How to Name and Classify Your Enzyme
This is a brief guide to the enzyme list and principles of classification.
The enzyme classification system
Each enzyme is assigned a recommended name; usually at the suggestion of the person who submits the details. The rules used to classify enzymes can be found at http://www.sbcs.qmul.ac.uk/iubmb/enzyme/rules.html. Each enzyme is allocated a four-digit EC number, the first three digits of which define the reaction catalysed and the fourth of which is a unique identifier (serial number). Each enzyme is also assigned a systematic name that uniquely defines the reaction catalysed.
The recommended names and EC number should be referred to in publications. This has a number of benefits: it will eliminate some of the ambiguities in the literature that have been caused by people using the same name for different enzymes and will also make the searching of literature databases more efficient. The EC number can also be used to find ancillary information, such as genes, sequences, properties and structures in other databases.
An enzyme should be listed IF:
An enzyme is not classified as a new enzyme IF:
- there is published evidence that it catalyses a distinct reaction that has not been listed previously.
- the reaction is similar to one already listed, but with a distinctly different substrate specificity, e.g. D- and L-amino-acid oxidases are classified as separate enzymes based on their different substrate specificities.
There are exceptions to these guidelines, for example, among the peptidases and ATPases/GTPases.
- the reaction is the same as that of an enzyme already listed, but the enzyme differs in source, structure or mechanism. Such differences may be mentioned in the �Comments� section and we would welcome your suggestions for such additions.
- the reaction represents an intermediate step in a reaction mechanism. Enzymes are classified based on the overall reaction that they catalyse.
- the enzyme is one that is already known to have a broad specificity and the reaction catalysed is just another specific example of the general reaction. In this case, the reaction is given a more general description (example: the reaction for alcohol dehydrogenase, EC 188.8.131.52, is written as "an alcohol + NAD+ = an aldehyde or ketone + NADH + H+").
An enzyme system, consisting of a number of proteins with different catalytic activities is named a system (e.g. fatty acid synthase system). The overall reaction is not normally given an EC number but each individual enzyme is given a number, and its involvement in the system is described in the comments.
To obtain a listing for a previously unlisted enzyme:
The procedure for recommending a new enzyme for inclusion in the enzyme database is straightforward. Complete the form available at http://www.expasy.ch/enzyme/enz_new_form.html, which will be sent to Prof K.F. Tipton (email@example.com) and Dr Sinéad Boyce (firstname.lastname@example.org), of Trinity College Dublin. They are responsible for assignment of EC numbers and maintenance of the enzyme list for the nomenclature committee of IUBMB. Enzymes that have been approved are displayed on the enzyme website at http://www.sbcs.qmul.ac.uk/iubmb/enzyme/ and those awaiting approval can be reviewed at http://www.sbcs.qmul.ac.uk/iubmb/enzyme/newenz.html.
Information you are requested to provide:
Then what happens:
- The overall reaction equation, including substrate(s), product(s), donor, acceptor, stoichiometry etc.
- Suggested name for the enzyme (see the list for examples).
- Other names by which the enzyme is known (if any).
- Full literature references (preferably journals, but books are also acceptable. To aid the classification process, please send reprints to Dr Ron Caspi, Bioinformatics Research Group, SRI International, Room AE217, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493), describing the properties of the enzyme. General review(s) about the enzyme are also helpful, if available.
- Any information that you know of, on the source of the enzyme, structure, cofactors, etc., to be included in the comments section. For examples, see the list.
- Any information that you know of, on the source of the enzyme, structure, cofactors, etc., as it may be suitable for inclusion in the Comments section.
Amendments to existing entries:
- A draft entry for the enzyme, including a provisional EC number, reaction, systematic name, recommended name etc., is prepared and sent to the nomenclature committee for refinement and approval.
- The enzyme entry is then displayed on the web, at http://www.sbcs.qmul.ac.uk/iubmb/newenz.html for a period of two months, to enable the biochemical community to make comments and suggest changes, if appropriate.
- The enzyme is then incorporated in the enzyme list, which is available at http://www.sbcs.qmul.ac.uk/iubmb/enzyme/.
You can also provide information about errors/updates to existing enzyme entries by completing the form available at http://www.expasy.ch/enzyme/enz_update_form.html. If an error necessitates changing the classification of an enzyme, i.e., its EC number, then the old entry will be marked as having been deleted or transferred and a link will be provided to the new entry.
Use of EC numbers
Enzyme entries, including EC numbers, may be quoted in any publication without permission. The copyright of the enzyme list rests with the IUBMB.
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