BRENDA is the main collection of enzyme functional data available to the scientific community. It is available free of charge via the internet (www.brenda-enzymes.org) and as an in-house database for commercial users (requests to our distributor geneXplain).
Today, as the large international genome sequence projects are gaining a great amount of public attention and huge sequence data bases are created, it becomes more and more obvious that we are very limited in our ability to access functional data for the gene products - the proteins, in particular for enzymes. Those data are inherently very difficult to collect, interpret and standardize as they are highly distributed among journals from different fields and are often subject to experimental conditions. Nevertheless a systematic collection is essential for our interpretation of the genome information and more so for possible applications of this knowledge in the fields of medicine, agriculture, etc. Recent progress on enzyme immobilisation, enzyme production, enzyme inhibition, coenzyme regeneration and enzyme engineering has opened up fascinating new fields for the potential application of enzymes in a large range of different areas.
The enzymes are classified according to the Enzyme Commission list of enzymes. Some 6500 "different" enzymes are covered. Frequently enzymes with very different properties are included under the same EC number. Although we intend to give a representative overview on the characteristics and variability of each enzyme the Handbook is not a compendium. The reader will have to go to the primary literature for more detailed information. Naturally it is not possible to cover all the numerous literature references for each enzyme (for some enzymes up to 40000) if the data representation is to be concise as is intended. Currently about 450 EC classes display a "B" in the 4th position of the EC number. A part of these enzymes is in the reviewing process of the enzyme commission of the IUBMB and awaiting their EC numbers. Another part is waiting for more data which are a prerequisite for being proposed to the IUBMB (e.g. a description of the purificatin procedure). Incompletely classified "B-enzymes" (preliminary BRENDA-supplied EC numbers) mostly fill gaps in otherwise established pathways.
The data collection is being developed into a metabolic network information system with links to Enzyme expression and regulation information.
2. Contents of BRENDA
Compilation of Data
BRENDA is maintained and developed at the Institute of Biochemistry and Bioinformatics at the Technical University of Braunschweig, Germany. Data on enzyme function are extracted directly from the primary literature by scientists holding a degree in Biology or Chemistry. Formal and consistency checks are done by computer programs, each data set on a classified enzyme is checked manually by at least one biologist and one chemist.
It should be mentioned here that the data are extracted from literature and critically evaluated by qualified scientists. On the other hand the original authors' nomenclature for enzyme forms and subunits is retained as is their nomenclature for organisms and strains even if the organism is reclassified in the meantime. In order to keep the tables concise redundant information is avoided as far as possible (e.g. if Km values are measured in the presence of an obvious cosubstrate, only the name of the cosubstrate is given in parentheses as a commentary without reference to its specific role).
3. Project History
The development of an enzyme data information system was started in 1987 at the German National Research Centre for Biotechnology in Braunschweig (GBF), continued at the University of Cologne, and is now curated and hosted at the Technical University of Braunschweig, Institute of Biochemistry and Bioinformatics.
If you have suggestion how to improve the usability of BRENDA, to include new information fields, or others, please send us an email.
5. References on BRENDA
- BRENDA in 2019: a European ELIXIR core data resource
Jeske L., Placzek S., Schomburg I., Chang A., Schomburg D., Nucleic Acids Res., in print (2019)View free full text paper
Other relevant publications
- BRENDA in 2017: new perspectives and new tools in BRENDA
Placzek S., Schomburg I., Chang A., Jeske L., Ulbrich M., Tillack J., Schomburg D., Nucleic Acids Res., 45:D380-388 (2017)View free full text paper
- The BRENDA enzyme information system-From a database to an expert system.
Schomburg I., Jeske L., Ulbrich M., Placzek S., Chang A., Schomburg D., J Biotechnol., 261:194-206 (2017)View free full text paper
- BRENDA - From a database to a centre of excellence.
Schomburg I., Schomburg D., Systembiologie.de, 10:18-21 (2016)View free full text paper
- BRENDA in 2015: exciting developments in its 25th year of existence
Chang A., Schomburg I., Placzek S., Jeske L., Ulbrich M., Xiao M., Sensen C.W., Schomburg D., Nucleic Acids Res., 43:D439-446 (2015)View free full text paper
- BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA.
Schomburg I., Chang A., Placzek S., Söhngen C., Rother M., Lang M., Munaretto C., Ulas S., Stelzer M., Grote A. Scheer M., Schomburg D., Nucleic Acids Res., 41:764-772 (2013)View free full text paper
- Development of a classification scheme for disease-related enzyme information.
Söhngen C., Chang A., Schomburg D., BMC Bioinformatics, 12:329 (2011)View free full text paper
- BRENDA, the enzyme information system in 2011.
Scheer M., Grote A., Chang A., Schomburg I., Munaretto C., Rother M., Söhngen C., Stelzer M., Thiele J., Schomburg D., Nucleic Acids Res., 39:670-676 (2011)View free full text paper
- The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources.
Gremse M., Chang A., Schomburg I., Grote A., Scheer M., Ebeling C., Schomburg D., Nucleic Acids Res., 39:D507-13 (2011)View free full text paper
- BKM-react, an integrated biochemical reaction databaseLang M., Stelzer M., Schomburg D., BMC Bioinformatics, 12:42 (2011)View free full text paper
- EnzymeDetector: an integrated enzyme function prediction tool and database.Quester S., Schomburg D., BMC Bioinformatics, 12:376 (2011)View free full text paper
- BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009.Chang A., Scheer M., Grote A., Schomburg I., Schomburg D., Nucleic Acids Res., 37: D588-D592 (2009)View free full text paper
- BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.Barthelmes J., Ebeling C., Chang A., Schomburg I., Schomburg D., Nucleic Acids Res., 35:D511-D514 (2007)View free full text paper
- Structural Analysis and Prediction of Protein Mutant Stability using Distance and Torsion Potentials: Role of Secondary Structure and Solvent Accessibility.Parthiban V, Gromiha MM, Hoppe C, Schomburg D., Proteins, 66(1):41-52 (2007)
- Computational modeling of protein mutant stability: analysis and optimization of statistical potentials and structural features reveal insights into prediction model development.Parthiban V, Gromiha MM, Abhinandan M., Schomburg D., BMC Structural Biology, 7:54 (2007)View free full text paper
- CUPSAT: prediction of protein stability upon point mutations.Parthiban V, Gromiha MM., Schomburg D., Nucleic Acid Res., 34:W239-42 (2006)View free full text paper
- 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., 32: D431-D433 (2004)View free full text paper
- Review of the BRENDA Database.Pharkya P., Nikolaev E.V., Maranas C.D., Metab Eng., 5(2):71-73 (2003)
- BRENDA: a resource for enzyme data and metabolic information.Schomburg I., Chang A., Hofmann O., Ebeling C., Ehrentreich F., Schomburg D., Trends Biochem Sci., 27(1):54-56 (2002)
- BRENDA, enzyme data and metabolic informationSchomburg, I., Chang, A., Schomburg, D., Nucleic Acids Res. 30, 47-49 (2002)View free full text paper
- 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 medicineSchomburg, I., Hofmann, O., Baensch, C., Chang, A., Schomburg, D., Gene Funct. Dis. 3-4, 109-18 (2000)
- BKM-react, an integrated biochemical reaction database