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The Cytochrome P450 Engineering Database: integration of biochemical propertiesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The online accessible version of the CYPED at http://www.cyped.uni-stuttgart.de provides a valuable tool for the analysis of sequences, structures and their relationships to biochemical properties. (Source: BMC Biochemistry)
Source: BMC Biochemistry - November 12, 2009 Category: Biochemistry Authors: Demet SirimFlorian WagnerAndrey LisitsaJuergen Pleiss Source Type: journals

Biosynthesis of the proteasome inhibitor syringolin A: the ureido group joining two amino acids originates from bicarbonateEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The results show that no additional syringolin A-specific genes were needed for the biosynthesis of the enigmatic ureido group joining two amino acids. They reveal the source of the ureido carbonyl group to be bicarbonate/carbon dioxide, which we hypothesize is incorporated by carbamylation of valine mediated by the sylC gene product(s). A similar mechanism may also play a role in the biosynthesis of other ureido-group-containing NRPS products known largely from cyanobacteria. (Source: BMC Biochemistry)
Source: BMC Biochemistry - October 28, 2009 Category: Biochemistry Authors: Christina RamelMicha ToblerMartin MeyerLaurent BiglerMarc-Olivier EbertBarbara SchellenbergRobert Dudler Source Type: journals

Ser170 of Bacillus thuringiensis Cry1Ab delta-endotoxin becomes anchored in a hydrophobic moiety upon insertion of this protein into Manduca sexta brush border membranesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Ion transport data for L157, S170, and S176, along with the mobility of the spin-labels, structural characterization of the resulting proteins, and toxicity assays against a target insect, suggest that the toxin undergoes conformational changes upon protein translocation into the midgut membrane. These conformational changes result in the midregion of the alpha-helix 5 being exposed to a hydrophobic-like environment. The location of these three residues in the toxin suggests that the entire alpha-helix becomes inserted in the insect midgut membrane. (Source: BMC Biochemistry)
Source: BMC Biochemistry - October 18, 2009 Category: Biochemistry Authors: Oscar AlzateCraig HemmanCristina OsorioRuss HilleDonald Dean Source Type: journals

Mapping of protein phosphatase-6 association with its SAPS domain regulatory subunit using a model of helical repeatsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The conserved SAPS domain in PP6R3 forms helical repeats similar to those in golgin p115 and negatively charged residues in interhelical loops are used to associate specifically with PP6. The results advance understanding of how distinctive helical repeat subunits uniquely distribute and differentially regulate closely related Ser/Thr phosphatases. (Source: BMC Biochemistry)
Source: BMC Biochemistry - October 15, 2009 Category: Biochemistry Authors: Julien GuergnonUrszula DerewendaJessica EdelsonDavid Brautigan Source Type: journals

Monitoring compartment-specific substrate cleavage by cathepsins B, K, L, and S at physiological pH and redox conditionsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The results revealed distinct cleavage patterns at all conditions analyzed, indicating compartment-specific processing of thyroglobulin by cysteine cathepsins. In particular, proteolytic activity of cathepsin S towards the substrate thyroglobulin can now be understood as instrumental for extracellular thyroid hormone liberation. Our study emphasizes that the proteolytic functions of cysteine cathepsins in the thyroid are not restricted to endo-lysosomes but include pivotal roles in extracellular substrate utilization. We conclude that understanding of the interplay and fine adjustment of protease networks in v...
Source: BMC Biochemistry - September 21, 2009 Category: Biochemistry Authors: Silvia JordansSasa Jenko-KokaljNicole KuhlSofia TedelindWolfgang SendtDieter BroemmeDusan TurkKlaudia Brix Source Type: journals

Identification of a nuclear localization motif in the serine/arginine protein kinase PSRPK of physarum polycephalumEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This study demonstrated that the 318PKKGDKYDKTD328 peptides localized in the C-terminal conserved domain of PSRPK with the Omega-loop structure could play a crucial role in the NLS function of PSRPK. (Source: BMC Biochemistry)
Source: BMC Biochemistry - August 24, 2009 Category: Biochemistry Authors: Shi-De LiuZhuo-Long ZhouZi-Yang LinQiu-Ling OuyangJian-Hua ZhangSheng-Li TianMiao Xing Source Type: journals

