Catalytic site atlas

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, catalytic site atlas, using defined criteria to catalytic site atlas catalytic residues, and an additional homologous set, containing annotations inferred by PSI-BLAST and sequence alignment to one of the original set.

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.

Catalytic site atlas

Present addresses: Gemma L. Julius O. Nicholas Furnham, Gemma L. Holliday, Tjaart A. Jacobsen, William R. Pearson, Janet M. Thornton, The Catalytic Site Atlas 2. 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. As biological catalysts they facilitate the many metabolic processes and pathways that are critical for life to exist and have been the focus of studies by biologists and chemists for over years. They are also some of the principal targets in pharmaceutical drug development, with many approved drugs acting to modify the action of enzymes implicated in disease processes. In addition they are often the focal point for biotechnology applications.

We are releasing M-CSA as a new website and underlying database architecture. Each entry contained a link to a list of homologous catalytic site atlas identified using the in-house homology methodand a link was also provided to other CSA entries identical EC numbers or UniProKB identifier to the entry currently being viewed.

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.

Craig T. Porter, Gail J. Bartlett, Janet M. CSA Version 1. Enzymes are amongst the most studied biological molecules and are vital for all processes of life.

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. Enzymes are the macromolecules that catalyze the chemical reactions of life. The study of enzymes draws from the fields of biochemistry, genomics, protein structure, organic chemistry, computational chemistry, thermodynamics, and metabolomics, amongst others. As discussed below, current literature and biological databases with enzyme information mirror this diversity. Enzymes are one of the most common products of the translation of genetic information. Protein sequence databases, most notably UniProtKB and its manually curated subset, Swiss-Prot, capture protein sequence data, including that for enzymes 1.

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It provides annotation on the protein, catalytic residues, cofactors, and the reaction mechanisms of hundreds of enzymes. Article Contents Abstract. Advanced Search. Evidence tags provide a direct link to the literature from which the annotations where derived. Science and Mathematics. When an entry was found by sequence comparison, it was possible to follow the link to the original entry. Funding for open access charge: The Wellcome Trust. Last updates Summer - More entries with mechanism details The number of entries with a detailed mechanism description has been extended from to thanks to Amelia Brasnett, Morwenna Hall, Charity Hornby, and James Willey who have worked as interns in the Thornton group over the Summer. You must accept the terms and conditions. BioJS: an open source JavaScript framework for biological data visualization.

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M-CSA is a database of enzyme reaction mechanisms. Published by Oxford University Press. The use of sequence comparisons extends these annotations to a further 32 structures annotated by homology, providing a total of 34 annotated structures out of possible 49 structures deposited in the PDB that are enzymatic. We would also like to thank Dr Syed A. 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. Oxford Academic. Advance article alerts. Tags Protein. Although the CSA and MACiE resources have been developed somewhat in tandem and thus share a common data model, it is currently challenging to link these to enzyme annotations in resources such as UniProtKB due to differences in the definitions of enzyme properties and the vocabularies used in their description. In Version 2, a JMol visualisation was added for the active site. Email alerts Article activity alert. The presence of D-amino acids protects the cell wall from proteases which can only recognise the L-isomer. Nicholas Furnham, Gemma L. 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.