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. 'Detailed mechanism' entries are more complete and show the individual chemical steps of the mechanism as schemes with electron flow arrows. 'Catalytic Site' entries annotate the catalytic residues necessary for the reaction, but do not show the mechanism.

Glutamate racemase

example mechanism

Biological species: Aquifex pyrophilus (Bacteria) Uniprot
Sequence: P56868 UniProt
PDB: 1b73 PDBe PDBsum 1b73
Catalytic CATH domains: 3.40.50.1860 CATHdb

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-alaline, 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.

Features

Latest Statistics

As of 29th May 2020, M-CSA contains 964 hand-curated entries, 684 of them with detailed mechanistic description. These represent 852 EC numbers. There are 73158 SwissProt sequences and 15487 PDB structures homologous to these entries that catalyse the same reaction and have an identical active site, and so probably follow the same mechanism.

Last updates

Summer 2018 - More entries with mechanism details
The number of entries with a detailed mechanism description has been extended from 423 to 684 thanks to Amelia Brasnett, Morwenna Hall, Charity Hornby, and James Willey who have worked as interns in the Thornton group over the Summer.
New Website
We have merged CSA (Catalytic Site Atlas) and MACiE (Mechanism Annotation and Classification in Enzymes) into the same database and website. The new website facilitates the data entry process and supports different mechanism proposals, among others improvements. It is powered by the Python Django web framework and a PostgreSQL database.

To cite M-CSA

(see complete list of related papers)
  • Ribeiro AJM et al. (2017), Nucleic Acids Res, 46, D618-D623. Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites. DOI:10.1093/nar/gkx1012. PMID:29106569.