Catalytic site atlas

Present addresses: Gemma L. Julius O.

M-CSA is a database of enzyme reaction mechanisms. It provides annotation on the protein, catalytic residues, cofactors, and the reaction mechanisms of hundreds of enzymes. There are two kinds of entries in M-CSA. Glutamate racemase is responsible for the synthesis of D-glutamate, an essential building block of peptidoglycan, found in bacterial cell walls where it provides structural integrity. Due to its uniqueness to bacteria, peptidoglycan, and enzymes involved in its biosynthesis, are targets for designing new antibacterial drugs. Peptidoglycan is formed from a repeating unit of a disaccharide, N-acetylglucosamine and N-acetylmuramic acid to which a small group of amino acids L-alanine, D-alanine, D-glutamate and either lysine or diaminopimelic acid are covalently attached.

Catalytic site atlas

Our objectives with M-CSA are to provide an open data resource for the community to browse known enzyme reaction mechanisms and catalytic sites, and to use the dataset to understand enzyme function and evolution. We are releasing M-CSA as a new website and underlying database architecture. At the moment, M-CSA contains entries, of these with detailed mechanism information, and with information on the catalytic site residues only. Oxford University Press is a department of the University of Oxford. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide. Sign In or Create an Account. NAR Journals. Advanced Search. Search Menu. Article Navigation.

Total Views 6, Users of this asynchronous service can either upload their own structure file or request a deposited structure if it has not already be annotated by the CSA to be searched using the new templates, catalytic site atlas. These authors contributed equally to the paper as first authors.

Understanding which are the catalytic residues in an enzyme and what function they perform is crucial to many biology studies, particularly those leading to new therapeutics and enzyme design. The curated entries are used, along with the variation in residue type from the sequence comparison, to generate 3D templates of the catalytic sites, which in turn can be used to find catalytic sites in new structures. The CSA database schema has been re-designed and both the CSA data and search capabilities are presented in a new modern web interface. The database consists of two types of annotated site: an original hand-annotated set containing information extracted from the primary literature, using defined criteria to assign catalytic residues, and an additional homologous set, containing annotations inferred by PSI-BLAST and sequence alignment to one of the original set. CSA Version 1.

Federal government websites often end in. The site is secure. Preview improvements coming to the PMC website in October Learn More or Try it out now. The database consists of two types of annotated site: an original hand-annotated set containing information extracted from the primary literature, using defined criteria to assign catalytic residues, and an additional homologous set, containing annotations inferred by PSI-BLAST and sequence alignment to one of the original set. CSA Version 1. The CSA will be updated on a monthly basis to include homologous sites found in new PDBs, and new hand-annotated enzymes as and when their annotatation is completed. Enzymes are amongst the most studied biological molecules and are vital for all processes of life. The catalytic activity of an enzyme is performed by a small, highly conserved constellation of residues within the active site. Unlike the catalytic residues, residues responsible for binding the substrate are not as vital to the catalytic function of the enzyme and can change through evolution, sometimes allowing the enzyme to accommodate new substrates.

Catalytic site atlas

Federal government websites often end in. The site is secure. Preview improvements coming to the PMC website in October Learn More or Try it out now. Understanding which are the catalytic residues in an enzyme and what function they perform is crucial to many biology studies, particularly those leading to new therapeutics and enzyme design.

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Structure of native four-repeat satellite III sequence with non-canonical base interactions. More from Oxford Academic. Submit a comment. Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis. Gene genome and annotation. For each catalytic site a search can be performed returning all other catalytic sites in the CSA that have the same catalytic residues grouped by their E. Holliday, Tjaart A. A number of people have contributed to the CSA over the years as annotators and developers. Publications The Catalytic Site Atlas 2. Journal Article. MACiE: exploring the diversity of biochemical reactions. Sign In or Create an Account. Submit a comment. Supplementary data. Please check for further notifications by email.

Craig T. Porter, Gail J.

Structure of native four-repeat satellite III sequence with non-canonical base interactions. Science and Mathematics. The origin recognition complex requires chromatin tethering by a hypervariable intrinsically disordered region that is functionally conserved from sponge to man. Glutamate racemase is responsible for the synthesis of D-glutamate, an essential building block of peptidoglycan, found in bacterial cell walls where it provides structural integrity. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Total Views 6, The evolution of enzyme function in the isomerases. Nucleic Acids Res. The CSA database schema has been re-designed and both the CSA data and search capabilities are presented in a new modern web interface. When an entry was found by sequence comparison, it was possible to follow the link to the original entry. The CSA database schema has been re-designed and both the CSA data and search capabilities are presented in a new modern web interface. Evidence tags provide a direct link to the literature from which the annotations where derived.