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EzCatDB: the Enzyme Catalytic-mechanism Database

N. Nagano
2004 Nucleic Acids Research  
The EzCatDB groups enzyme data in the Protein Data Bank (PDB) and the SWISS-PROT database with identical domain compositions, Enzyme Commission (EC) numbers and catalytic mechanisms.  ...  The EzCatDB (Enzyme Catalytic-mechanism Database) specifically includes catalytic mechanisms of enzymes in terms of sequences and tertiary structures of enzymes, and proposed catalytic mechanisms, along  ...  ACKNOWLEDGEMENTS I would like to thank Yuko Hasegawa, Keitarou Nonaka, Kenji Morita, Munehiro Sugiyama and Junko Some, who assisted in the annotation of enzyme data and collection of the literature.  ... 
doi:10.1093/nar/gki080 pmid:15608227 pmcid:PMC540034 fatcat:4efuckypgbbg5djef7yb2ecoru

Organic cofactors in the metabolism of Dehalococcoides mccartyi strains

C. J. Schipp, E. Marco-Urrea, A. Kublik, J. Seifert, L. Adrian
2013 Philosophical Transactions of the Royal Society of London. Biological Sciences  
(d) Cofactors and vitamins in Dehalococcoides strains Organic cofactors play crucial roles in the catalysis of biochemical reactions in the metabolism of all living organisms.  ...  This was in accordance with the expectations at least for the enzyme-bound cofactor biosynthesis enzymes because such cofactor biosynthesis enzymes are needed in much lower amounts than enzymes involved  ... 
doi:10.1098/rstb.2012.0321 pmid:23479751 pmcid:PMC3638462 fatcat:j3bf2o6nnfgvdmc3gwem6kptoq

On the Metal Cofactor in the Tyrosinase Family

Francisco Solano
2018 International Journal of Molecular Sciences  
The production of pigment in mammalian melanocytes requires the contribution of at least three melanogenic enzymes, tyrosinase and two other accessory enzymes called the tyrosinase-related proteins (Trp1  ...  The last two proteins are paralogues to tyrosinase, and they appeared late in evolution by triplication of the tyrosinase gene. Tyrosinase is a copper-enzyme, and Trp2 is a zinc-enzyme.  ...  Zinc is the second most abundant transition metal in organisms after iron, and it is the only metal that appears in all enzyme classes as a catalytic or structural cofactor, so that the biological impact  ... 
doi:10.3390/ijms19020633 pmid:29473882 pmcid:PMC5855855 fatcat:5vumalqvmngpro7unzce2haiz4

The methanogenic redox cofactor F420 is widely synthesized by aerobic soil bacteria

Blair Ney, F Hafna Ahmed, Carlo R Carere, Ambarish Biswas, Andrew C Warden, Sergio E Morales, Gunjan Pandey, Stephen J Watt, John G Oakeshott, Matthew C Taylor, Matthew B Stott, Colin J Jackson (+1 others)
2016 The ISME Journal  
F 420 is a low-potential redox cofactor that mediates the transformations of a wide range of complex organic compounds.  ...  Considered one of the rarest cofactors in biology, F 420 is best known for its role in methanogenesis and has only been chemically identified in two phyla to date, the Euryarchaeota and Actinobacteria.  ...  smegmatis mc 2 4517 and the three anonymous reviewers for their helpful suggestions.  ... 
doi:10.1038/ismej.2016.100 pmid:27505347 pmcid:PMC5315465 fatcat:k4bd7zazc5e43dg2b5fyid3moe

Crystal structure of the human adenovirus proteinase with its 11 amino acid cofactor

J. Ding, W. J. McGrath, R. M. Sweet, W. F. Mangel
1996 EMBO Journal  
To ascertain which residues are involved in catalysis, hence the class of the proteinase, and to determine the structural basis of substrate specificity and of cofactor activation of the enzyme, we have  ...  In (B), the residues involved in catalysis in papain are shown after alignment of the papain molecule to fit the equivalent residues in AVP.  ... 
doi:10.1002/j.1460-2075.1996.tb00526.x fatcat:wg3iii7hgna4litqfruidmligi

