BIOCHEMICAL NOMENCLATURE
COMMITTEES

INTERNATIONAL UNION OF PURE AND APPLIED CHEMISTRY
and
INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY

IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN)

Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB)

http://www.chem.qmul.ac.uk/iupac/jcbn/

World Wide Web home page maintained by G. P. Moss

School of Biological and Chemical Sciences, Queen Mary University of London,
Mile End Road, London, E1 4NS, UK
g.p.moss@qmul.ac.uk


Contents


Purpose of the committees

The purpose of the committees is to facilitate communication of biochemical information by encouraging scientists to use generally understood terminology.

They make recommendations with this aim. The committees seek advice from experts in the diverse fields of biochemistry about matters where communication is difficult because of inconsistent practices. This is the starting point of most of the initiatives of the committees. The experts consulted include journal editors and database managers. For example, the recommendations for a Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences (1984) arose out of an attempt by an international group of experts to resolve the confusion that previously resulted from the existence of many different systems to represent combinations such as "G or C", which had been written in at least five different ways.

Origins

The present nomenclature committees were created by the International Union of Biochemistry (IUB; now the International Union of Biochemistry and Molecular Biology, IUBMB) and the International Union of Pure and Applied Chemistry (IUPAC) to replace the IUPAC-IUB Commission on Biochemical Nomenclature (CBN), which was discontinued in 1977. Formally there are two committees: with somewhat different terms of reference. JCBN is jointly responsible to both International Unions, and deals with matters of biochemical nomenclature that have importance in both biochemistry and chemistry. NC-IUBMB is responsible only to IUBMB and deals with matters of biochemical nomenclature that are more remote from the interests of chemists.

In practice there is considerable overlap in the tasks of the two committees and they always work and meet as a single body, with a common Chairman and a common Secretary. The present members are listed on the web. Unless otherwise indicated, therefore, the term "nomenclature committees" in this page refers equally to JCBN and to NC-IUBMB.

Procedures for establishing new recommendations

The initial recommendations for any topic are always prepared by experts in the subject area, but are subsequently studied by the nomenclature committees in an effort to harmonize them with recommendations in related areas of biochemistry, or indeed in chemistry and other disciplines. Although this step often appears unnecessary to experts in a restricted area of the subject, its importance emerges when one attempts to present information on a broader scale or to a broader audience. As an example, some years ago the nomenclature committees were asked to advise on some draft recommendations in which I (in ordinary roman type and without any qualifiers) was proposed as a standard symbol that could be used without definition for a particular immunoglobulin; they had to point out that this could only be acceptable in a very narrow context, as it would be confusing whenever the chemical symbol for iodine might be needed, or if the one-letter code for isoleucine and the symbol for ionic strength were also used (quite apart from confusion with the personal pronoun, as, for example, in "I mixed I with 131I-labelled thyroxine in a solution of I = 0.5 mol/l containing 5mM I"). Further review is required after the nomenclature committees are satisfied with any recommendations, as the International Unions, which have ultimate responsibility for any publication, need to be satisfied that they represent the views of a broad range of experts. The actual review procedures of the two Unions differ somewhat, but their aims are the same, and they also have the additional consequence that preparing any document is inevitably slow. Even the most rapidly produced documents, such as the Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences noted above, which encountered no serious obstacles on the way to approval, typically take at least two years.

Connections with other bodies

There is inevitably some overlap between the work of the biochemical nomenclature committees and similar bodies in other disciplines, especially through IUPAC Division VIII, Chemical Nomenclature and Structure Representation. Many IUPAC nomenclature recommendations are available through the web. To avoid arriving at conflicting recommendations the nomenclature committees maintain close relations with such bodies (and during the existence of the present committees they have always included present or former members of CNOC among their members). Input from other committees concerned with biochemical nomenclature is always welcomed, and any such body interested in sending an Observer to meetings of JCBN and NC-IUBMB is invited to contact the Secretary, Professor R. Caspi.

Publication of recommendations

Apart from Enzyme Nomenclature, discussed below, recommendations of the nomenclature committees are published in the primary research literature. All JCBN recommendations are published in Pure and Applied Chemistry, and all JCBN and NC-IUBMB recommendations are currently published in the European Journal of Biochemistry, by courtesy of FEBS. Many documents appear also in other journals, and any journal wishing to republish a document can normally obtain reproduction-quality proofs from the European Journal of Biochemistry, to avoid the need for re-setting. However, it is not obligatory to use these proofs, and journals that prefer to set the type themselves may do so without any copyright complications. From time to time these documents are published together as a Compendium, Biochemical Nomenclature and Related Documents; the most recent edition was published by Portland Press for IUBMB in 1992 (ISBN 1 85578 005 4).

