The Enzyme Commission number (EC number) is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze.[1] As a system of enzyme nomenclature, every EC number is associated with a recommended name for the corresponding enzyme-catalyzed reaction.
EC numbers do not specify enzymes but enzyme-catalyzed reactions. If different enzymes (for instance from different organisms) catalyze the same reaction, then they receive the same EC number.[2] Furthermore, through convergent evolution, completely different protein folds can catalyze an identical reaction (these are sometimes called non-homologous isofunctional enzymes)[3] and therefore would be assigned the same EC number. By contrast, UniProt identifiers uniquely specify a protein by its amino acid sequence.[4]
Format of number
editEvery enzyme code consists of the letters "EC" followed by four numbers separated by periods. Those numbers represent a progressively finer classification of the enzyme. Preliminary EC numbers exist and have an 'n' as part of the fourth (serial) digit (e.g. EC 3.5.1.n3).[2]
For example, the tripeptide aminopeptidases have the code "EC 3.4.11.4", whose components indicate the following groups of enzymes:
- EC 3 enzymes are hydrolases (enzymes that use water to break up some other molecule)
- EC 3.4 are hydrolases that act on peptide bonds
- EC 3.4.11 are those hydrolases that cleave off the amino-terminal amino acid from a polypeptide
- EC 3.4.11.4 are those that cleave off the amino-terminal end from a tripeptide
Top level codes
editNB:The enzyme classification number is different from the 'FORMAT NUMBER'
| Class | Reaction catalyzed | Typical reaction | Enzyme example(s) with trivial name |
|---|---|---|---|
| EC 1 Oxidoreductases |
Oxidation/reduction reactions; transfer of H and O atoms or electrons from one substance to another |
AH + B → A + BH (reduced) A + O → AO (oxidized) |
Dehydrogenase, oxidase |
| EC 2 Transferases |
Transfer of a functional group from one substance to another. The group may be methyl-, acyl-, amino- or phosphate group | AB + C → A + BC | Transaminase, kinase |
| EC 3 Hydrolases |
Formation of two products from a substrate by hydrolysis | AB + H2O → AOH + BH | Lipase, amylase, peptidase, phosphatase |
| EC 4 Lyases |
Non-hydrolytic addition or removal of groups from substrates. C-C, C-N, C-O or C-S bonds may be cleaved | RCOCOOH → RCOH + CO2 or [X-A+B-Y] → [A=B + X-Y] | Decarboxylase |
| EC 5 Isomerases |
Intramolecule rearrangement, i.e. isomerization changes within a single molecule | ABC → BCA | Isomerase, mutase |
| EC 6 Ligases |
Join together two molecules by synthesis of new C-O, C-S, C-N or C-C bonds with simultaneous breakdown of ATP | X + Y + ATP → XY + ADP + Pi | Synthetase |
| EC 7 Translocases |
Catalyse the movement of ions or molecules across membranes or their separation within membranes | Transporter |
Reaction similarity
editSimilarity between enzymatic reactions can be calculated by using bond changes, reaction centres or substructure metrics (formerly EC-BLAST], now the EMBL-EBI Enzyme Portal).[6]
History
editBefore the development of the EC number system, enzymes were named in an arbitrary fashion, and names like old yellow enzyme and malic enzyme that give little or no clue as to what reaction was catalyzed were in common use. Most of these names have fallen into disuse, though a few, especially proteolyic enzymes with very low specificity, such as pepsin and papain, are still used, as rational classification on the basis of specificity has been very difficult.
By the 1950s the chaos was becoming intolerable, and after Hoffman-Ostenhof[7] and Dixon and Webb[8] had proposed somewhat similar schemes for classifying enzyme-catalyzed reactions, the International Congress of Biochemistry in Brussels set up the Commission on Enzymes under the chairmanship of Malcolm Dixon in 1955. The first version was published in 1961, and the Enzyme Commission was dissolved at that time, though its name lives on in the term EC Number. The current sixth edition, published by the International Union of Biochemistry and Molecular Biology in 1992 as the last version published as a printed book, contains 3196 different enzymes. Supplements 1-4 were published 1993–1999. Subsequent supplements have been published electronically, at the website of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology.[5] In August 2018, the IUBMB modified the system by adding the top-level EC 7 category containing translocases.[9]
See also
edit- List of EC numbers
- List of enzymes
- TC number (classification of membrane transport proteins)
References
edit- ^ Webb, E. C. (1992). Enzyme nomenclature 1992: recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzymes. Academic Press. ISBN 978-0-12-227164-9.
- ^ a b "ENZYME (Enzyme nomenclature database)". ExPASy. Archived from the original on 21 March 2019. Retrieved 24 April 2019.
- ^ Omelchenko MV, Galperin MY, Wolf YI, Koonin EV (2010). "Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution". Biology Direct. 5 (1): 31. doi:10.1186/1745-6150-5-31. PMC 2876114. PMID 20433725.
- ^ Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS (Jan 2004). "UniProt: the Universal Protein knowledgebase". Nucleic Acids Research. 32 (Database issue): D115–9. doi:10.1093/nar/gkh131. PMC 308865. PMID 14681372.
- ^ a b Moss GP. "Recommendations of the Nomenclature Committee". International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes by the Reactions they Catalyse. Archived from the original on 2018-09-10. Retrieved 2006-03-14.
- ^ Rahman SA, Cuesta SM, Furnham N, Holliday GL, Thornton JM (Feb 2014). "EC-BLAST: a tool to automatically search and compare enzyme reactions". Nature Methods. 11 (2): 171–174. doi:10.1038/nmeth.2803. PMC 4122987. PMID 24412978.
- ^ Hoffman-Ostenhof, O (1953). "Suggestions for a more rational classification and nomenclature of enzymes". Advances in Enzymology and Related Subjects of Biochemistry. 14: 219–260. doi:10.1002/9780470122594.ch7. ISBN 9780470122594. PMID 13057718.
- ^ Dixon, M; Webb, E.C. (1958). Enzymes. London: Longmans Green. pp. 183–227.
- ^ Tipton, Keith (August 2018). "Enzyme Nomenclature News: Translocases (EC 7): A new EC Class". ExplorEnz: the primary source of the IUBMB enzyme list. Archived from the original on 10 September 2018. Retrieved 3 November 2018.
External links
edit
EC enzyme number (P591) (see uses)
- Enzyme Nomenclature, authoritative website by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology, maintained by G.P. Moss
- Enzyme nomenclature database — by ExPASy
- List of all EC numbers — by BRENDA
- Browse PDB structures by EC number
- Browse SCOP domains by EC number — by dcGO
- Compare EC numbers using EC-Blast Archived 2019-05-30 at the Wayback Machine
