Catalytic site atlas

Present addresses: Gemma L. Julius O. Nicholas Furnham, Gemma L.

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.

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, 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 annotation is completed. Database Commons a catalog of worldwide biological databases. Home Database. Database Profile CSA. Year founded: Last update: NA Version: v2. Real time : Checking Gene genome and annotation Structure. Publications The Catalytic Site Atlas 2.

More metrics information. Approximately half of the entries had 2D-SVG animations associated with them. Nicholas Furnham.

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.

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. Sequence is but a small part of understanding how enzymes work, but due to the explosion of sequencing data there are, at the moment, more than 89 million sequences in UniProtKB across proteomes , it is an essential tool if one wants to extend current knowledge throughout the tree of life. Currently,

Catalytic site atlas

Craig T. Porter, Gail J. Bartlett, Janet M.

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Your comment will be reviewed and published at the journal's discretion. Present addresses: Gemma L. Authoring Open access Purchasing Institutional account management Rights and permissions. More from Oxford Academic. Annotators provide a brief free-text description of the enzyme as well as a more detailed summary of the enzyme mechanism. The origin recognition complex requires chromatin tethering by a hypervariable intrinsically disordered region that is functionally conserved from sponge to man. Citing articles via Web of Science Supplementary data. PMID: 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. Entries to be manually annotated are chosen from the PDB based on the quality of the structure and available experimental evidence of the reaction catalysed. 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. Holliday, Gail J. This version contained entries that were non-homologous and based from the CatRes dataset see: Bartlett et al. Each entry contained a link to a list of homologous entries identified using the in-house homology method , and a link was also provided to other CSA entries identical EC numbers or UniProKB identifier to the entry currently being viewed.

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This includes details of the catalytic mechanism, also validated by experimental data where possible. Your comment will be reviewed and published at the journal's discretion. Previous Next. In addition the database schema has been re-designed, integrating it into a sister database of enzyme mechanisms: the Mechanism, Annotation and Classification in Enzymes MACiE database 4. Tjaart A. Article Navigation. Bartlett GJ et al. The Catalytic Site Atlas 2. MACiE: exploring the diversity of biochemical reactions. The expansion of curated entries also permits the addition of new 3D structural templates, which have been used in a revision of the Catalytic Site Search service. In addition individual users can access both curated and homology derived entries to gain details of the catalytic residues in a structure of interest, which has the potential to be useful in design of further experiments. 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.