BRENDA

BRENDA (The Comprehensive Enzyme Information

System) is an information system representing one of the most
BRENDA (The
comprehensive enzyme repositories. It is an electronic resource Comprehensive Enzyme
that comprises molecular and biochemical information on Information System)
enzymes that have been classified by the IUBMB. Every
classified enzyme is characterized with respect to its catalyzed
Content
biochemical reaction. Kinetic properties of the corresponding
reactants (that is, substrates and products) are described in detail. Description molecular and
BRENDA contains enzyme-specific data manually extracted biochemical
from primary scientific literature and additional data derived information on
from automatic information retrieval methods such as text enzymes that
mining. It provides a web-based user interface that allows a have been
convenient and sophisticated access (https://web.archive.org/we classified by the
b/20150506193454/http://www.brenda-enzymes.org/) to the
IUBMB
data.
Contact

History Research center Technische

Universität
BRENDA was founded in 1987 at the former German Research Braunschweig,
Centre for Biotechnology (now the Helmholtz Centre for BRICS -
Infection Research) in Braunschweig and was originally Braunschweig
published as a series of books. Its name was originally an Integrated Centre
acronym for the BRaunschweig ENzyme DAtabase. From of Systems
1996 to 2007, BRENDA was located at the University of Biology
Cologne. There, BRENDA developed into a publicly accessible
Primary citation PMID 33211880
enzyme information system.[1][2][3] In 2007, BRENDA
returned to Braunschweig. Currently, BRENDA is maintained (https://pubmed.nc
and further developed at the BRICS ( Braunschweig Integrated bi.nlm.nih.gov/332
Centre of Systems Biology) at the TU Braunschweig. 11880)
Release date 2021
In 2018 BRENDA was appointed to ELIXIR Core Data
Resource with fundamental importance to biological and Access
biomedical research and long-term preservation of biological Website http://www.brenda-
data. enzymes.org
Download URL form (https://www.
Updates brenda-enzymes.o
rg/brenda_downlo
A major update of the data in BRENDA is performed twice a ad)
year. Besides the upgrade of its content, improvements of the
user interface are also incorporated into the BRENDA database. Web service URL soap (https://www.
brenda-enzymes.o
rg/soap/)
Content and features
Database:
The database contains more than 40 data fields with enzyme-specific information on more than 8300 EC
numbers that are classified according to the IUBMB. The different data fields cover information on the
enzyme's nomenclature, reaction and specificity, enzyme structure, isolation and preparation, enzyme
stability, kinetic parameters such as Km value and turnover number, occurrence and localization, mutants
and engineered enzymes, application of enzymes and ligand-related data. Currently, BRENDA contains
manually annotated data from over 165,000 different scientific articles. Each enzyme entry is clearly linked
to at least one literature reference, to its source organism, and, where available, to the protein sequence of
the enzyme.[3]

An in-house development of the BRENDA team is the BRENDA tissue ontology (BTO),[4] a
comprehensive, structured encyclopedia with controlled vocabulary for terms and names for tissues, organs,
anatomical structures, plant parts, cell cultures, cell types, and cell lines in organisms from all taxonomic
groups.

An important part of BRENDA represent the almost 260,000 enzyme ligands, which are available on their
names, synonyms or via the chemical structure. The term "ligand" is used in this context to all low
molecular weight compounds which interact with enzymes. These include not only metabolites of primary
metabolism, co-substrates or cofactors but also enzyme inhibitors or metal ions. The origin of these
molecules ranges from naturally occurring antibiotics to synthetic compounds that have been synthesized
for the development of drugs or pesticides. Furthermore, cross-references to external information resources
such as sequence and 3D-structure databases, as well as biomedical ontologies, are provided.

Extensions:

Since 2006, the data in BRENDA is supplemented with information extracted from the scientific literature
by a co-occurrence based text mining approach. For this purpose, four text-mining repositories FRENDA
(Full Reference ENzyme DAta), AMENDA (Automatic Mining of ENzyme DAta), DRENDA (Disease-
Related ENzyme information DAtabase) and KENDA (Kinetic ENzyme DAta) were introduced. These
text-mining results were derived from the titles and abstracts of all articles in the literature database
PubMed.[3][5][6]

Data access:

There are several tools to obtain access to the data in BRENDA. Some of them are listed here.

Several different query forms (e.g., quick and advanced search)

EC tree browser
Taxonomy tree browser
Ontologies for different biological domains (e.g., BRENDA tissue ontology, Gene Ontology)
Thesaurus for ligand names
Chemical substructure search engine for ligand structures
BRENDA Pathway Maps

Download options:

SOAP-API
SBML-download
BRENDA download (textfile oder JSON-Format])

Availability
The use of BRENDA is free of charge. BRENDA is subject to the terms of the Creative Commons license
(CC BY 4.0).

Other databases
BRENDA provides links to several other databases with a different focus on the enzyme, e.g., metabolic
function or enzyme structure. Other links lead to ontological information on the corresponding gene of the
enzyme in question. Links to the literature are established with PubMed. BRENDA links to some further
databases and repositories such as:

BRENDA tissue ontology

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

References
1. Chang A, Jeske L, Ulbrich S, Hofmann J, Koblitz J, Schomburg I, Neumann-Schaal M, Jahn
D, Schomburg D (2021). "BRENDA, the ELIXIR core data resource in 2021: new
developments and updates" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779020).
Nucleic Acids Res. 49 (Database issue): D498–D508. doi:10.1093/nar/gkaa1025 (https://doi.
org/10.1093%2Fnar%2Fgkaa1025). PMC 7779020 (https://www.ncbi.nlm.nih.gov/pmc/articl
es/PMC7779020). PMID 33211880 (https://pubmed.ncbi.nlm.nih.gov/33211880).
2. Schomburg I, Jeske L, Ulbrich M, Placzek S, Chang A, Schomburg D (2021). "The BRENDA
enzyme information system-From a database to an expert system" (https://doi.org/10.1016%
2Fj.jbiotec.2017.04.020). J. Biotechnol. 261 (Database issue): 194–206.
doi:10.1016/j.jbiotec.2017.04.020 (https://doi.org/10.1016%2Fj.jbiotec.2017.04.020).
PMID 28438579 (https://pubmed.ncbi.nlm.nih.gov/28438579).
3. Chang A, Scheer M, Grote A, Schomburg I, Schomburg D (2008). "BRENDA, AMENDA and
FRENDA the enzyme information system: new content and tools in 2009" (https://www.ncbi.
nlm.nih.gov/pmc/articles/PMC2686525). Nucleic Acids Res. 37 (Database issue): D588-92.
doi:10.1093/nar/gkn820 (https://doi.org/10.1093%2Fnar%2Fgkn820). PMC 2686525 (https://
www.ncbi.nlm.nih.gov/pmc/articles/PMC2686525). PMID 18984617 (https://pubmed.ncbi.nl
m.nih.gov/18984617).
4. M. Gremse, A. Chang, I. Schomburg, A. Grote, M. Scheer, C. Ebeling, D. Schomburg: The
BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for
enzyme sources. (http://nar.oxfordjournals.org/content/39/suppl_1/D507.long) In: Nucleic
Acids Res. 39 (Database issue), 2011, S. D507–D513
5. Schomburg I, Chang A, Placzek S, Söhngen C, Rother M, Lang M, Munaretto C, Ulas S,
Stelzer M, Grote A, Scheer M, Schomburg D: "BRENDA in 2013: integrated reactions, kinetic
data, enzyme function data, improved disease classification: new options and contents in
 BRENDA (https://archive.today/20131007234938/http://nar.oxfordjournals.org/content/41/D1/
D764.long)", Nucleic Acids Res., 41 (Database issue): D764-D772
6. Barthelmes J, Ebeling C, Chang A, Schomburg I, Schomburg D (2006). "BRENDA,
AMENDA and FRENDA: the enzyme information system in 2007" (https://www.ncbi.nlm.nih.
gov/pmc/articles/PMC1899097). Nucleic Acids Res. 35 (Database issue): D511-4.
doi:10.1093/nar/gkl972 (https://doi.org/10.1093%2Fnar%2Fgkl972). PMC 1899097 (https://w
ww.ncbi.nlm.nih.gov/pmc/articles/PMC1899097). PMID 17202167 (https://pubmed.ncbi.nlm.
nih.gov/17202167).

Further reading
Chang A, Schomburg I, Placzek S, Jeske L, Ulbrich M, Xiao M, Sensen CW, Schomburg D
(2015). "BRENDA in 2015: exciting developments in its 25th year of existence" (https://www.
ncbi.nlm.nih.gov/pmc/articles/PMC4383907). Nucleic Acids Res. 43 (Database issue):
D439–D446. doi:10.1093/nar/gku1068 (https://doi.org/10.1093%2Fnar%2Fgku1068).
PMC 4383907 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383907). PMID 25378310
(https://pubmed.ncbi.nlm.nih.gov/25378310).
Schomburg I, Schomburg D (2016). "BRENDA: From a database to a centre of excellence".
Systembiologie.de. 10: 18–21.
Chang A, Scheer M, Grote A, Schomburg I, Schomburg D (2009). "BRENDA, AMENDA and
FRENDA the enzyme information system: new content and tools in 2009" (https://www.ncbi.
nlm.nih.gov/pmc/articles/PMC2686525). Nucleic Acids Res. 37 (Database issue): D588–92.
doi:10.1093/nar/gkn820 (https://doi.org/10.1093%2Fnar%2Fgkn820). PMC 2686525 (https://
www.ncbi.nlm.nih.gov/pmc/articles/PMC2686525). PMID 18984617 (https://pubmed.ncbi.nl
m.nih.gov/18984617).
Schomburg D, Schomburg I, Chang A (2006). Springer Handbook of Enzymes (2nd ed.).
Heidelberg: Springer.
Pharkya P, Nikolaev EV, Maranas CD (2003). "Review of the BRENDA Database". Metab
Eng. 5 (2): 71–73. doi:10.1016/S1096-7176(03)00008-9 (https://doi.org/10.1016%2FS1096-
7176%2803%2900008-9). PMID 12850129 (https://pubmed.ncbi.nlm.nih.gov/12850129).
Schomburg I, Chang A, Schomburg D (2002). "BRENDA, enzyme data and metabolic
information" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC99121). Nucleic Acids Res. 30
(1): 47–49. doi:10.1093/nar/30.1.47 (https://doi.org/10.1093%2Fnar%2F30.1.47).
PMC 99121 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC99121). PMID 11752250 (http
s://pubmed.ncbi.nlm.nih.gov/11752250).
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): 109–118. doi:10.1002/1438-826X(200010)1:3/4<109::AID-
GNFD109>3.0.CO;2-O (https://doi.org/10.1002%2F1438-826X%28200010%291%3A3%2F
4%3C109%3A%3AAID-GNFD109%3E3.0.CO%3B2-O).

External links
Official BRENDA website (https://web.archive.org/web/20150506193454/http://www.brenda-
enzymes.org/)
Enzyme Nomenclature (http://www.chem.qmul.ac.uk/iubmb/enzyme/)
Springer Handbook of Enzymes (https://www.springer.com/series/4621/)
Worthington Enzyme Manual (https://www.worthington-biochem.com/tools-resources/enzym
e-manual/)
ExplorEnz The Enzyme Database (https://www.enzyme-database.org/index.php/)
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