The BRENDA database is an enzyme database that provides extensive functional data on enzymes. These include details on nomenclature, reactions and specificity, enzyme structure, isolation/preparation and stability. The data are extracted from the primary literature and experimental details and references are given, as are data provided by the NC-IUBMB.
Part of the EXPASY database is ENZYME which is a repository of information relative to the nomenclature of enzymes. It provides information on each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided. The data provided comprise the EC number, recommended name, alternative names (if any), details of the reaction catalysed and of the cofactors required (if any). From ENZYME, there are also pointers to the SWISS-PROT protein sequence entries that correspond to the enzyme (if any) and to human disease(s) that are associated with a deficiency of the enzyme (if any).
This database of Thermodynamics of Enzyme-Catalysed Reactions provides information on the thermodynamics of enzyme-catalysed reactions. The data comprise direct equilibrium and calorimetric measurements, as determined under in vitro conditions, and presented in scientific publications. For each entry in the database, the reference for the data; the reaction studied; the name and EC number of the enzyme used; the method of measurement; the conditions of measurement [temperature, pH, ionic strength, and the buffer(s) and cofactor(s) used]; the data and an evaluation of it and, sometimes, commentary on the data and on any corrections that have been applied to it, where available, are provided.
KEGG (Kyoto Encyclopedia of Genes and Genomes) provides information on molecular and cellular biology in terms of the information pathways that consist of interacting molecules or genes. It also provides links from the gene catalogs produced by genome sequencing projects. The KEGG database also provides metabolic pathway maps and regulatory pathways maps, which can be viewed in terms of a specific organism. KEGG provides enzyme data with links to pathways, genes, diseases (OMIM database), motif and PDB (Protein Data Bank) structures.
The MEROPS (Merops, father-in-law to Priam, the King of Troy) database is an integrated resource for information on peptidases (subclass 3.4). The underlying classification assigns the peptidases to families on the basis of amino acid sequence similarities, and then groups the families in clans according to three-dimensional structures. Information provided in the database includes amino acid and nucleotide sequence identifiers, gene names and loci, images of three-dimensional molecular structures, alignments of amino acid sequences, evolutionary trees, and alignments of matching expressed sequence tags. Data for the catalytic activities of the peptidases include a specificity search and comments on biological functions of the enzymes.
MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways for primary metabolism and secondary metabolism. It stores compounds, proteins, protein complexes and genes associated with these pathways.
The PDB (Protein Data Bank) is a repository of 3-D macromolecular structural data primarily determined experimentally by X-ray crystallography and NMR. The link is to an index of enzymes in the PDB database.
UM-BBD (The University of Minnesota Biocatalysis/Biodegradation Database) This database contains information on microbial biocatalytic reactions and biodegradation pathways, primarily for xenobiotics. The UM-BBD provides information on microbial enzyme-catalysed reactions that are important for that area of biotechnology. Individual reactions and metabolic pathways are presented with information on the starting and intermediate chemical compounds, the organisms that transform the compounds, the enzymes, and the relevant genes.
CAS registry number The CAS (Chemical Abstracts Service) registry number is a unique identifier which can be used in an on-line search of the Chemical Abstracts database. It saves using either the EC number or any of the names under which the enzyme is known for searching. The registry file will provide a list of synonyms and the main database will identify all references which refer to the enzyme.