The ENZYME data bank is a repository of information related to the nomenclature of enzymes. In recent years it has become an indispensable resource for the development of metabolic databases. The current version contains information on 3704 enzymes. It is available through the ExPASy WWW server (http://www.expasy.ch/

Bairoch, Amos

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 1999 Oxford University Press310–311 Nucleic Acids Research, 1999, Vol. 27, No. 1The ENZYME data bank in 1999Amos Bairoch*Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, SwitzerlandReceived October 7, 1998; Revised October 9, 1998; Accepted October 28, 1998ABSTRACTThe ENZYME data bank is a repository of informationrelated to the nomenclature of enzymes. In recentyears it has become an indispensable resource for thedevelopment of metabolic databases. The currentversion contains information on 3704 enzymes. It isavailable through the ExPASy WWW server (http://www.expasy.ch/ ).INTRODUCTIONThe ENZYME data bank is a repository of information related tothe nomenclature of enzymes. It is primarily based on therecommendations of the Nomenclature Committee of the Interna-tional Union of Biochemistry and Molecular Biology (IUBMB)(1) and it contains the following data for each type ofcharacterized enzyme for which an EC (Enzyme Commission)number has been provided: (i) EC number; (ii) recommendedname; (iii) alternative names (if any); (iv) catalytic activity;(v) cofactors (if any); (vi) pointers to the SWISS-PROT (2)protein sequence entrie(s) that correspond to the enzyme (if any);(vii) pointers to the PROSITE (3) entrie(s) describing the proteinfamilie(s) of which the enzyme is a member (if any);(viii) pointers to human disease(s) (4) associated with a defi-ciency of the enzyme (if any).We believe that the ENZYME data bank would be useful toanybody working with enzymes and that it can be of help in thedevelopment of computer programs involved in the manipulationof metabolic pathways. In recent years it has became anindispensable resource for the development of metabolic data-bases (5). Such databases typically describe collections ofenzymes, reactions and biochemical pathways and are used inconjunction with software that allows the user to query andvisualize metabolic information. They are used in variouscontexts and have gained recognition in the context of thereconstruction of metabolic pathways from the sequence ofcomplete bacterial or archebacterial genomes (6,7).The main source for the data in the ENZYME data bank comesfrom the recommendations of the IUBMB, but additionalinformation has been extracted from the literature. Finally, it isimportant to note that the tight coupling that exists between theENZYME database and the SWISS-PROT protein sequencedatabase is of benefit to both resources as it allows updates andcorrections to be propagated efficiently between them.Figure 1. Two sample ENZYME entries.FORMATThe entries in the database are structured so as to be usable byhuman readers as well as by computer programs. An entry in thedatabase is composed of defined line types, each with its ownformat; they are used to record the various types of data whichmake up the entry. For standardization purposes the format ofENZYME follows as closely as possible that of the SWISS-PROT (2) protein and EMBL (8) nucleotide sequence databases.Two sample ENZYME entries are shown in Figure 1.PRACTICAL INFORMATIONContent of the current releaseRelease 23.0 of ENZYME (July 1998) contains information on3704 enzymes. The data file (ENZYME.DAT) requires ∼1.5 Mbof disk storage space. The database is distributed with a usermanual (ENZUSER.TXT); a file describing the various classes,subclasses and sub-subclasses of enzymes (ENZCLASS.TXT);and a file that describes how the database can be obtained(ENZYME.GET).