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BRENDA Enzyme Database Overview

BRENDA is a comprehensive enzyme information system that provides data on enzymes classified by the Enzyme Nomenclature, including molecular biology and biochemistry information. Established in 1987, it has evolved from a series of books to a relational database, now maintained at TU Braunschweig, and is freely accessible to the scientific community. BRENDA features over 1.9 million different enzymes and more than 3 million manually annotated enzyme data entries from extensive literature sources.

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4 views8 pages

BRENDA Enzyme Database Overview

BRENDA is a comprehensive enzyme information system that provides data on enzymes classified by the Enzyme Nomenclature, including molecular biology and biochemistry information. Established in 1987, it has evolved from a series of books to a relational database, now maintained at TU Braunschweig, and is freely accessible to the scientific community. BRENDA features over 1.9 million different enzymes and more than 3 million manually annotated enzyme data entries from extensive literature sources.

Uploaded by

RedhaLav
Copyright
© All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd

BRENDA Tutorial

Introduction to the Enzyme


Information System
Facts about BRENDA

o BRENDA (BRaunschweig ENzyme DAtabase)

o one of the most comprehensive enzyme information repositories

o all enzymes, classified by the Enzyme Nomenclature (IUBMB)

o data of molecular biology, biochemistry, medical research, and


biotechnology

o furthermore BRENDA includes data from interconnected databases


containing results from text mining methods and bioinformatic approaches.

o BRENDA is freely available to the scientific community

o more than 80,000 visits of the BRENDA website each month

o major updates of the data in BRENDA are performed twice a year


History and major developments of BRENDA
o BRENDA was created at the former German National Research Center
for Biotechnology (GBF, now HZI, Helmholtz Zentrum für
Infektionsforschung) in 1987
o BRENDA was originally published as a series of book
• 1st Edition 1990-1997 (Enzyme Handbook)
• 2nd Edition 2001-... (Handbook of Enzymes)
o BRENDA moved to the University of Cologne
o First online version in 1998 via the SRS system at the EBI
o First website of BRENDA in Cologne
o Transfer of BRENDA into a fully relational database system
o BRENDA moved back to Braunschweig in 2007
o BRENDA is now maintained and further developed at the Department of
Bioinformatics & Biochemistry at the TU Braunschweig
Facts about BRENDA
o the main categories are based on the Enzymes and the Metabolites
/ Ligands
o enzyme-related data encompasses information on:
• Enzyme and ligand nomenclature
• Organism
• reaction and specificity
• Kinetic properties
• Structure and role of the ligands
• Stability information
• Ligand-enzyme information
• Enzyme sequence and structure
• Mutants and disease
• Occurence, isolation and properties
BRENDA data and information fields „classic view“
BRENDA is the most comprehensive information system on:

o 6671 EC Numbers (January 2015)


o more than 1.9 Mill. different enzymes
o more than 3 Mill. enzyme data, manually annotated from more than
130,000 literature references

Enzyme Commission numbers (EC Numbers) are defined according to the


catalyzed reaction
Enzyme nomenclature is defined by the IUBMB
(International Union of Biochemistry and Molecular Biology)‫‏‬

Format: Four numbers separated by periods, e.g. [Link]


Numbers represent from left to right a progressively finer classification scheme

Main Enzyme Classes: EC [Link] Formate + NAD+ = CO2 + NADH

1 Oxidoreductases formate dehydrogenase


2 Transferases
3 Hydrolases with NAD+ or NADP+ as acceptor
4 Lyases
5 Isomerases
acting on the aldehyde or oxo group of donors
6 Ligases oxidoreductase (main class)
(A)

(B)

Two main search options:


o quick access (A)
o and more specific queries (B)

…further details in the corresponding


BRENDA tutorials
Data sources & updates: Merge and process of data
Text mining data Manual annotation External databases
FRENDA und ontologies
Enzyme name + organism

AMENDA
Enzyme name + organism IUBMB enzyme classes
+ occurence

DRENDA Literature
Disease-related enzyme
data

KENDA Literature annotation


Kinetic data

BTO
Tissue
Ontology

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