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Enzyme Commission number

 

Enzyme Commission number

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 respective enzyme.

Strictly speaking, 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 and therefore would be assigned an identical EC number (these are called non-homologous isofunctional enzymes, or NISE).[3] By contrast, UniProt identifiers uniquely specify a protein by its amino acid sequence.[4]

Contents

  • Format of number 1
  • Top level codes 2
  • Reaction Similarity 3
  • History 4
  • See also 5
  • References 6
  • External links 7

Format of number

Every 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

Top-level EC numbers[5]
Group Reaction catalyzed Typical reaction Enzyme example(s) with trivial name
EC 1
Oxidoreductases
To catalyze 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
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

Reaction Similarity

Similarity between enzymatic reactions (EC) can be calculated by using bond changes, reaction centres or substructure metrics (i.e. EC-BLAST).[6]

History

The enzyme nomenclature scheme was developed starting in 1955, when the International Congress of Biochemistry in Brussels set up an Enzyme Commission. The first version was published in 1961. The current sixth edition, published by the International Union of Biochemistry and Molecular Biology in 1992, 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]

See also

References

  1. ^ Webb EC (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. San Diego: Published for the International Union of Biochemistry and Molecular Biology by Academic Press.  
  2. ^ a b "ENZYME (Enzyme nomenclature database)". ExPASy. Retrieved 2006-03-14. 
  3. ^ Omelchenko MV, Galperin MY, Wolf YI, Koonin EV (2010). "Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution". Biol. Direct 5: 31.  
  4. ^ 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 (January 2004). "UniProt: the Universal Protein knowledgebase". Nucleic Acids Res. 32 (Database issue): D115–9.  
  5. ^ 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. Retrieved 2006-03-14. 
  6. ^ Rahman, SA; Cuesta, SM; Furnham, N; Holliday, GL; Thornton, JM (2014). "EC-BLAST: a tool to automatically search and compare enzyme reactions". Nature Methods 11: 171–174.  

External links

  • 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
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