The BRENDA Enzyme Information System

The BRENDA Enzyme Information System

1The Enzyme Information System BRENDA

BRENDA Training

The BRENDA Enzyme Information System developed and maintained at

Technische Universität Braunschweig, GermanyDepartment of Bioinformatics and Biochemistry


Introduction to BRENDA

The BRENDA Enzyme Information System developed and maintained at

Technische Universität Braunschweig, GermanyDepartment of Bioinformatics and Biochemistry

Director of the department and founder of BRENDA: Prof. Dietmar Schomburg



Module B0Introduction to BRENDA● History, scope and content● Data sources and updates● BRENDA on the web

Module B1 Web interface● Search modes● Enzyme flat file● EC Explorer● Quick Search

Module B2 Web interface● Sequence Search● Genome Explorer● 3D Structure● Functional Enzyme Parameters

Overview

4

Module B3 Web interface● Ontology Explorer● TaxTree Explorer

Module B4 Web interfaceEnzyme ligands● Ligand Search● Substructure Search

Module B5Computer-based access●SOAP●Textfile with BRENDA core data●SBML output

Excercises

The Enzyme Information System BRENDA



Module B0Introduction to BRENDA● History, scope and content● Data sources and updates● BRENDA on the web


History

March, 2nd 2009 4BRENDA - Technical and bioinformatical aspects 6The Enzyme Information System BRENDA

A short history of BRENDA


History


A short history of BRENDA BRaunschweig ENzyme DAtabase

1987 project started at German National Research Centre for Biotechnology in Braunschweig


History




History




originally published as a series of books 1st Edition 1990-1997 2nd Edition 2000-2009 (45 Volumes) available in print and pdf-format


History





1996 BRENDA and Dietmar Schomburg moved to University of Cologne

here BRENDA was further curated and transformed into a publicly available database


History







2007 BRENDA moved back to Braunschweig (Technische Universität)


History







2007 BRENDA moved back to Braunschweig (Technische Universität)

continuous curation, technical improvement and further development


Scope and content



Most comprehensive information systems on● Enzymes

Scope and content



Most comprehensive information systems on● Enzymes > 1,000,000 different enzymes > 65,000 manually curated

5,300 EC numbers

Scope and content



Most comprehensive information systems onEnzymes > 1,000,000 different enzymes

> 65,000 manually curated 5,300 EC numbers

Enzyme Commision numbers are defined according to the catalyzed reactionEnzyme nomenclature is defined by the IUBMB(International Union of Biochemistry and Molecular Biology)

Scope and content






Main class (1st digit)

1 Oxidoreductases2 Transferases3 Hydrolases4 Lyases5 Isomerases6 Ligases

Scope and content






Format: Four numbers separated by periods → e.g. 1.2.1.2

Numbers represent from left to right a progressively finer classification scheme

EC 1.2.1.2 Formate + NAD+ = CO2 + NADH

formate dehydrogenase

with NAD+ or NADP+ as acceptor

acting on the aldehyde or oxo group of donors

oxidoreductases

Main class (1st digit)

1 Oxidoreductases2 Transferases3 Hydrolases4 Lyases5 Isomerases6 Ligases

Scope and content



Most comprehensive information system on Enzymes > 1,000,000 different enzymes > 65,000 manually curated

5,300 EC numbers

Data categories

Scope and content




5,300 EC numbers

Data categories

● Enzymes (module B1)

● Classification and Nomenclature

● Reaction & Specificity

● Enzyme Structure

● Isolation & Preparation

● Stability

● Kinetic data

● Links & Literature References

Scope and content




5,300 EC numbers

Data categories

● Enzymes (module B1)

● Classification and Nomenclature

● Reaction & Specificity

● Enzyme Structure

● Isolation & Preparation

● Stability

● Kinetic data

● Links & Literature References

● Metabolites/Ligands (module B4)

● Nomenclature

● Structure

● Role

● Occurrence/concentration

Scope and contentIntroduction to BRENDA


Biochemical and molecular properties of enzymes stored in BRENDA:

Scope and content



BRENDA 2011_1 (entry/organism/reference relationships)