Biochemical characterization of malate synthase G of P. aeruginosaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The implication of the glyoxylate bypass in the pathology of various microorganisms makes malate synthase G an attractive new target for antibacterial therapy. The purification procedure and biochemical characterization assist in the development of antibacterial components directed against this target in P. aeruginosa. (Source: BMC Biochemistry)
Source: BMC Biochemistry - June 23, 2009 Category: Biochemistry Authors: Bart RoucourtNikki MinneboPatrick AugustijnsKirsten HertveldtGuido VolckaertRob Lavigne Source Type: journals

Insights into the role of Val45 and Gln182 of Escherichia coli MutY in DNA substrate binding and specificityEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The substrate specificities are altered in V45A, Q182L, and V45A/Q182L EcMutY mutants. V45A and Q182L mutants had reduced binding and glycosylase activities for A/G and A/8-oxoG mismatches and increased affinities towards T/G mismatch. However, in contrast to a previous report that Mig.MthI thymine DNA glycosylase can be converted to a MutY-like adenine glycosylase by replacing two residues (A50V and L187Q), both V45A and Q182L EcMutY mutants did not exhibit any T/G or T/8-oxoG glycosylase activity. The dominant negative phenotype of V45A EcMutY mutant protein is probably caused by its increased binding affinit...
Source: BMC Biochemistry - June 11, 2009 Category: Biochemistry Authors: Po-Wen ChangAmrita MadabushiA-Lien Lu Source Type: journals

DNA binding kinetics of two response regulators, PlnC and PlnD, from the bacteriocin regulon of Lactobacillus plantarum C11Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: We have characterised the DNA binding kinetics of the two regulators PlnC and PlnD from the bacteriocin locus in L. plantarum C11. Our data show that PlnC and PlnD, despite their strong homology to each other, differ greatly from each other in terms of binding affinity and cooperativity to the different promoters of the pln regulon. (Source: BMC Biochemistry)
Source: BMC Biochemistry - June 10, 2009 Category: Biochemistry Authors: Daniel StraumeRune JohansenMagnar BjorasIngolf NesDzung Diep Source Type: journals

Analysis of DNA relaxation and cleavage activities of recombinant Mycobacterium tuberculosis DNA topoisomerase I from a new expression and purification protocolEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Recombinant M. tuberculosis DNA topoisomerase I can be expressed as a soluble protein and purified in high yield from E. coli host with a new protocol. Analysis of DNA cleavage with M. tuberculosis DNA substrate showed that the preferred DNA cleavage sites have a C nucleotide in the -4 position. (Source: BMC Biochemistry)
Source: BMC Biochemistry - June 10, 2009 Category: Biochemistry Authors: Thirunavukkarasu AnnamalaiNeil DaniBokun ChengYuk-Ching Tse-Dinh Source Type: journals

TIPT2 and geminin interact with basal transcription factors to synergize in transcriptional regulationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Together, our study introduces a novel transcriptional regulator and its function in cooperation with chromatin associated factors and the basal transcription machinery. (Source: BMC Biochemistry)
Source: BMC Biochemistry - June 9, 2009 Category: Biochemistry Authors: Mara PitulescuMartin TeichmannLingfei LuoMichael Kessel Source Type: journals

TIPT2 and geminin interact with basal transcription factors to synergize in transcriptional regulationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Together, our study introduces a novel transcriptional regulator and its function in cooperation with chromatin associated factors and the basal transcription machinery. (Source: BMC Biochemistry)
Source: BMC Biochemistry - June 9, 2009 Category: Biochemistry Authors: Mara PitulescuMartin TeichmannLingfei LuoMichael Kessel Source Type: journals

A novel human NatA N-alpha-terminal acetyltransferase complex: hNaa16p-hNaa10p (hNat2-hArd1)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: At least two distinct NatA protein N-alpha-terminal acetyltransferases coexist in human cells potentially creating a more complex and flexible system for N-alpha-terminal acetylation as compared to lower eukaryotes. (Source: BMC Biochemistry)
Source: BMC Biochemistry - May 29, 2009 Category: Biochemistry Authors: Thomas ArnesenDarina GromykoDiane KagaboMatthew BettsKristian StarheimJan Erik VarhaugDave AndersonJohan Lillehaug Source Type: journals

