What is the relationship between Rhea and the IUBMB enzyme classification (EC numbers)?
Content:
- What is NC-IUBMB?
- Enzyme classification and EC numbers
- Enzyme classification and reactions
- Related documents
What is NC-IUBMB?
NC-IUBMB, the nomenclature committee of the international union of biochemistry and molecular biology, is in charge of classifying enzymes according to the reaction(s) they catalyze.
See also A Brief Guide to Enzyme Nomenclature and Classification (Keith Tipton and Andrew McDonald)
ExplorEnz is an open-access database. It is the definitive IUBMB Enzyme Nomenclature list, produced by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB), in consultation with the IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN).
Who is involved?
Enzyme entries are authorized on behalf of NC-IUBMB by a subcommitee comprising Kristian Axelsen* (Switzerland), Richard Cammack (UK), Ron Caspi (USA), Athel Cornish Bowden (France), Minoru Kanehisa (Japan), Masaaki Kotera (Japan), Andrew McDonald (Ireland), Gerry Moss (UK), Dietmar Schomburg (Germany), Ida Schomburg (Germany) and Keith Tipton (Ireland).
Members of each of these team projects are part of the NC-IUBMB.
Kristian Axelsen* is the head of the SIB ENZYME project and a member of the Rhea project.
Enzyme classification and EC numbers
The first Enzyme Commission, in its report in 1961, devised a system for classification of enzymes that also serves as a basis for assigning code numbers to them. These code numbers, prefixed by EC, contain four elements separated by points
Example: D-alanine 2-hydroxymethyltransferase (EC 2.1.2.7 )
The seven main enzymes classes
| EC number | Class name | Description |
|---|---|---|
| 1 | Oxidoreductases | All enzymes that catalyse oxido-reductions belong in this class. The substrate oxidized is regarded as a hydrogen or electron donor. The classification is based on 'donor:acceptor oxidoreductase'. The common name is 'dehydrogenase', wherever this is possible; as an alternative, 'acceptor reductase' can be used. 'Oxidase' is used only where O2 is an acceptor. Classification is difficult in some cases, because of the lack of specificity towards the acceptor. |
| 2 | Transferases | Transferases are enzymes that transfer a group, for example, the methyl group or a glycosyl group, from one compound (generally regarded as donor) to another compound (generally regarded as acceptor). The classification is based on the scheme 'donor:acceptor grouptransferase'. The common names are normally formed as 'acceptor grouptransferase' or 'donor grouptransferase'. In many cases, the donor is a cofactor (coenzyme) that carries the group to be transferred. The aminotransferases constitute a special case (EC 2.6). |
| 3 | Hydrolases | These enzymes catalyse the hydrolysis of various bonds. Some of these enzymes pose problems because they have a very wide specificity, and it is not easy to decide if two preparations described by different authors are the same, or if they should be listed under different entries. While the systematic name always includes 'hydrolase', the common name is, in most cases, formed by the name of the substrate with the suffix -ase. It is understood that the name of the substrate with this suffix, and no other indicator, means a hydrolytic enzyme. It should be noted that enzymes in EC 3.4 (peptidases) have recommended names rather than common names. |
| 4 | Lyases | Lyases are enzymes that cleave C-C, C-O, C-N and other bonds by means other than by hydrolysis or oxidation. They differ from other enzymes in that two (or more) substrates are involved in one reaction direction, but there is one compound fewer in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring. The systematic name is formed according to 'substrate group-lyase'. In common names, expressions like decarboxylase, aldolase, etc. are used. 'Dehydratase' is used for those enzymes that eliminate water. In cases where the reverse reaction is the more important, or the only one to be demonstrated, 'synthase' may be used in the name. |
| 5 | Isomerases | These enzymes catalyse changes within a single molecule. |
| 6 | Ligases | Ligases are enzymes that catalyse the joining of two molecules or two parts of a molecule with concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate. 'Ligase' is often used for the common name, but, in a few cases, 'synthase' or 'carboxylase' is used. 'Synthetase' may be used in place of 'synthase' for enzymes in this class. |
| 7 | Translocases | These enzymes catalyse the movement of ions or molecules across membranes or their separation within membranes. The reaction is designated as a transfer from 'side 1' to 'side 2' because the designations 'in' and 'out', which had previously been used, can be ambiguous. The subclasses designate the types of components transferred and the sub-subclasses indicate the reaction processes that provide the driving force for the translocation. |
Enzyme classification and reactions
If ExplorEnz resource is the definitive list of EC numbers, the data are used by many other databases:
- SIB ENZYME (we also call it ENZYME@ExPASy)
- KEGG ENZYME
- MetaCyc ENZYME
- BRENDA ENZYME
ExplorEnz: textual representation + comment
--> lead to interpretations (different resources == different interpretations)
ENZYME@ExPASy and Rhea
Excepted for a few exceptions (i.e reactions described in natural language), the textual description of IUBMB reactions is translated into Rhea reactions.