Nomenclature Enzyme Structure Reaction & Specificity

EC-Number 5258 Molecular Weight 34477 Substrates/Products 304941

Enzyme Names 78724 Subunits 32010 Inhibitors 180218

Common Name 5258 6121 Cofactors 23365

Systematic Name 4071 Functional Parameters Metals/Ions 37048

Synonyms 108875 Km Value 114610 Activating Compounds 27528

Isolation & Preparation Ki Value 30178 References

Purification 36441 IC50 29370 References 152735

Cloned 33085 pI Value 3790 Application & Engineering

Renatured 993 Turnover Number 44479 Application 14084

Crystallization 8266 2668 Engineering 52946

Stability Specific Activity 45062 Organism-releated information

pH stability 6088 pH Optimum 37637 Organism 425676

Temp. Stability 17133 pH Range 8774 Source Tissue 79701

General Stability 7372 Temperature Optimum 23095 Localization 28521

Org. Solv. Stability 1259 Temperature Range 3411

Oxidation Stability 690

Storage Stability 10095

Posttranslational Modifications

kcat/Km NEW

Scope and content




5,300 EC numbers

● Enzyme ligand data, e.g. → catalyzed reactions → enzyme ligands

Scope and content



of enzyme-catalyzed reactions

of enzymes


5,300 EC numbers

● Enzyme ligand data, e.g. → catalyzed reactions → enzyme ligands

substratesproductscofactors

activatorsinhibitors

Scope and content




of enzymes


5,300 EC numbers

● Enzyme ligand data, e.g. → catalyzed reactions > 10,000 → enzyme ligands >100,000



Explore enzyme-ligandInteractions inModule B4

Scope and content




of enzymes


5,300 EC numbers

● Enzyme ligand data, e.g. → catalyzed reactions > 10,000 → enzyme ligands >100,000



Data sources & updates



Updates of BRENDA

Frequency:

- normally every six months (January and July)

1) Data content:

- Ensure that the web-accessible database contains latest data

- Inclusion of new types of information (e.g. textmining data)

2) Query engine and web interface:

- Integration of new features

Data sources & updates


Manually curatedBRENDA data


External databases & ontologies

UniRef

UniProt

EMBLGenomes

IntEnzIUBMB

KEGG NCBITaxonomy Tree

ChEBIPDB

> 40 OntologiesBRENDA Tissue Ontology, Gene Ontology, ...



Data sources & updatesIntroduction to BRENDA



UniRef

UniProt

KEGG PDB ChEBI EMBLGenomes


IntEnzIUBMB

NCBITaxonomy Tree



Merge and process data- Prediction of protein domains (e.g. membrane helices)- Structure-based recognition of ligand synonyms (via Inchis)- Draw molecule pictures- Compute fingerprints for substructure search- Complete Pubmed references



UniRef

UniProt

KEGG PDB ChEBI EMBLGenomes


IntEnzIUBMB

NCBITaxonomy Tree



Cooccurrence-basedTextmining approach

Merge and process data- Prediction of protein domains (e.g. membrane helices)- Structure-based recognition of ligand synonyms (via Inchis)- Draw molecule pictures- Compute fingerprints for substructure search- Complete Pubmed references


BRENDA on the Web

Access to BRENDA via

www.brenda-enzymes.org

BRENDA on the Web


Web usage:

~ 100,000 requests per day

2,000 - 5,000 visits per day


BRENDA on the Web


How to explore the BRENDA data

● Quick Search for Enzymes● Avanced Enzyme Search

● Sequence Search● Genome Explorer

● Ontologies● Taxonomy Tree

● Search Enzyme Ligands

● Computer-based access


module B1

module B2

module B3

module B4

module B5

Financial support to BRENDA by European Union projects FELICS and SLING is gratefully acknowledged.

This BRENDA training session was funded by the SLING project.

March, 2nd 2009 4BRENDA - Technical and bioinformatical aspectsSept., 8th 2009 35The Enzyme Information System BRENDA

Acknowledgements


Acknowledgements

Team

Dietmar Schomburg (Supervision)

Ida Schomburg Andreas GroteAntje Chang Carola SöhngenMichael Rother Cornelia MunarettoJuliane Thiele Maurice Scheer

... the external annotators


Documents

The BRENDA Enzyme Information System