The endocannabinoid anandamide is a precursor for the signaling lipid N-arachidonyl glycine through two distinct pathwaysEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: These data support the hypothesis that the signaling lipid NAGly is a metabolic product of AEA by both oxidative metabolism of the AEA ethanolamine moiety and through the conjugation of glycine to AA that is released during AEA hydrolysis by FAAH. (Source: BMC Biochemistry)
Source: BMC Biochemistry - May 21, 2009 Category: Biochemistry Authors: Heather BradshawNeta RimmermanSherry Shu-Jung HuValery BentonJordyn StuartKim MasudaBenjamin CravattDavid O'DellJ Michael Walker Source Type: journals

Biochemical characterization of bovine plasma thrombin-activatable fibrinolysis inhibitor (TAFI)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The findings presented here suggest that the properties of these two orthologous proteins are similar and that conclusions reached using the bovine TAFI may be extrapolated to the human protein. (Source: BMC Biochemistry)
Source: BMC Biochemistry - May 5, 2009 Category: Biochemistry Authors: Zuzana Valnickova, Morten Thaysen-Andersen, Peter Højrup, Trine Christensen, Kristian W Sanggaard, Torsten Kristensen and Jan J Enghild Source Type: journals

Biochemical characterization of bovine plasma thrombin-activatable fibrinolysis inhibitor (TAFI).Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: These findings suggest that the properties of these two orthologous proteins are similar and that conclusions reached using the bovine TAFI may be extrapolated to the human protein. (Source: BMC Biochemistry)
Source: BMC Biochemistry - May 5, 2009 Category: Biochemistry Authors: Zuzana Valnickova, Morten Thaysen-Andersen, Peter Hojrup, Trine Christensen, Kristian W Sanggaard, Torsten Kristensen and Jan J Enghild Source Type: journals

Exploring the functional interaction between POSH and Alix and the relevance to HIV-1 releaseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Thus, the cumulative results identified ALIX as an ubiquitination substrate of POSH and indicate that POSH and ALIX cooperate to facilitate efficient virus release. However, while ALIX is obligatory for the release of YPXnL-dependent HIV-1, POSH, albeit rate-limiting, may be functionally interchangeable. (Source: BMC Biochemistry)
Source: BMC Biochemistry - April 24, 2009 Category: Biochemistry Authors: Joerg Voetteler, Elena Iavnilovitch, Orit Fingrut, Vivian Shemesh, Daniel Taglicht, Omri Erez, Stefan Sorgel, Torsten Walther, Norbert Bannert, Ulrich Schubert and Yuval Reiss Source Type: journals

Identification of distinct SET/TAF-Ibeta domains required for core histone binding and quantitative characterisation of the interactionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This type of analysis allowed us to assess the relative affinities of SET/TAF-Ibeta for different histones and identify the domains of the protein required for effective histone recognition. Our findings are consistent with recent structural studies of SET/TAF-Ibeta and can be valuable to understand the role of SET/TAF-Ibeta in chromatin function. (Source: BMC Biochemistry)
Source: BMC Biochemistry - April 9, 2009 Category: Biochemistry Authors: Zoe Karetsou, Anastasia Emmanouilidou, Ioannis Sanidas, Stamatis Liokatis, Eleni Nikolakaki, Anastasia S Politou and Thomais Papamarcaki Source Type: journals

alpha-Sarcin catalytic activity is not required for cytotoxicityEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We conclude that although protein synthesis inhibition likely contributes to cell death, it is not required. Thus, our results suggest that alpha-sarcin can promote cell death through a previously unappreciated mechanism that is independent of rRNA cleavage and JNK activation. (Source: BMC Biochemistry)
Source: BMC Biochemistry - April 3, 2009 Category: Biochemistry Authors: Spencer C Alford, Joel D Pearson, Amanda Carette, Robert J Ingham and Perry L Howard Source Type: journals

