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.

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. The presence of D-amino acids protects the cell wall from proteases which can only recognise the L-isomer.

Catalytic site atlas

Enzyme-catalysed reactions are ubiquitous and essential to the chemistry of life. A great deal of knowledge, including structures, gene sequences, mechanisms, metabolic pathways and kinetic data exists, but is spread between many different databases and throughout the literature. To consolidate much of this information, two databases were developed:. The first version of the M-CSA was released in September publication in preparation and represents a major update of both the data and underlying resource architecture. The M-CSA now contains entries of which have a complete mechanism, and describe the catalytic site only. These duplicates were retained within the curator-defined parent entry. A literature review has also been performed to update the citations and, where appropriate, mechanisms. To date, approximately a third of the entries have had this review completed. This version of MACiE also represents a change in how the data are stored and updated. This aspect of the collaboration incorporated the expertise of CERM with metalloproteins and we developed Metal MACiE , a database of catalytic metal ions, with a view to understanding the functions of the roles and activity of catalytic metals in enzymes. This version contained entries that were non-homologous and based from the CatRes dataset see: Bartlett et al. DOI: Approximately half of the entries had 2D-SVG animations associated with them. Several changes were made during the release cycle of Version 2 from version 2. This version of MACiE represented a shift in emphasis for new entries, from non-homologous representatives covering EC reaction space to enzymes with mechanisms of interest to our users and collaborators with a view to exploring the chemical diversity of life.

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Present addresses: Gemma L. Julius O. Nicholas Furnham, Gemma L. Holliday, Tjaart A. Jacobsen, William R. Pearson, Janet M.

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.

Catalytic site atlas

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.

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Views 6, Close mobile search navigation Article Navigation. Volume Sign In or Create an Account. 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. Abstract 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. Your comment will be reviewed and published at the journal's discretion. 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. 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 CoFactor database: organic cofactors in enzyme catalysis.

Federal government websites often end in. The site is secure. Preview improvements coming to the PMC website in October

Detailed information on catalytic residues and enzyme active sites are essential for understanding the relationship between protein structure and functions, design of inhibitors and enzyme design. Pearson, Janet M. Download all slides. The evolution of enzyme function in the isomerases. 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. Article Contents Abstract. This version of MACiE represented a shift in emphasis for new entries, from non-homologous representatives covering EC reaction space to enzymes with mechanisms of interest to our users and collaborators with a view to exploring the chemical diversity of life. The data are stored in a MySQL database. Permissions Icon Permissions. Version 2 of the CSA implemented a more stringent homology search using FASTA and also implemented chemical similarity information for the substrate and products of the enzyme overall chemical transformations using SMSD.