Enzyme Classification and Nomenclature


The variety of different names that had been used for the same enzyme and the fact that some different enzymes were known by the same name necessitated the development of a rational system for their classification and nomenclature. The International Union of Biochemistry devised a system of classification that allows the unambiguous identification of enzymes in terms of the reactions they catalyse. This relies on a numerical system (the EC number) to class enzymes in groups according to the types of reaction catalysed and systematic naming that describes the chemical reaction involved. This is now in widespread use and the official list of enzymes classified can be found at ExplorEnz – The Enzyme Database ( http://www.enzyme‐database.org).

Key Concepts

  • Many enzymes have several alternative names and the same name has sometimes been used for different enzymes. This necessitates the use of an unambiguous naming system.
  • Enzymes are classified in the IUBMB Enzyme List according to the reactions they catalyse.
  • The EC number is a unique identifier for each enzyme classified according to this system.
  • Each enzyme has a short entry in the Enzyme List describing what it catalyses and some other key details.
  • Commonly used enzyme names may contain ambiguities and an Accepted name is provided to avoid this.
  • A Glossary is provided to relate compound names used by biochemists to those used by chemists.
  • Systematic names describe the catalysed reaction in more detail but can be cumbersome.
  • There are now over 5500 classified enzymes and the list is being continuously expanded and updated.
  • The official list is available at http://www.enzyme‐database.org/ – where searches by old names, or EC number are possible.

Keywords: enzymes; classification; nomenclature


BioCyc Pathway/Genome Database Collection (2015) http://biocyc.org/

BRENDA Enzyme Information System (2015) http://www.brenda‐enzymes.org/

Berman HM, Kleywegt GJ, Nakamura H and Markley JL (2014) The Protein Data Bank archive as an open data resource. Journal of Computer Aided Molecular Design. 28: 1009–1014.

Caspi R, Altman T, Billington R, et al. (2014) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Resesearch 42 (Database issue): D459–D471.

ChemSpider (2015) Chemical Structure Database. http://www.chemspider.com/

Dixon M and Webb EC (1958) Enzymes, pp. 183–227. London & New York: Longmans Green & Academic Press.

Eawag Biocatalysis/Biodegradation Database (2015) http://eawag‐bbd.ethz.ch

Favre A and Powell WH (2013) Nomenclature of Organic Chemistry. IUPAC Recommendations and Preferred Name 2013. Cambridge, UK: The Royal Society of Chemistry.

Gao J, Ellis LB and Wackett LP (2010) The University of Minnesota Biocatalysis/Biodegradation Database: improving public access. Nucleic Acids Research 38 (Database issue): D488–D491.

Gasteiger E, Gattiker A, Hoogland C, et al. (2003) ExPASy: The proteomics server for in‐depth protein knowledge and analysis. Nucleic Acids Research 31: 3784–3788.

IUPAC (1993) Nomenclature of Organic Chemistry. http://www.acdlabs.com/iupac/nomenclature/

IUPAC & IUBMB (2013) Nomenclature Recommendations. http://www.chem.qmul.ac.uk/iupac/

Kanehisa M, Goto S and Sato Y (2014) Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Research 42 (Database issue): D199–D205.

Kyoto Encyclopedia of Genes and Genomes, KEGG (2015). http://www.genome.ad.jp/kegg/

McDonald AG and Tipton KF (2014) Fifty‐five years of enzyme classification: advances and difficulties. FEBS Journal 281: 583–592.

MEROPS (2014) The Peptidase Database. http://merops.sanger.ac.uk/

NIST Standard Reference Database on the Thermodynamics of Enzyme‐Catalyzed Reactions (2015) http://www.bmcd.nist.gov:8080/enzyme/enzyme.html

Protein Data Bank (PDB) (2015) http://www.rcsb.org/pdb/

Rawlings ND, Waller M, Barrett AJ and Bateman A (2014) MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Research 42 (Database issue): D503–D509.

Schomburg I, Chang PS, et al. (2013) BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA. Nucleic Acids Research 41 (Database issue): D764–D772.

SWISSPROT ENZYME (2015) Swiss Institute of Bioinformatics (SIB) Enzyme nomenclature database primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) http://www.ca.expasy.org/enzyme/

Williams A and Tkachenko V (2014) The Royal Society of Chemistry and the delivery of chemistry data repositories for the community. Journal of Computer Aided Mololecular Design 28: 1023–1030.

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 by the Reactions they Catalyse. New York: Academic Press.

Further Reading

Alberty RA, Cornish‐Bowden A, Goldberg RN, et al. (2011) Recommendations for terminology and databases for biochemical thermodynamics. Biophysical Chemistry 155: 89–103.

Boyce S and Tipton KF (2000) History of the enzyme nomenclature system. S. Boyce and K.F. Tipton. Bioinformatics 16: 34–40.

Copeland RA (2000) Enzymes: A Practical Introduction to Structure, Mechanism, and Data Analysis. New York: Wiley‐VCH Inc.

Kotera M, McDonald AG, Boyce S and Tipton KF (2008) Functional group and substructure searching as a tool in metabolomics. PLoS One 3 (2): e1537.

McDonald AG, Boyce S, Moss GP, et al. (2007) ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature. BMC Biochemistry 27 (8): 14.

McDonald AG, Tipton KF and Boyce S (2009) Tracing metabolic pathways from enzyme data. Biochimica et Biophysica Acta 1794: 1364–1371.

Tipton KF, Armstrong RN, Bakker BM, et al. (2014) Standards for Reporting Enzyme Data: The STRENDA Consortium: what it aims to do and why it should be helpful. Perspectives in Science 1: 131–137.

Panico R, Richer J‐C and Powell WH (1994) A Guide to IUPAC Nomenclature of Organic Compounds. Oxford: Blackwell Science.

Webb EC (1993) Enzyme nomenclature: a personal retrospective. FASEB Journal 7: 1192–1194.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
McDonald, Andrew G, Boyce, Sinead, and Tipton, Keith F(Apr 2015) Enzyme Classification and Nomenclature. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000710.pub3]