Characterisation of the paralytic shellfish toxin biosynthesis gene clusters in Anabaena circinalis AWQC131C and Aphanizomenon sp. NH-5Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The PST biosynthesis gene cluster presents a mosaic structure, whereby genes have apparently transposed in segments of varying size, resulting in different gene arrangements in all three sxt clusters sequenced so far. The gene cluster organizational structure and sequence similarity seems to reflect the phylogeny of the producer organisms, indicating that the gene clusters have an ancient origin, or that their lateral transfer was also an ancient event. The knowledge we gain from the characterisation of the PST biosynthesis gene clusters, including the identity and sequence of the genes involved in the biosynt...
Source: BMC Biochemistry - March 30, 2009 Category: Biochemistry Authors: Troco K Mihali, Ralf Kellmann and Brett A Neilan Source Type: journals

The roles of aldehyde dehydrogenases (ALDHs) in the PDH bypass of ArabidopsisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The PDH bypass is active in sporophytic tissue of plants. Blocking this pathway via triple ALDH mutants does not uncover obvious visible phenotypes. (Source: BMC Biochemistry)
Source: BMC Biochemistry - March 25, 2009 Category: Biochemistry Authors: Yanling Wei, Ming Lin, David J. Oliver and Patrick S. Schnable Source Type: journals

A novel method for screening the glutathione transferase inhibitorsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: It appears that the F2 peptide can be used as a new potent specific GST inhibitor. It is proposed that the novel method, described in this report, might be useful for screening the inhibitors of not only GST but also other enzymes. (Source: BMC Biochemistry)
Source: BMC Biochemistry - March 16, 2009 Category: Biochemistry Authors: Zhijun Wang, Li Jin, Grzegorz Wegrzyn and Alicja Wegrzyn Source Type: journals

Human Rad51 mediated DNA unwinding is facilitated by conditions that favour Rad51-dsDNA aggregationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: RAD52 itself being a highly aggregated protein perhaps acts as scaffold to bring together RAD51 and DNA molecules into large co-aggregates of RAD52-RAD51-DNA complexes to promote RAD51 mediated DNA unwinding reaction, when appropriate nucleotide cofactors are available, presumably through macromolecular crowding effects. Our work highlights the functional link between aggregation of protein-DNA complexes and DNA unwinding in RAD51 system. (Source: BMC Biochemistry)
Source: BMC Biochemistry - January 9, 2009 Category: Biochemistry Authors: Kamakshi Balakrishnan, Neeraja M Krishnan, Anagha Kulkarni and Basuthkar J Rao Source Type: journals

Modification of carbonic anhydrase II with acetaldehyde, the first metabolite of ethanol, leads to decreased enzyme activityEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The acetaldehyde-derived modifications in CA II molecule may have physiological consequences in alcoholic patients. (Source: BMC Biochemistry)
Source: BMC Biochemistry - November 27, 2008 Category: Biochemistry Authors: Fatemeh Bootorabi, Janne Janis, Jarkko Valjakka, Sari Isoniemi, Pirjo Vainiotalo, Daniela Vullo, Claudiu T Supuran, Abdul Waheed, William S Sly, Onni Niemela and Seppo Parkkila Source Type: journals

Lipid bilayer composition influences small multidrug transportersEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions These findings show that the physical state of the membrane modifies drug transport and that substrate translocation is dependent on in vitro lipid composition. Multidrug transport activity seems to respond to alterations in the lateral forces exerted upon the transport proteins by the bilayer. (Source: BMC Biochemistry)
Source: BMC Biochemistry - November 25, 2008 Category: Biochemistry Authors: Kalypso Charalambous, David Miller, Paul Curnow and Paula J Booth Source Type: journals

The FF domains of yeast U1 snRNP protein Prp40 mediate interactions with Luc7 and Snu71Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Prp40, Luc7, and Snu71 appear to form a subcomplex within the yeast U1snRNP. Our data suggests that the N-terminal FF domains are critical for these interactions. Crystallization of Prp40, Luc7, and Snu71 have failed so far but co-crystallization of pairs or the whole tri-complex may facilitate crystallographic and further functional analysis. (Source: BMC Biochemistry)
Source: BMC Biochemistry - November 11, 2008 Category: Biochemistry Authors: Claudia Ester and Peter Uetz Source Type: journals

Displacement affinity chromatography of protein phosphatase one (PP1) complexesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This modification of the microcystin-Sepharose technique offers an effective means of purifying novel PP1 regulatory subunits and provides a simple method to uncover a link between PP1 and additional cellular processes. (Source: BMC Biochemistry)
Source: BMC Biochemistry - November 10, 2008 Category: Biochemistry Authors: Greg BG Moorhead, Laura Trinkle-Mulcahy, Mhairi Nimick, Veerle G De Wever, David G Campbell, Robert Gourlay, Yun W Lam and Angus I Lamond Source Type: journals