A list of JCBN and NC-IUBMB publications is available through the web, and the full texts of the following are also there. Others will be added as time permits.

RecommendationURL
Amino Acids and Peptideshttp://www.chem.qmul.ac.uk/iupac/AminoAcid/
Biochemical thermodynamicshttp://www.chem.qmul.ac.uk/iubmb/thermod/
Branched nucleic acidshttp://www.chem.qmul.ac.uk/iubmb/misc/bran.html
Carbohydrateshttp://www.chem.qmul.ac.uk/iupac/2carb/
Carotenoidshttp://www.chem.qmul.ac.uk/iupac/carot/
Corrinoids (vitamin B12)http://www.chem.qmul.ac.uk/iupac/misc/B12.html
Cyclitolshttp://www.chem.qmul.ac.uk/iupac/cyclitol/
Electron transport proteinshttp://www.chem.qmul.ac.uk/iubmb/etp/
Enzyme kineticshttp://www.chem.qmul.ac.uk/iubmb/kinetics/
Enzyme nomenclaturehttp://www.chem.qmul.ac.uk/iubmb/enzyme/
   EC 1 Oxidoreductaseshttp://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/
   EC 2 Transferaseshttp://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/
   EC 3 Hydrolaseshttp://www.chem.qmul.ac.uk/iubmb/enzyme/EC3/
   EC 4 Lyases http://www.chem.qmul.ac.uk/iubmb/enzyme/EC4/
   EC 5 Isomerases http://www.chem.qmul.ac.uk/iubmb/enzyme/EC5/
   EC 6 Ligases http://www.chem.qmul.ac.uk/iubmb/enzyme/EC6/
Folic acidhttp://www.chem.qmul.ac.uk/iupac/misc/folic.html
Glycolipidshttp://www.chem.qmul.ac.uk/iupac/misc/glylp.html
Glycoproteinshttp://www.chem.qmul.ac.uk/iupac/misc/glycp.html
myo-Inositol numberinghttp://www.chem.qmul.ac.uk/iupac/cyclitol/myo.html
Lignan Nomenclaturehttp://www.chem.qmul.ac.uk/iupac/lignan/
Lipid Nomenclaturehttp://www.chem.qmul.ac.uk/iupac/lipid/
Membrane transport proteinshttp://www.chem.qmul.ac.uk/iubmb/mtp/
Multienzymeshttp://www.chem.qmul.ac.uk/iubmb/misc/menz.html
Multiple forms of enzymeshttp://www.chem.qmul.ac.uk/iubmb/misc/isoen.html
Nucleic acid constituentshttp://www.chem.qmul.ac.uk/iupac/misc/naabb.html
Nucleic acid sequence
(incompletely specified bases)
http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
Peptide hormones
http://www.chem.qmul.ac.uk/iubmb/misc/phorm.html
Phosphorus containing compounds
http://www.chem.qmul.ac.uk/iupac/misc/phospho.html
Polymerized amino acidshttp://www.chem.qmul.ac.uk/iupac/misc/polypep.html
Polypeptide conformationhttp://www.chem.qmul.ac.uk/iupac/misc/ppep1.html
Polynucleotide conformationhttp://www.chem.qmul.ac.uk/iupac/misc/pnuc1.html
Polysaccharide conformationhttp://www.chem.qmul.ac.uk/iupac/misc/psac.html
Prenol nomenclaturehttp://www.chem.qmul.ac.uk/iupac/misc/prenol.html
Pyridoxal (vitamin B6)http://www.chem.qmul.ac.uk/iupac/misc/B6.html
Quinones with an Isoprenoid Chain http://www.chem.qmul.ac.uk/iupac/misc/quinone.html
Retinoidshttp://www.chem.qmul.ac.uk/iupac/misc/ret.html
Steroidshttp://www.chem.qmul.ac.uk/iupac/steroid/
Tetrapyrroleshttp://www.chem.qmul.ac.uk/iupac/tetrapyrrole/
Tocopherols (vitamin E)http://www.chem.qmul.ac.uk/iupac/misc/toc.html
Translation Factorshttp://www.chem.qmul.ac.uk/iubmb/misc/trans.html
Vitamin Dhttp://www.chem.qmul.ac.uk/iupac/misc/D.html
Chemical recommendations of use to biochemists
Bioinorganic glossarywww.chem.qmul.ac.uk/iupac/bioinorg/
Class nameswww.chem.qmul.ac.uk/iupac/class/
Gold Book - chemical glossarywww.chem.qmul.ac.uk/iupac/bibliog/gold.html
Isotopic modificationwww.chem.qmul.ac.uk/iupac/sectionH/
Medicinal chemistry glossarywww.chem.qmul.ac.uk/iupac/medchem/
Natural product nomenclaturewww.chem.qmul.ac.uk/iupac/sectionF/
Physical organic chemistry glossarywww.chem.qmul.ac.uk/iupac/gtpoc/
Stereochemical terminologywww.chem.qmul.ac.uk/iupac/stereo/
If you want to search all these files then two searches are needed. All those which start www.chem.qmul.ac.uk/iupac/ can be searched, and separately those which start www.chem.qmul.ac.uk/iubmb/ may be searched.

