Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2018 Jan 4;46(D1):D618-D623.
doi: 10.1093/nar/gkx1012.

Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites

António J M Ribeiro  1 , Gemma L Holliday  1 , Nicholas Furnham  2 , Jonathan D Tyzack  1 , Katherine Ferris  1 , Janet M Thornton  1
Affiliations

Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites

António J M Ribeiro et al. Nucleic Acids Res. .

Abstract

M-CSA (Mechanism and Catalytic Site Atlas) is a database of enzyme active sites and reaction mechanisms that can be accessed at www.ebi.ac.uk/thornton-srv/m-csa. 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. M-CSA results from the merging of two existing databases, MACiE (Mechanism, Annotation and Classification in Enzymes), a database of enzyme mechanisms, and CSA (Catalytic Site Atlas), a database of catalytic sites of enzymes. We are releasing M-CSA as a new website and underlying database architecture. At the moment, M-CSA contains 961 entries, 423 of these with detailed mechanism information, and 538 with information on the catalytic site residues only. In total, these cover 81% (195/241) of third level EC numbers with a PDB structure, and 30% (840/2793) of fourth level EC numbers with a PDB structure, out of 6028 in total. By searching for close homologues, we are able to extend M-CSA coverage of PDB and UniProtKB to 51 993 structures and to over five million sequences, respectively, of which about 40% and 30% have a conserved active site.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Frequencies and catalytic propensity of the 20 amino acids as they appear in current the M-CSA dataset.
Figure 2.
Figure 2.
The browse page. Example of how to find all M-CSA entries with detailed mechanism, CATH:1.10.-.- and at least one His and one Cys in the catalytic site. The bottom three rows of the results table are omitted in the screenshot.
See this image and copyright information in PMC

References

    1. The UniProt Consortium UniProt: the universal protein knowledgebase. Nucleic Acids Res. 2017; 45:D158–D169. - PMC - PubMed
    1. Burley S.K., Berman H.M., Kleywegt G.J., Markley J.L., Nakamura H., Velankar S.. Protein Data Bank (PDB): the single global macromolecular structure archive. Protein Crystallography, Methods in Molecular Biology. 2017; NY: Humana Press; 627–641. - PMC - PubMed
    1. de Beer T.A., Berka K., Thornton J.M., Laskowski R.A.. PDBsum additions. Nucleic Acids Res. 2014; 42:D292–D296. - PMC - PubMed
    1. Kirby A.J. The lysozyme mechanism sorted — after 50 years. Nat. Struct. Mol. Biol. 2001; 8:737–739. - PubMed
    1. Sillitoe I., Lewis T.E., Cuff A., Das S., Ashford P., Dawson N.L., Furnham N., Laskowski R.A., Lee D., Lees J.G. et al. . CATH: comprehensive structural and functional annotations for genome sequences. Nucleic Acids Res. 2015; 43:D376–D381. - PMC - PubMed

Publication types

LinkOut - more resources