Immunoaffinity purification and characterization of mitochondrial membrane-bound D-3-hydroxybutyrate dehydrogenase from Jaculus orientalisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: This study applies immunoaffinity chromatography to purify BDH, the membrane-bound and lipid-dependent enzyme, as a 31 kDa single polypeptide chain. In addition, bacterial BDH isolation was achieved in a two-step purification procedure, improving the knowledge of an enzyme involved in the lipid metabolism of a unique hibernating mammal. Sequence alignment revealed conserved putative amino acids for possible NAD+ interaction. (Source: BMC Biochemistry)
Source: BMC Biochemistry - September 30, 2008 Category: Biochemistry Authors: Driss Mountassif, Pierre Andreoletti, Zakaria El Kebbaj, Adnane Moutaouakkil, Mustapha Cherkaoui-Malki, Norbert Latruffe and M'hammed Saïd El Kebbaj Source Type: journals

Immuno-affinity purification and characterization of the mitochondrial membrane bound D-3-hydroxybutyrate dehydrogenase from Jaculus orientalisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This study applies immunoaffinity chromatography to purify BDH, the membrane-bound and lipid-dependent enzyme, as a 31 kDa single polypeptide chain. In addition, bacterial BDH isolation was achieved in a two-step purification procedure, improving the knowledge of an enzyme involved in the lipid metabolism of a unique hibernating mammal. Sequence alignment revealed conserved putative amino acids for possible NAD+ interaction. (Source: BMC Biochemistry)
Source: BMC Biochemistry - September 30, 2008 Category: Biochemistry Authors: Driss Mountassif, Pierre Andreoletti, Zakaria El Kebbaj, Adnane Moutaouakkil, Mustapha Cherkaoui Malki, Norbert Latruffe and M'hammed Said El Kebbaj Source Type: journals

The serine/threonine kinase Stk33 exhibits autophosphorylation and phosphorylates the intermediate filament protein VimentinEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We hypothesize that Stk33 is involved in the in vivo dynamics of the intermediate filament cytoskeleton by phosphorylating vimentin. (Source: BMC Biochemistry)
Source: BMC Biochemistry - September 23, 2008 Category: Biochemistry Authors: Bastienne Brauksiepe, Alejandro O Mujica, Harald Herrmann and Erwin R Schmidt Source Type: journals

YB-1 promotes microtubule assembly in vitro through interaction with tubulin and microtubulesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: These results suggest that YB-1 may regulate microtubule assembly in vivo and that its interaction with tubulin may contribute to the control of mRNA translation. (Source: BMC Biochemistry)
Source: BMC Biochemistry - September 15, 2008 Category: Biochemistry Authors: Konstantin G Chernov, Alain Mechulam, Nadezhda V Popova, David Pastre, Elena S Nadezhdina, Olga V Skabkina, Nina A Shanina, Viktor D Vasiliev, Anne Tarrade, Judith Melki, Vandana Joshi, Sonia Baconnais, Flavio Toma, Lev P Ovchinnikov and Patrick A Curmi Source Type: journals

The central proline rich region of POB1/REPS2 plays a regulatory role in epidermal growth factor receptor endocytosis by binding to 14-3-3 and SH3 domain-containing proteinsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Our findings are relevant to the characterization of the molecular mechanism underlying the involvement of POB1/REPS2, SH3 and 14-3-3 proteins in receptor endocytosis, suggesting that 14-3-3 could work by bridging the EGF receptor and the scaffold protein POB1/REPS2. (Source: BMC Biochemistry)
Source: BMC Biochemistry - July 22, 2008 Category: Biochemistry Authors: Laura Tomassi, Anna Costantini, Salvatore Corallino, Elena Santonico, Martina Carducci, Gianni Cesareni and Luisa Castagnoli Source Type: journals

