ENZYME nomenclature database

The ENZYME nomenclature database, a repository of information based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB), currently contains 4435 enzyme entries (Release 38.0, September 2005). Of these, 545 entries are superseded, resulting in a final list of 3,890 enzymes, 224 sub-subclasses, and 65 subclasses. 

The ENZYME nomenclature database (Figure 7.3) of ExPASy (Expert Protein Analysis System) at http //www.expasy.ch/enzyme/ can be searched by entering EC number or enzyme names. The query returns information on EC number, enzyme name, catalytic activity, cofactors (if any) and pointers to Swiss-Prot sequence, ProSite, and human disease(s) of the enzyme deficiency. 

The complex nature and interconnectivity of plant cell wall polymers preclude straightforward enzymatic digestion. There are dozens of enzyme families involved in plant cell wall hydrolysis, including cellulases, hemicellu-lases, pectinases, and lignin-modifying enzymes. The Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) has classified cellulases and hemicellulases, like all enzymes, into different classes based on activity. Table 33.2 and Table 33.3, compiled from the IUBMB enzyme nomenclature database (http //www.chem.qmul.ac.uk/iubmb/ enzyme/), list the IUBMB enzyme classifications for cellulases and hemicellulases.153... 

Swissprot Enzyme (Enzyme nomenclature database) http / / us. expasy. org / enzyme /... 

For identifying synonyms or finding out the correct name of an enzyme, the Enzyme Nomenclature Database (EC database) can be searched or downloaded under http // www.expasy.ch/enzyme/. 

DIPPR Pure Compound Database Dortmund Data Bank Enzyme Nomenclature Database Enzyme Structures Database European Bioinformatics Institute... 

Enzyme Nomenclature Database European Bioinformatics Institute... 

Of the 14500 entries currently in PDB, there are roughly 7200 enzyme structures. The Enzymes Structures Database, maintained by University College, University of London, focuses on this portion of PDB and offers links between the E.C. nomenclature of the IUBMB and the corresponding PDB entries. 

Thus, the EC numbers provide unique identifiers for enzyme functions, and give us useful keyword entries in database searches (http //www.chem.qmw.ac.uk/iubmb/ enzyme/). Enzyme nomenclature/common names and properties are also available at ENZYME (http //www.expasy.org/enzyme) and BRENDA (http //www.brenda.uni-koeln. de). IntEhz (http //www.ebi.ac.uk/intenzy) is the integrated enzyme database and enzyme nomenclature. Table 11.1 lists some enzyme resource sites providing general information. 

Carbohydrates constitute one the of most complex structures occurring in nature (with nucleic acids and proteins) due to i) the monosaccharide diversity, ii) the type of linkage and iii) the nature of carbohydrate-linked molecules. As a result, GHs present a wide range of activities, which have necessitated the creation of a specific classification more explicit than the lUB Enzyme Nomenclature. In 1998, the Carbohydrate-Active Enzymes (CAZy) database was created, gathering glycosidases in famiUes based on amino-acid sequence and protein structures similarities. ... 

Portal to databases of chemical suppliers lUBMB nomenclature for enzymes Nucleotide and protein sequences, protein structures, enzyme nomenclature and reactions Infrared, Raman, and mass spectra Portal to Infotherm, Acronyms, thermophysical properties See B.6... 

Merops (http //merops.sanger.ac.uk), database of peptidases and their proteinaceous inhibitors. Includes enzyme classification and nomenclature, external links to literature, and the structure of proteins of interest (if known). Enables one to find the gene coding for a given peptidase or to find the best enzyme to digest a chosen substrate. 

The ENZYME database (Bairoch, 1996) is also used to generate standardized description lines for enzyme entries and to allow information such as catalytic activity, cofactors, and relevant keywords to be taken from ENZYME and to be added automatically to TrEMBL entries. Additionally, specialized databases such as FlyBase (FlyBase Consortium, 1999) and MGD (Blake et al., 1999) are used to transfer information such as the correct gene nomenclature and cross references to these databases into TrEMBL entries. The automatic analysis and annotation of TrEMBL entries are redone and updated every TrEMBL release. 

An overview of databases yields the number of publicly accessible genomes 112 finished microbial and two eukaryotic genomes with over 300 overall in progress (as of April 2003). The number of enzymes with E.C. nomenclature is 4159 according to the ExPASy website and 3225 according to Brenda databases the number of accessible 3D structures totals 20 946, 18 872 of which are proteins. 

Databases such as Enzyme [12], Brenda [5], Ligand [28] and EMP [6] contain enzymes which are involved in a large number of reactions. Each enzyme with known enzyme function are catalogued and named by a nomenclature committee. Also included in the databases is information on the reaction and specificity of the enzyme and the various conditions the enzyme will be active under. Information about the structure and stability of the enzyme and the preparation of the reaction may also be included. 

Thermodynamic and thermophysical properties of ionic liquids and mixtures Miscibility and other properties of organic liquids Enzyme and nucleic acid nomenclature Portal to crystallographic databases See B.13 See B.13.b... 

LocusLink is an NCBI project to link information applicable to specific genetic loci from several disparate databases. Information maintained by LocusLink includes official nomenclature, aliases, sequence accessions (particularly RefSeq accessions), phenotypes. Enzyme Commission numbers, map information, and Mendelian Inheritance in Man numbers. Each locus is assigned a unique identification number, which additional databases can then reference. LocusLink is described in greater detail in Chapter 7. 

Proteins include the enzyme molecules that carry out many of the biological reactions we study, and their sequences are an intrinsic part of the submission process. Their importance, which is discussed in Chapter 2, is also reflected in the submission process, and this information must be captured for representation in the various databases. Also important are the protein product and gene names, if these are known. There are a variety of resources (many present in the lists that conclude these chapters) that offer the correct gene nomenclature for many organisms (cf. Genetic nomenclature guide, Trends in Genetics, 1998). 

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