Enzyme Nomenclature

The continuous process of discovering new enzymes requires a somewhat different approach for their nomenclature and classification; this is probably the single largest task of the committees. The system used is to allot each enzyme a recommended name and number to allow it to be identified, and the list so obtained has been published at intervals. Its most recent printed edition is Enzyme Nomenclature, published by Academic Press for IUBMB in 1992 (ISBN 0-12-227164-5 hardback or 0-12-227165-3 paper). Several supplements have also been published. This list is now available on the web, at:

      http://www.chem.qmul.ac.uk/iubmb/enzyme/

classified under:

EC 1 oxidoreductases
EC 2 transferases
EC 3 hydrolases
EC 4 lyases
EC 5 isomerases
EC 6 ligases
This site is searchable. It contains the recommended name and number of each enzyme. An increasing fraction of these entries have links to the specifications of the enzymes, allowing these to be obtained on screen. These specifications include links to other bioinformatic databases as well as references and comments on the nature of the enzymes. It includes all enzymes approved or updated since the 1992 edition of Enzyme Nomenclature.

It is perhaps worth noting, as it has been a matter of long-standing confusion, that enzyme nomenclature is primarily a matter of naming reactions catalysed, not the structures of the proteins that catalyse them. This has allowed assignment of newly-discovered catalytic activities before anything is known about the structures of the enzymes. The links to databases of genes and protein structure allow the relationships between functional and structural classifications to be more readily accessed. The system of naming enzymes in terms of reactions, rather than structures, is one that works far better for enzymes that act on relatively small molecules than for those that handle polymers. Because of this a rather different system is used for the nomenclature of peptidases.

Information about new enzymes or corrections to existing entries may be reported directly from these web pages or by using the form printed in the back of of the 1992 edition of Enzyme Nomenclature. Comments and suggestions on enzyme classification and nomenclature also may be sent to Dr Andrew McDonald (Department of Biochemistry, Trinity College Dublin, Dublin 2, Ireland). All new material is considered by the committees before approval. The work on enzyme nomenclature and its transfer to the web have been greatly facilitated by grants to K.F. Tipton from the European Commission (Framework 4 Programme) and the National Institutes of Health.

Newsletters

The nomenclature committees publish newletters from time to time in various journals of biochemistry as a way of drawing attention to new recommendations, revisions to existing ones, current problems that are being studied, and to make minor recommendations that are too small to demand a full-scale document. In the future the committees hope that many of these functions will be fulfilled by these web pages. The complete 1996, 1999, 2004 and 2009 Newsletters are available, and a list of useful contents from earlier Newsletters, which has links to extracts from several of them.

Procedure for drawing attention to problems of nomenclature

Certain major areas of biochemistry require almost continuous review: the recommendations on carbohydrates, lipids, nucleic acids, proteins and enzymes are in this category, and are inevitably in a continuous state of revision as new discoveries are made. More restricted areas of the subject can have nomenclature that may survive for a decade or more without requiring any changes, but even then there are never any "definitive" recommendations fixed for all time. In the past published recommendations were often described as Rules, but the present committees prefer to avoid this term as far as possible, replacing it with Recommendations, which expresses more accurately their status. It is important to realize that the nomenclature committees do not have (and do not seek to have) any authority to enforce the adoption of their recommendations. Only journal editors have such authority, and follow nomenclature recommendations only to the extent that they choose to do so. In practice the Instructions to Authors of numerous journals do include references to most of the documents prepared by JCBN and NC-IUBMB, but only because this is the policy of the journals themselves.

Any subject can be reexamined, and it is open to any biochemist or other scientist concerned with biochemistry to draw attention to problem areas, whether because no conventions exist or because the existing recommendations fail to take account of the current state of knowledge. The most efficient way to do this is to write to the contact the Secretary of JCBN and NC-IUBMB, Professor R. Caspi, outlining the problem, and when appropriate suggesting a possible solution.


Last update 22 May 2013.

Comments and corrections to the Secretary Professor R. Caspi

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