Functional and biochemical characterization of the 20S proteasome in a yeast temperature-sensitive mutant, rpt6-1Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Two alpha-subunits (alpha1 and alpha7) of the 20S proteasome in the rpt6-1 mutant differed from their wild-type counterparts and peptidase activities were found to be lower in the mutant than in the wild-type strain. (Source: BMC Biochemistry)
Source: BMC Biochemistry - July 21, 2008 Category: Biochemistry Authors: Aktar UZZAMAN Chouduri, Toshinobu Tokumoto, Hideo Dohra, Takashi Ushimaru and Shinpei Yamada Source Type: journals

Modulation of the pharmacological effects of enzymatically-active PLA2 by BTL-2, an isolectin isolated from the Bryothamnion triquetrum red algaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The unexpected results observed for the PLA2-BTL-2 complex strongly suggest that the pharmacological activity of this PLA2 is not solely dependent on the presence of enzymatic activity, and that other pharmacological regions may also be involved. In addition, we describe for the first time an interaction between two different molecules, which form a stable complex with significant changes in their original biological action. This opens new possibilities for understanding the function and action of crude venom, an extremely complex mixture of different molecules. (Source: BMC Biochemistry)
Source: BMC Biochemistry - June 6, 2008 Category: Biochemistry Authors: Simone CB Oliveira, Fabiana V Fonseca, Edson Antunes, Enilton A Camargo, Rafael P Morganti, Ricardo Aparício, Daniela O Toyama, Luís OS Beriam, Eudismar V Nunes, Benildo S Cavada, Celso S Nagano, Alexandre H Sampaio, Kyria S Nascimento and Marcos H Toya Source Type: journals

Isolation, characterization and molecular cloning of Duplex-Specific Nuclease from the hepatopancreas of the Kamchatka crabEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: We describe a new DSN from Kamchatka crab hepatopancreas, determining its primary structure and developing a preparative method for its purification. We found that DSN had unique substrate specificity, cleaving only DNA duplexes longer than 8 base pairs, or DNA in DNA-RNA hybrids. Interestingly, the DSN primary structure is homologous to well-known Serratia-like non-specific nucleases structures, but the properties of DSN are distinct. The unique substrate specificity of DSN should prove valuable in certain molecular biology applications. (Source: BMC Biochemistry)
Source: BMC Biochemistry - May 21, 2008 Category: Biochemistry Authors: Veronika E. Anisimova, Denis V. Rebrikov, Dmitry A. Shagin, Valery B. Kozhemyako, Natalia I. Menzorova, Dmitry B. Staroverov, Rustam Ziganshin, Laura L. Vagner, Valery A. Rasskazov, Sergey A. Lukyanov and Alex S. Shcheglov Source Type: journals

The Mycobacterium tuberculosis Rv2540c DNA sequence encodes a bifunctional chorismate synthaseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This is the first report showing that a bacterial CS is bifunctional. Primary deuterium kinetic isotope effects show that C4-proS hydrogen is being transferred during the reduction of FMNox by NADH and that hydride transfer contributes significantly to the rate-limiting step of FMN reduction reaction. Solvent kinetic isotope effects and proton inventory results indicate that proton transfer from solvent partially limits the rate of FMN reduction and that a single proton transfer gives rise to the observed solvent isotope effect. Multiple isotope effects suggest a stepwise mechanism for the reduction of FMNox. ...
Source: BMC Biochemistry - April 29, 2008 Category: Biochemistry Authors: Fernanda Ely, Jose ES Nunes, Evelyn K Schroeder, Jeverson Frazzon, Mario S Palma, Diogenes S Santos and Luiz A Basso Source Type: journals

Regulation of 5'-adenosine monophosphate deaminase in the freeze tolerant wood frog, Rana sylvaticaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Maintenance of long term viability under the ischemic conditions in frozen muscle requires attention to the control of cellular energetics. Differential regulatory controls on AMPD by mechanisms including binding to muscle proteins, actions of allosteric effectors, glucose and temperature effects, and reversible phosphorylation adjust enzyme function for an optimal role in controlling cellular adenylate levels in ischemic frozen muscle. Stable modification of AMPD properties via freeze-responsive phosphorylation may contribute both to AMPD control and to coordinating AMPD function with other enzymes of energy m...
Source: BMC Biochemistry - April 22, 2008 Category: Biochemistry Authors: Christopher A Dieni and Kenneth B Storey Source Type: journals