LUCApedia: a database for the study of ancient life

Aaron David Goldman, Tess M. Bernhard, Egor Dolzhenko, Laura F. Landweber
2012 Nucleic Acids Research  
Organisms represented by the root of the universal evolutionary tree were most likely complex cells with a sophisticated protein translation system and a DNA genome encoding hundreds of genes.  ...  ACKNOWLEDGEMENTS The authors thank the members of the Landweber lab for useful comments and for help testing the web server.  ...  The authors also thank John Baross and Ram Samudrala for early discussions of the LUCApedia concept. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gks1217 pmid:23193296 pmcid:PMC3531223 fatcat:p6qttuzl25hzvodraejht7ylti

The Biosynthesis of Flavin Cofactors in Listeria monocytogenes

Maria Sebastián, Sonia Arilla-Luna, Jacques Bellalou, Inmaculada Yruela, Milagros Medina
2019 Journal of Molecular Biology  
Our data exemplify alternative strategies for FMN and FAD biosynthesis and homeostasis, envisaging that in Listeria two FADSs might be required to fulfill the supply of flavin cofactors under niches that  ...  As FADSs are attractive antimicrobial targets, understanding of FADSs traits in different species is essential to help in the discovery of specific antimicrobials.  ...  Acknowledgments This work has been supported by the Spanish Ministry of Economy, Industry and Competitiveness (MINECO) (BIO2016-75183-P AEI/FEDER, UE, to M.M.) and the Government of Aragón-FEDER  ... 
doi:10.1016/j.jmb.2019.05.029 pmid:31132361 fatcat:luloegtxyralpowtd6gvg2dmkm

Diversity and Functional Analysis of the FeMo-Cofactor Maturase NifB

Simon Arragain, Emilio Jiménez-Vicente, Alessandro A. Scandurra, Stefan Burén, Luis M. Rubio, Carlos Echavarri-Erasun
2017 Frontiers in Plant Science  
The product of NifB activity is called NifB-co, a complex [8Fe-9S-C] cluster that serves as obligate intermediate in the biosyntheses of the active-site cofactors of all known nitrogenases.  ...  In addition, purified C. tepidum NifB exhibited activity in the in vitro NifB-dependent nitrogenase reconstitution assay.  ...  The curated NifB database contains 45 Firmicutes species likely to be diazotrophic organisms.  ... 
doi:10.3389/fpls.2017.01947 pmid:29250084 pmcid:PMC5715403 fatcat:7c3jvzgby5exdgx2qmyrvroi2y

The Role of the Nucleotides in the Insertion of the bis-Molybdopterin Guanine Dinucleotide Cofactor into apo-Molybdoenzymes

Kim Tiedemann, Chantal Iobbi-Nivol, Silke Leimkühler
2022 Molecules  
the role of the nucleotides of bis-MGD and bis-MPT cofactors in Moco insertion and the activity of molybdoenzymes in direct comparison.  ...  Using the well-known E. coli TMAO reductase TorA as a model enzyme for cofactor insertion, we were able to show that the GMP nucleotides of bis-MGD are crucial for the insertion of the bis-MGD cofactor  ...  With the exception of nitrogenase, the molybdenum cofactor (Moco) is the common element in all molybdoenzymes from different organisms.  ... 
doi:10.3390/molecules27092993 pmid:35566344 pmcid:PMC9103625 fatcat:y5l6efwnyba4naxe3yheuppc74

Structural Investigation of the GlmS Ribozyme Bound to Its Catalytic Cofactor

Jesse C. Cochrane, Sarah V. Lipchock, Scott A. Strobel
2007 Chemistry and Biology  
, but instead functions as a catalytic cofactor for the reaction.  ...  This demonstrates that RNA, like protein enzymes, can employ the chemical diversity of small molecules to promote catalytic activity.  ...  This work was supported by grants from the National Science Foundation (MCB0544255) and the National Institutes of Health (GM022778) to S.A.S.  ... 
doi:10.1016/j.chembiol.2006.12.005 pmid:17196404 pmcid:PMC1847778 fatcat:s3rd3q3j3rfefl7caajcnyjc5y

Effects of deletions at the C-terminus of tobacco acetohydroxyacid synthase on the enzyme activity and cofactor binding

