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.
Biological species: Aquifex pyrophilus (Bacteria) 
Sequence: P56868
PDB: 1b73 
Catalytic CATH domains:
3.40.50.1860 
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.
Features
Latest Statistics
As of 4th February 2026, M-CSA contains 1003 hand-curated entries, 734 of them with detailed mechanistic description. The entries in M-CSA represent 895 EC numbers. 73211 SwissProt sequences and 15541 PDBs are homologous to these entries, catalyse the same reaction and have an identical active site, probably follwing the same mechanism.
Last updates
- December 2025 - Search catalytic motifs in protein structures with EnzyMM
- We added a web-based search for catalytic motifs in protein structures with EnzyMM - The Enzyme Motif Miner. Search any structure in the PDB or the AlphafoldDB (or upload your own) for geometric similarity to our library of 6870 templates representing catalytic sites in the M-CSA in various (partial) conformations. Matches are reported interactively, so you can quickly explore the catalytic functions of your protein, and can be traced back to the associated M-CSA entry and the original literature references.
- Summer 2021 - A Round of Remote Curation
- Noa Marson, Marko Babic, Yordanos Abeje, and Trung Nguyen, working remotely as interns over the summer, have increased the number of detailed mechanism entries to 734, bringing the total entries to 1003.
- 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.