A new classification system for bacterial Rieske non-heme iron aromatic ring-hydroxylating oxygenasesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The new classification system provides the following features. First, the new classification system analyzes RHO enzymes as a whole. Second, the new classification system is not static but responds dynamically to the growing pool of RHO enzymes. Third, our classification can be applied reliably to the classification of incomplete RHOs. Fourth, the classification has direct applicability to experimental work. Fifth, the system provides new insights into the evolution of RHO systems based on enzyme interaction. (Source: BMC Biochemistry)
Source: BMC Biochemistry - April 3, 2008 Category: Biochemistry Authors: Ohgew Kweon, Seong-Jae Kim, Songjoon Baek, Jong-Chan Chae, Michael D Adjei, Dong-Heon Baek, Young-Chang Kim and Carl E Cerniglia Source Type: journals

Pro-protein convertases control the maturation and processing of the iron-regulatory protein, RGMc/hemojuvelinEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our results support a key role for PCs in maturation of RGMc that has implications for the physiological actions of this critical iron-regulatory protein. (Source: BMC Biochemistry)
Source: BMC Biochemistry - April 2, 2008 Category: Biochemistry Authors: David Kuninger, Robin Kuns-Hashimoto, Mahta Nili and Peter Rotwein Source Type: journals

The pyrroloquinoline quinone biosynthesis pathway revisited: a structural approachEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: PQQ is derived from the two amino acids glutamate and tyrosine encoded in the precursor peptide PqqA. Five reactions are necessary to form this quinone cofactor. The PqqA peptide is recognised by PqqE, which links the C9 and C9a, afterwards it is accepted by PqqF which cuts out the linked amino acids. The next reaction (Schiff base) is spontaneous, the following dioxygenation is catalysed by an unknown enzyme. The last cyclization and oxidation steps are catalysed by PqqC. Taken together the known facts of the different proteins we assign a putative function to all six proteins in PQQ biosynthesis pathway. (Sou...
Source: BMC Biochemistry - March 27, 2008 Category: Biochemistry Authors: Sandra Puehringer, Moritz Metlitzky and Robert Schwarzenbacher Source Type: journals

Functional role of the additional domains in inulosucrase (IslA) from Leuconostoc citreum CW28.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The C-terminal domain may have been acquired to anchor inulosucrase to the cell surface. Furthermore, the acquired domains in IslA interact with the catalytic core resulting in a new conformation that renders the enzyme more stable and switch the specificity from a hydrolytic to a transglycosylase mechanism. Based on these results, chimeric constructions may become a strategy to stabilize and modulate biocatalysts based on FTF activity. (Source: BMC Biochemistry)
Source: BMC Biochemistry - January 31, 2008 Category: Biochemistry Authors: Sandra del Moral, Clarita Olvera, Maria Elena Rodriguez and Agustin Lopez Munguia Source Type: journals

Components of the ubiquitin-proteasome pathway compete for surfaces on Rad23 family proteinsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We conclude that the competition of ubiquitin-proteasome pathway components for surfaces on Rad23 is important for the role of the Rad23 family proteins in proteasomal targeting. (Source: BMC Biochemistry)
Source: BMC Biochemistry - January 30, 2008 Category: Biochemistry Authors: Amanda M Goh, Kylie J Walters, Suzanne Elsasser, Rati Verma, Raymond J Deshaies, Daniel Finley and Peter M Howley Source Type: journals

Thermal dependency of RAG1 self-association propertiesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Together these results confirm that the functional form of RAG1 in V(D)J recombination is in the dimeric state, and that its stability under physiological conditions likely requires complex formation with RAG2. Additionally, in future structural and functional studies of RAG1, it will be important to take into account the temperature-dependent self-association properties of RAG1 described in this study. (Source: BMC Biochemistry)
Source: BMC Biochemistry - January 30, 2008 Category: Biochemistry Authors: Pallabi De, Shuying Zhao, Lori M Gwyn, LeAnn J Godderz, Mandy M Peak and Karla K Rodgers Source Type: journals

Blocking Binding of Bacillus thuringiensis Cry1Aa to Bombyx mori Cadherin Receptor Results in Only a Minor Reduction of ToxicityEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The results identify a novel receptor-binding epitope and demonstrate that virtual elimination of binding to cadherin BR-175 does not completely remove toxicity in the case of B. mori. (Source: BMC Biochemistry)
Source: BMC Biochemistry - January 24, 2008 Category: Biochemistry Authors: Taek H. You, Mi K. Lee, Jeremy L. Jenkins, Oscar Alzate and Donald H. Dean Source Type: journals