*Tel: +41 22 702 5477; Fax: +41 22 702 5502; Email: amos.bairoch@medecine.unige.ch311Nucleic Acids Research, 1994, Vol. 22, No. 1Nucleic Acids Research, 1999, Vol. 27, No. 1 311The present distribution frequency is four releases per year. Norestrictions are placed on the use or redistribution of the data.Interactive access to SWISS-PROT and TrEMBLThe most efficient and user-friendly way to browse interactivelyin ENZYME is to use the World-Wide Web (WWW) molecularbiology server ExPASy (9). The ExPASy Web server was madeavailable to the public in September 1993. In October 1998 acumulative total of 33 million connections was attained. It maybe accessed through its URL, which is: http://www.expasy.ch/You can directly access the section of ExPASy that allows youto browse through the ENZYME database by opening the URL:http://www.expasy.ch/sprot/enzyme.htmlThe electronic version of the Boehringer MannheimBiochemical Pathways WallchartThe Biochemical Pathways Wallchart edited by retired Boeh-ringer Mannheim researcher Dr Gerhard Michal (see http://biochem.boehringer-mannheim.com/techserv/metmap.htm ), hasa long tradition of prominence on the walls of life scienceslaboratories. It consists of a graphical representation of the mainmetabolic pathways. We provide, on the ExPASy server, anelectronic version of the chart as a series of linked images. Eachenzyme mentioned in the chart is linked to its corresponding entryin ENZYME. The converse is also true. The BiochemicalPathways can be accessed from the URL: http://www.expasy.ch/cgi-bin/search-biochem-indexHow to obtain ENZYMEIf you have access to a computer system linked to the Internet youcan obtain ENZYME using anonymous FTP (File TransferProtocol), from the following servers: ExPASy (Expert ProteinAnalysis System), ftp.expasy.ch; EBI, ftp.ebi.ac.uk.A version of the database in the ASN.1 data exchange formatcompatible with the databases and software developed by theNational Center for Biotechnology Information (NCBI) (10) isalso available on the above servers.How to submit new data or updates/corrections toENZYMEWe do not assign EC numbers for newly characterized enzymes,this is the responsibility of the Nomenclature Committee ofIUBMB (NC-IUBMB) (see http://www.chem.qmw.ac.uk/iupac/jcbn/ ). To contact the person responsible for the assignment ofEC numbers in that committee one should write to: Prof. K.Tipton, Department of Biochemistry, Trinity College, Dublin 2,Republic of Ireland. Tel: +353 1 608 1608; Fax: +353 1 677 2400;Email: ktipton@tcd.ie.The ENZYME data bank is distributed with a form that can beused to fill in the information necessary for the NC-IUBMB toassign an EC number. Such a form is also available from the Webat the URL: http://www.expasy.ch/sprot/enz_new_form.htmlA separate form is available to send updates or corrections:http://www.expasy.ch/sprot/enz_update_form.htmlThe commission regularly sends us updates and additions to thenomenclature so that they can be integrated into the data bank ina timely manner.REFERENCES1 Enzyme Nomenclature, Recommendations of the Nomenclature Committeof the International Union of Biochemistry and Molecular Biology on theNomenclature and Classification of Enzymes, NC-IUBMB (1992)Academic Press, New York.2 Bairoch,A. and Apweiler,R. (1998) Nucleic Acids Res., 26, 38–42.3 Bairoch,A., Bucher,P. and Hofmann,K. (1997) Nucleic Acids Res., 25,217–221.4 Pearson,P.L., Francomano,C., Foster,P., Bocchini,C., Li,P. andMcKusick,V.A. (1994) Nucleic Acids Res., 22, 3470–3473.5 Karp,P. (1998) Trends Biochem. Sci., 23, 114–116.6 Galperin,M.Y. and Brenner,S.E. (1998) Trends Genet., 14, 332–333.7 Bono,H., Ogata,H., Goto,S. and Kanehisa,M. (1998) Genome Res., 8,203–210.8 Stoesser,G., Moseley,M.A., Sleep,J., McGowran,M., Garcia-Pastor,M. andSterk,P. (1998) Nucleic Acids Res., 26, 8–15.9 Appel,R.D., Bairoch,A. and Hochstrasser,D.F. (1994) Trends Biochem.Sci., 19, 258–260.10 Benson,D.A., Boguski,M.S., Lipman,D.J., Ostell,J. and Ouellette,B.F.F.(1998) Nucleic Acids Res., 26, 1–7.

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