Development of the Enzyme List

Changes in the format.

In the future, it is intended that references will be cited at the end of each entry with full title and pagination. In the past the earliest available reference to a specific enzyme has usually been cited. It is hoped in the future, and starting with new additions to the list, to give more complete and up-to-date references. Good reviews on the properties of any specific enzyme would be particularly valuable citations.

We intend to expand the Comments section for individual enzymes to include information on metabolic significance, relation to other listed enzymes, possible isoenzymes, codification of enzymes of specific interest to clinical chemists, sequence database information, etc. Suggestions for material to include for individual enzymes are always welcome.

Work for the provision of enzyme nomenclature in database format is in progress.

Links with other relevant databases.

Several other nomenclature systems and databases are in existence. These include the World Health Organization (WHO) list of International Nonproprietary Names (INNs), the QU number system of the Commitee on Nomenclature, Properties and Units (C-NPU) for classifying enzymes of relevance to clinical chemistry, the ReBase of restriction enzymes, etc.

The Enzyme nomenclature database must link to these and the most appropriate ways of doing this are under discussion. Comments and suggestions are welcome.

Deficiencies in the list of enzymes.

Advice and suggestions concerning deficiencies or omissions are always welcome. Problems in the classification of monooxygenases, protein kinases/phosphatases, restriction enzymes and other nucleases, are obvious and it would be most helpful if expert groups could be formed to advise on how these might best be classified and unambiguously named.

Submission of new enzymes and corrections to existing enzymes.

These can be made on forms available from Keith F. Tipton, Biochemistry Department, Trinity College, Dublin 2, Ireland. Fax: +353 1 677-2400. E-mail: ktipton@mail.tcd.ie

Submissions concerning peptidases (EC 3.4.-.-) should be sent to Alan J. Barrett, Peptidase Laboratory, Department of Immunology, Babraham Institute, Babraham, England CB2 4AT. Fax: +44 1223 83-7952. E-mail: alan.barrett@bbsrc.ac.uk

Forms for electronic submission are available on the World Wide Web through the home page of JCBN and NC-IUBMB at http://www.sbcs.qmul.ac.uk/iupac/jcbn/

and from Swiss-Prot at http://www.expasy.ch/sprot/enz_new_form.html

and at http://www.expasy.ch/sprot/enz_update_form.html

respectively.

As enzymes are named and classified in terms of the reaction that they catalyse, any new enzyme must differ significantly from any of those already listed. This rules out minor species and tissue differences, which can adequately be described in the Comments section for an enzyme already on the list. Copies of relevant publications should be sent in support of any new entry.

Catalytic antibodies.

Like enzyme nomenclature, it is proposed that the nomenclature of catalytic antibodies should be based on the reaction catalysed, rather than on structural features. As more than one different 'abzyme' catalysing the same general reaction may be produced, there is clearly a possibility for confusion. However, the catalytic behaviour and specificities may not be identical. Several possibilities are under discussion: they may be included in the Comments section for existing enzymes where they catalyse similar reactions, they might be given EC numbers or they might be given an 'AB' numbering system in a separate list based on the enzyme nomenclature classes. Examples of a possible classification of catalytic antibodies are given below. Comments on these possibilities and on the general value of such a listing would be most welcome.

AB 2.1.1.1 (or EC 2.1.1.?)

Recommended name: Aromatic alcohol acyltransferase (antibody).

Reaction: An alcohol + a carboxylate = a carboxyl ester + H2O.

Systematic name: Aromatic alcohol:ester acyltransferase (antibody).

Antibody details: Monoclonal IgG raised in mice. Author's designation 21H3. Not commercially available.

Comments: Active towards benzyl and phenyl alcohols. The reaction catalysed is the reverse of that of the carboxylic ester hydrolases (EC 3.1.1.-). Such reactions may be catalysed by these enzymes at very low concentrations of water (e.g. lipases in organic solvents) or when the ester product has limited solubility.

Reference

1. Wirshing, P., Ashley, J. A., Benkovic, S. J., Janda, K. D. & Lerner, R. A. (1991) An unexpectedly efficient catalytic antibody operating by ping-pong and induced fit mechanisms, Science (Wash. DC) 252, 680-684.

AB 3.1.1.1 (or EC 3.1.1.?)

Recommended name: Carboxylesterase (antibody).

Reaction: A carboxylic ester + H2O = an alcohol + a carboxylate.

Systematic name: Carboxylic ester hydrolase (antibody).

Antibody details: Polyclonal IgG raised in sheep. Author's designation PCA 270-22. Not commercially available.

Comments: Catalyses the hydrolysis of carbonates and anilides in addition to carboxylic esters. Reaction involves the OH- ion. Compare: EC 3.1.1.1, carboxyl esterase and other non-specific esterases.

References

1. Gallacher, G., Jackson, C. S., Searcey, M., Badman, G. T., Goel, R., Topman, C. M., Mellor, G. W. & Brocklehurst, K. (1992) A polyclonal antibody preparation with Michaelian catalytic properties, Biochem. J. 279, 871-881.

2. Gallacher, G., Jackson, C. S., Searcey, M., Goel, R., Mellor, G. W., Smith, C. Z. & Brocklehurst, K. (1993) Catalytic antibody activity elicited by active immunisation. Evidence for natural variation involving preferential stabilization of the transition state, Eur. J. Biochem. 214, 197-207.

Other catalytic molecules.

As in the case of catalytic antibodies the listing of natural and artificial catalytic nucleotides and engineered enzymes with novel specificities could be of use. Advice and comments as to how this could be most helpfully effected are invited.


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