Association of SAP130/SF3b-3 with Cullin-RING ubiquitin ligase complexes and its regulation by the COP9 signalosomeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: SAP130 is a cullin binding protein that is likely involved in the Nedd8 pathway. The association of SAP130 with various cullin member proteins such as Cul1, Cul2 and Cul4A is modulated by CAND1 and CSN. As an established component of transcription and RNA processing complexes, we hypothesis that SAP130 may link CRL mediated ubiquitination to gene expression. (Source: BMC Biochemistry)
Source: BMC Biochemistry - January 3, 2008 Category: Biochemistry Authors: Suchithra Menon, Tomohiko Tsuge, Naoshi Dohmae, Koji Takio and Ning Wei Source Type: journals

Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interactionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: In the present study we have analysed the binding specificity of the POB1 EH domain. We show that it differs from other EH domains since it interacts with both NPF- and DPF-containing sequences. These unusual binding properties could be attributed to a different conformation of the binding pocket that allows to accommodate negative charges; moreover, we identified a cluster of solvent exposed Lys residues, which are only found in the EH domain of POB1, and influence binding to both NPF and DPF motifs. The characterization of structures of the DPF ligands described in this study and the POB1 EH domain will clea...
Source: BMC Biochemistry - December 21, 2007 Category: Biochemistry Authors: Elena Santonico, Simona Panni, Mattia Falconi, Luisa Castagnoli and Gianni Cesareni Source Type: journals

Downregulation of COP9 signalosome subunits differentially affects CSN complex and target protein stabilityEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: There exists a coordinated downregulation of CSN subunits in the CSN1 and CSN3 knockdowns. The underlying regulatory mechanisms are obscure. CSN5 seems to possess a specific status in HeLa cells. Its reduction is not connected with coordinated downregulation of other subunits. CSN knockdowns confirm that the stabilization of the CRL component Rbx1 is a major CSN function. In addition, downregulation of CSN subunits influences the stability of important cellular regulators such as c-Jun and p27. (Source: BMC Biochemistry)
Source: BMC Biochemistry - December 19, 2007 Category: Biochemistry Authors: Andreas Peth, Christoph Berndt, Wolfgang Henke and Wolfgang Dubiel Source Type: journals

Glutathionylation of beta-actin via a cysteinyl sulfenic acid intermediaryEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We conclude that glutathionylation of beta-actin may occur via spontaneous oxidation of a cysteinyl residue to a sulfenic acid that readily reacts with GSH to form a mixed disulfide. We also show that the reactivity and oxidation to a reactive protein thiol intermediary differ between different actin isoforms. (Source: BMC Biochemistry)
Source: BMC Biochemistry - December 10, 2007 Category: Biochemistry Authors: Magnus Johansson and Mathias Lundberg Source Type: journals

Metabolic signature of breast cancer cell line MCF-7: profiling of modified nucleosides via LC-IT MS couplingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The obtained results are discussed against the background of pathological changes in cell metabolism, resulting in new perspectives for modified nucleosides and related metabolites as possible biomedical markers for breast carcinoma in vivo. (Source: BMC Biochemistry)
Source: BMC Biochemistry - November 29, 2007 Category: Biochemistry Authors: Dino Bullinger, Hans Neubauer, Tanja Fehm, Stefan Laufer, Christoph H Gleiter and Bernd Kammerer Source Type: journals

Membrane binding of the neuronal calcium sensor recoverin - modulatory role of the charged carboxy-terminusEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our data indicate a small, but evident electrostatic contribution to the overall binding energy of recoverin association with lipid bilayer. Properties of the charged carboxy-terminus are consistent with a role of this region as an internal effector region that prolongs the time recoverin stays on the membrane by influencing its Ca2+-sensitivity. (Source: BMC Biochemistry)
Source: BMC Biochemistry - November 22, 2007 Category: Biochemistry Authors: Ivan I Senin, Valeriya A Churumova, Pavel P Philippov and Karl-Wilhelm Koch Source Type: journals