ExplorEnz is the MySQL database that is used for the curation and dissemination of the International Union of Biochemistry and Molecular Biology (IUBMB) Enzyme Nomenclature. A simple web-based query interface is provided, along with an advanced search engine for more complex Boolean queries. The WWW front-end is accessible at http://www.enzyme-database.org, from where downloads of the database as SQL and XML are also available. An associated form-based curatorial application has been developed to facilitate the curation of enzyme data as well as the internal and public review processes that occur before an enzyme entry is made official. Suggestions for new enzyme entries, or modifications to existing ones, can be made using the forms provided at http://www.enzyme-database.org/forms.php.

Naming things is essential for people to understand one another, no matter what language or field of interest is involved. This is as true for enzymes, genes and chemicals as it is for birds, food, flowers, etc. Effective communication requires a lack of ambiguity, but, in practice, ambiguities abound even between people who use the same language in different parts of the world, or even within the same country. Whereas ambiguities in the words used for common objects or actions have been the basis for many, more-or-less memorable jokes, they can also cause a great deal of confusion. Such linguistic chaos is welcomed by many as being a part of a diverse heritage that should be preserved at all costs to prevent us from descending into Orwellian 'newspeak'. However, in the sciences, there are distinct advantages in others being able to understand what one is doing. Many groups have stressed the need for standardized, universally accepted systems of nomenclature in chemistry, genetics, enzymology, etc. However, it is the universal acceptance that usually causes the problem. It is rare to find people who will admit that they find nomenclature to be an interesting subject, but many who profess contempt for it will get very excited if it is suggested that their pet nomenclature should be changed in the interest of clarity or uniformity. This account will consider the development of the enzyme nomenclature system, its benefits, shortcomings and future prospects.

Photoaffinity labelling of rat adrenal mitochondrial preparations with [3H]PK 14105 resulted in a single 3H-labelled band on SDS/PAGE gels with an apparent-molecular-mass peak of 18 kDa. This represents a polypeptide associated with the peripheral-type benzodiazepine-binding site. Solubilization of photoaffinity-labelled membranes with 6 M-guanidine hydrochloride, followed by gel filtration and reversed-phase h.p.l.c. of the solubilized material, resulted in the purification to homogeneity of the [3H]PK 14105-labelled polypeptide. This purified polypeptide was used to raise a rabbit polyclonal antiserum which recognized the immunogen in pure form and exclusively recognized it in a crude preparation of rat adrenal mitochondria as judged by immunoblotting. By the same analysis the antiserum identified the corresponding polypeptide from rat kidney and salivary gland, demonstrating its cross-reactivity. Subsequent immunocytochemical studies localized the polypeptide to the cortex of the adrenal gland, the distal tubules of kidney, the interstitial cells of testis, the biliary epithelium of liver and the choroid plexus and ependyma cells within the brain. This selective localization within organs may provide an insight into the physiological role of the peripheral-type benzodiazepine acceptor.

The development of metabolomics has resulted in the discovery of an increasing number of orphan metabolites, which are defined as compounds that are known to be present in living organisms but whose synthetic/degradation pathways are unknown. In this paper, we describe a procedure for identifying possible products and/or precursors of such orphan metabolites and for suggesting complete reaction equations and the corresponding EC (Enzyme Commission) number simultaneously. Chemical structure comparison is performed for a pair of compounds consisting of a reported substrate and its corresponding product and also for pairs of randomly selected compounds. Possible combinations of compounds registered in the KEGG database were used for generating putative enzyme reaction equations, which resulted in 77% of the reported equations being generated, as most of the remainder represent classes of compounds, rather than specific compounds, or contain Markush structures. The quality was checked using chemical structure comparison and the random-tree method, which gave 98% accuracy in suggesting EC subsubclasses for reported equations in cross-validation tests. The equations generated in this study can be seen using the Web-based program GREP (Generator of Reaction Equations & Pathways; http://bisscat.org/GREP/ ). The usefulness of our method for constructing possible metabolic pathways was demonstrated by mapping the generated equations for several groups of compounds, such as the betalain alkaloids. The possible development of our method so that alternative substrates for reported enzymes can be found and for annotating enzyme functions in genomic research is also discussed.

Background: We describe the database ExplorEnz, which is the primary repository for EC numbers and enzyme data that are being curated on behalf of the IUBMB. The enzyme nomenclature is incorporated into many other resources, including the ExPASy-ENZYME, BRENDA and KEGG bioinformatics databases.