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4263969 Sat, 18 Dec 2010 13:52:33 +0100 4263969 http://www.medworm.com/index.php?rid=4263977&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fme0434 (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4263977 Thu, 16 Dec 2010 00:00:00 +0100 4263977 http://www.medworm.com/index.php?rid=4263976&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5173 SgrAI is a type II restriction endonuclease that cuts an unusually long recognition sequence and exhibits allosteric self-activation with expansion of DNA-sequence specificity. The three-dimensional crystal structures of SgrAI bound to cleaved primary-site DNA and Mg2+ and bound to secondary-site DNA with either Mg2+ or Ca2+ are presented. All three structures show a conformation of enzyme and DNA similar to the previously determined dimeric structure of SgrAI bound to uncleaved primary-site DNA and Ca2+ [Dunten et al. (2008), Nucleic Acids Res. 36, 5405–5416], with the exception of the cleaved bond and a slight shifting of the DNA in the SgrAI/cleaved primary-site DNA/Mg2+ structure. In addition, a new metal ion binding site is located in one of the two active sites in this structure, w... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4263976 Thu, 16 Dec 2010 00:00:00 +0100 4263976 http://www.medworm.com/index.php?rid=4263975&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5172 Thymidylate synthase (TS) is a well validated target in cancer chemotherapy. Here, a new crystal form of the R163K variant of human TS (hTS) with five subunits per asymmetric part of the unit cell, all with loop 181–197 in the active conformation, is reported. This form allows binding studies by soaking crystals in artificial mother liquors containing ligands that bind in the active site. Using this approach, crystal structures of hTS complexes with FdUMP and dUMP were obtained, indicating that this form should facilitate high-throughput analysis of hTS complexes with drug candidates. Crystal soaking experiments using oxidized glutathione revealed that hTS binds this ligand. Interestingly, the two types of binding observed are both asymmetric. In one subunit of the physiological dimer co... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4263975 Thu, 16 Dec 2010 00:00:00 +0100 4263975 http://www.medworm.com/index.php?rid=4263974&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5218 In this study, procedures for extracting more accurate anomalous signals by merging data from multiple crystals are devised and tested. SAD phasing tests were made with a relatively large (1456 ordered residues) poorly diffracting (dmin = 3.5 Å) selenomethionyl protein (20 Se). It is quantified that the anomalous signal, success in substructure determination and accuracy of phases and electron-density maps all improve with an increase in the number of crystals used in merging. Structure solutions are possible when no single crystal can support structural analysis. It is proposed that such multi-crystal strategies may be broadly useful when only weak anomalous signals are available. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=4263974 Thu, 16 Dec 2010 00:00:00 +0100 4263974