Joungmok KIM, Dong-Gil BEAK, Young-Tae KIM, Jung-Do CHOI, Moon-Young YOON
2004 Biochemical Journal  
within contact distance of the cofactors.  ...  Owing to the unique presence of these biosynthetic pathways in plants and micro-organisms, AHAS has been widely investigated as an attractive target of several classes of herbicides.  ...  The branched-chain amino acids are not synthesized in animals, but are made by micro-organisms and plants.  ... 
doi:10.1042/bj20040427 pmid:15521822 pmcid:PMC1134088 fatcat:e4vpoqteejhs3h32zrtmlg6z7q

Shared-intermediates in the biosynthesis of thio-cofactors: Mechanism and functions of cysteine desulfurases and sulfur acceptors

Katherine A. Black, Patricia C. Dos Santos
2015 BBA - Molecular Cell Research  
Acknowledgements The research in PDS laboratory is supported by the National Science Foundation (MCB-1054623).  ...  of these enzymes in catalysis.  ...  However, the presence of additional cysteine desulfurases in these organisms suggests that the biosynthesis of Fe-S clusters in this organism is decoupled from the synthesis of other thio-cofactors.  ... 
doi:10.1016/j.bbamcr.2014.10.018 pmid:25447671 fatcat:xup372ultjemtb64vuncrshm6e

C–C bond forming radical SAM enzymes involved in the construction of carbon skeletons of cofactors and natural products

Kenichi Yokoyama, Edward A. Lilla
2018 Natural product reports (Print)  
An emerging group of radical SAM enzymes that catalyze C–C bond formations in natural product and cofactor biosynthesis are discussed.  ...  We thank Dr Margot Wuebbens for proofreading the manuscript and providing feedbacks.  ...  Acknowledgments Funding source statement This work was supported by the Duke University Medical Center and National Institute of General Medical Sciences R01 GM112838 and R01 GM115729 (to K. Y.).  ... 
doi:10.1039/c8np00006a pmid:29633774 pmcid:PMC6051890 fatcat:jif5a7pmhjae3oktmzuybujotm

Determinants of Cofactor Specificity for the Glucose-6-Phosphate Dehydrogenase from Escherichia coli: Simulation, Kinetics and Evolutionary Studies

Matias Fuentealba, Rodrigo Muñoz, Pablo Maturana, Adriana Krapp, Ricardo Cabrera, Claudio M Soares
2016 PLoS ONE  
Throughout the different stages of purification, the enzyme activity was followed by the Determinants of Cofactor Specificity in the G6PDH from E. coli PLOS ONE |  ...  In the absence of both positive charges the enzyme was unable to discriminate NADP + from NAD + .  ...  Phylogenetic Analysis of Bacterial G6PDHs In order to generate a phylogenetic tree of bacterial G6PDHs, we first searched the Swiss-Prot and TrEMBL (UniProtKB) databases for sequences of enzymes that have  ... 
doi:10.1371/journal.pone.0152403 pmid:27010804 pmcid:PMC4807051 fatcat:jpnewgx37nfddkmcrmhzfap4wm

Cofactor Editing by the G-protein Metallochaperone Domain Regulates the Radical B12Enzyme IcmF

Zhu Li, Kenichi Kitanishi, Umar T. Twahir, Valentin Cracan, Derrell Chapman, Kurt Warncke, Ruma Banerjee
2017 Journal of Biological Chemistry  
Adenosyltransferase in turn converts cob(II)alamin to AdoCbl in the presence of ATP and a reductant. The repaired cofactor is then reloaded onto IcmF in a GTPase-gated step.  ...  DeMartino IcmF is a 5-deoxyadenosylcobalamin (AdoCbl)-dependent enzyme that catalyzes the carbon skeleton rearrangement of isobutyryl-CoA to butyryl-CoA.  ...  B. helped conceive the experiments, analyzed the data, and co-wrote the manuscript. All authors approved the final version of the manuscript.  ... 
doi:10.1074/jbc.m117.775957 pmid:28130442 pmcid:PMC5354503 fatcat:sm5t7xsv5je55mswivlknvnc3u
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