Databases enzyme

BRENDA [191,192] The BRaunschweig ENzyme DAtabase http //www.brenda enzymes.info/... 

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. 

Schomburg I, Chang A, Ebehng C, et al. (2004) BRENDA, the enzyme database Updates and major new developments. Nucl. Acids Res. 32 D431-D433. http //www.brenda.uni-koeln.de/. 

Fleischmann A, Darsow M, Degtyarenko K et al. (2004) IntEnz, the integrated relational enzyme database. Nucleic Acids Res 32 D434-D437... 

In this section, enzymes in the EC 2.4. class are presented that catalyze valuable and interesting reactions in the field of polymer chemistry. The Enzyme Commission (EC) classification scheme organizes enzymes according to their biochemical function in living systems. Enzymes can, however, also catalyze the reverse reaction, which is very often used in biocatalytic synthesis. Therefore, newer classification systems were developed based on the three-dimensional structure and function of the enzyme, the property of the enzyme, the biotransformation the enzyme catalyzes etc. [88-93]. The Carbohydrate-Active enZYmes Database (CAZy), which is currently the best database/classification system for carbohydrate-active enzymes uses an amino-acid-sequence-based classification and would classify some of the enzymes presented in the following as hydrolases rather than transferases (e.g. branching enzyme, sucrases, and amylomaltase) [91]. Nevertheless, we present these enzymes here because they are transferases according to the EC classification. 

P. M. Coutinho, B. Henrissat, in Recent Advances in Carbohydrate Bioengineering (Eds. H.). H.). Gilbert, G. Davies, B. Henrissat, B. Svensson), The Royal Society of Chemistry, Cambridge, 1999, p. 3 P. M. Coutinho, B. Henrissat, Carbohydrate Active Enzymes database http //afmb.cnrs-mrs.ff/CAZY/ 1999. 

REBASE-The Restriction Enzyme Database Restriction enzyme directory and action http //rebase. neb.com/... 

The ENZYME database at http //www.expasy.ch/enzyme/ provides information on EC number, name, catalytic activity, and hyperlinks to sequence data of enzymes. The 3D structures of enzymes can be accessed via Enzyme Structures Database at http //www.biochem.ucl.ac.uk/bsm/enzyme/index.html. Some other enzyme databases are listed in Table 7.1. 

SEARCH AND ANALYSIS OF ENZYME DATA 7.3.1. Search for Enzyme Database... 

Figure 7.5. Search enzyme information at Brenda. Brenda is the comprehensive enzyme database for retrieving chemical, kinetic, and structural properties of enzymes via EC number, enzyme name, and organism (biological source). The search page by EC number is shown.

Search enzyme databases for information to construct a database of glucosidases (EC 3.2.1.x) with retrievable fields on substrate (anomeric) specificity, catalytic mechanism (stereochemical, e.g., inversion versus retention) and kinetic constants (e.g., Km and V). 

In addition to the metabolic databases listed above, some of the enzyme databases described in the previous chapter (Chapter 6) also serve as useful metabolic resources. All of the enzyme and metabolic databases make use of EC (Enzyme Commission) numbers which are available at the International Union of Biochemistry and Molecular Biology (IUBMB) site (http //www.chem.qmw.ac.uk/ iubmb/enzyme/). 

Enzyme Commission, EC ENZYME database Enzyme Structures Database Esther Esterases G6P dehydrogenase Leonora Enzyme kinetics LIGAND... 

Bairoch, A., The ENZYME database in 2000. Nucleic Acids Research 2000, 28, 304-305. 

MichaeUs-Menten (MM) kinetics, although not perfect and in many cases inadequate for a number of reasons, have been used widely to describe the dynamics of catalysis of most enzymes. Databases such as BRENDA [5], containing sets of MM kinetic constants for most enzymes in a wide array of organisms, are widely available. The basic MM equation (Fig. 7-2) is derived for a simple system as shown ... 

The ENZYME database1501, maintained by the Swiss Institute for Bioinformatics (SIB), provides a comprehensive list of all IUBMB classifications, together with associated information such as systematic and alternative enzyme names, cofactor requirements, and pointers to the corresponding entry in the SWISS-PROT database of protein sequences1511. In addition, there is a concise free-text description of the reaction catalyzed, together with a description of preferential substrates and products. Currently, the ENZYME database holds entries for approximately 3700 enzymes. 

A much more ambitious database that builds on the IUBMB classification is BRENDA, maintained by the Institute of Biochemistry at the University of Cologne. In addition to the data provided by the ENZYME database, the BRENDA curators have extracted a large body of information from the enzyme literature and incorporated it into the database. The database format strives to be readable by both humans and machines. The categories of data stored in BRENDA comprise the EC-number, systematic and recommended names, synonyms, CAS-registry numbers, the reaction catalyzed, a list of known substrates and products, the natural substrates, specific activities, KM values, pH and temperature optima, cofactor and ion requirements, inhibitors, sources, localization, purification schemes, molecular weight, subunit structure, posttranslational modifications, enzyme stability, database links, and last but not least an extensive bibliography. Currently, BRENDA holds entries for approximately 3500 different enzymes. 

Approximately 3700 different types of enzymes, each of which catalyzes a single chemical reaction or set of closely related reactions, have been classified in the enzyme database. Certain enzymes are found in the majority of cells because they catalyze the synthesis of common cellular products (e.g., proteins, nucleic acids, and phospholipids) or take part in the... 

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