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