BRENDA

BRENDA is the comprehensive enzyme information database. It is maintained and developed at the Institute of Biochemistry at the University of Cologne. Data on enzyme functions are extracted directly from the primary literature. Formal and consistency checks are done by computer programs and each data set is checked manually. The latest update was in January, 2004 which included:

• Large increase in updating speed
• Development of new EC-tree browser
• Taxonomy-tree browser
• Chemical substructure search engine for ligand structure
• Development of controlled vocabulary
• Ontology for some information fields
• Thesaurus for ligand names.

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Usage

The database covers 40 data fields with information about nomenclature, reaction and specificity, enzyme structure, isolation/preparation, stability, literature references and cross references to sequence and 3D-structure data banks.

The resource is available free of charge for academic, non-profit users; commercial use requires a license. For use it requires registration by email. The database can be searched by EC number, enzyme name, organism, or an advanced search combining these terms.

Example

As an example you can use the quick search to search for pyruvate dehydrogenase. This search gives several forms of the enzyme. If you click on pyruvate dehydrogenase (NADP+) it takes you to a page it gives you information on:

• Enzyme nomenclature
• Enzyme ligand interactions
• Functional parameters
• Organism related information
• Enzyme structure
• Molecular properties
• Bibliography/links/Disease

This page also shows all the organisms that contain this enzyme. If you wanted to determine the pyruvate dehydrogenase enzyme found in humans you can use the advance search using this query:

enzyme name = pyruvate dehydrogenase organism = homo sapiens

This query gives the result pyruvate dehydrogenase (lipoamide).

Other methods of searching include full text search, substructure search, TaxTree search (search an organism in taxonomy tree), search the EC tree and it is possible to do a sequence search.

Other databases

BRENDA also links to other databases. Including KEGG which provides information about the pathway that the enzyme is involved in. It also links to gene ontology information through the GO website. There is also links to the literature through PubMed. Other databases that BRENDA link to include:

• ExPASy
• NCBI databases (Protein, nucleotide, structure, genome, OMIM, Domains
• IUBMB enzyme nomenclature
• PDB database (3D information)
• PROSITE
• SYSTERS
• Protein mutant database
• SCOP
• CATH
• InterPro

Database extensions

As of January 2007, the data repository was complemented by text-mining data in^[1]:

• AMENDA (Automatic Mining of ENzyme DAta); and
• FRENDA (Full Reference ENzyme DAta)

References

1. ^ Barthelmes J, Ebeling C, Chang A, Schomburg I, Schomburg D (2007). BRENDA, AMENDA and FRENDA: the enzyme information system in 2007. Nucleic Acids Res, 35(Database issue):D511-4.

• Schomburg I, Hofmann O, Bänsch C, Chang A, Schomburg D (2000). Enzyme data and metabolic information: BRENDA, a resource for research in biology, biochemistry, and medicine. Gene Funct Dis, 3-4:109-18.
• Schomburg D, Schomburg I (2001). Springer Handbook of Enzymes, 2nd Ed. Springer, Heidelberg.
• Schomburg I, Chang A, Schomburg D (2002). BRENDA, enzyme data and metabolic information. Nucleic Acids Res, 30:47-9.
• Schomburg I, Chang A, Hofmann O, Ebeling C, Ehrentreich F, Schomburg D (2002). BRENDA: a resource for enzyme data and metabolic information. Trends Biochem Sci, 27(1):54-6.
• Pharkya P, Nikolaev EV, Maranas CD (2003). Review of the BRENDA Database. Metab Eng, 5(2):71-3.
• Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, Huhn G, Schomburg D (2004). BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res, 32(Database issue):D431-3.