Catalytic site atlas

M-CSA is a database of enzyme reaction mechanisms.

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.

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.

Rahman SA et al. Developers involved in the prediction of proteins of unknown function can use the extended number of curated entries to train and test the methodologies being developed.

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.

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. 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.

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. 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.

Adams and jarret

Nicholas Furnham, Gemma L. Article Navigation. Email alerts Article activity alert. Authoring Open access Purchasing Institutional account management Rights and permissions. For each residue in each catalytic site the functional part of the residue is recorded as well as its function and target described using a controlled vocabulary and a short free-text description of how the residue performs the function. Andreini C et al. The data are stored in a MySQL database. Open in new tab Download slide. Jonathan D Tyzack. You must accept the terms and conditions. These authors contributed equally to the paper as first authors. Comments 0. A new method for reliably extrapolating the annotations and identification of catalytic residues to homologous structures has been implemented. Google Scholar Crossref.

Federal government websites often end in.

This version contained entries that were non-homologous and based from the CatRes dataset see: Bartlett et al. The CSA database schema has been re-designed and both the CSA data and search capabilities are presented in a new modern web interface. Figure 3. A literature review has also been performed to update the citations and, where appropriate, mechanisms. 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. NAR Journals. Torrance JW et al. The M-CSA now contains entries of which have a complete mechanism, and describe the catalytic site only. Approximately half of the entries had 2D-SVG animations associated with them. 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. Evidence tags provide a direct link to the literature from which the annotations where derived. The template made from each curated entry can be accessed from relevant the CSA entry page as well as collectively being made available for download. DOI: Thank you for submitting a comment on this article. All the data in the CSA is downloadable and freely available to the academic community.