BRENDA
Encyclopedia
BRENDA is an enzyme information system representing one of the most comprehensive enzyme
repositories.
and biochemical
information on enzymes that have been classified by the IUBMB. Every classified enzyme
is characterized with respect to its catalyzed
biochemical
reaction
. Kinetic properties of the corresponding reactants; i.e., substrates
and products
are described in detail.
BRENDA provides a web-based user interface
that allows a convenient and sophisticated access to the data.
BRENDA was founded in 1987 at the former German National Research Centre for Biotechnology (now: Helmholtz Centre for Infection Research) in Braunschweig
and was originally published as a series of books. From 1996 to 2007, BRENDA was located at the University of Cologne
. There, BRENDA developed into a publicly accessible enzyme information system. In 2007, BRENDA returned to Braunschweig
. Currently, BRENDA is maintained and further developed at the Department of Bioinformatics and Biochemistry at the TU Braunschweig.
BRENDA contains enzyme-specific data manually extracted from primary scientific literature
and additional data derived from automatic information retrieval
methods such as text mining
.
A major update of the data in BRENDA is performed twice a year. Besides the upgrade of its content, improvements of the user interface are also incorporated into the BRENDA database.
The latest update was performed .
The database contains more than 40 data fields with enzyme-specific information on more than 4800 EC number
s 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. The data originates from almost 85,000 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. 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, two text-mining repositories FRENDA (Full Reference ENzyme DAta) and AMENDA (Automatic Mining of ENzyme DAta) were introduced. These text-mining results were derived from the titles and abstracts of all articles in the literature database PubMed
.
Data access:
There are several tools to obtain access to the data in BRENDA. Some of them are listed here.
, 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:
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
repositories.
Introduction
BRENDA is an electronic information resource that comprises molecularBiomolecule
A biomolecule is any molecule that is produced by a living organism, including large polymeric molecules such as proteins, polysaccharides, lipids, and nucleic acids as well as small molecules such as primary metabolites, secondary metabolites, and natural products...
and biochemical
Biochemistry
Biochemistry, sometimes called biological chemistry, is the study of chemical processes in living organisms, including, but not limited to, living matter. Biochemistry governs all living organisms and living processes...
information on enzymes that have been classified by the IUBMB. Every classified enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
is characterized with respect to its catalyzed
Catalysis
Catalysis is the change in rate of a chemical reaction due to the participation of a substance called a catalyst. Unlike other reagents that participate in the chemical reaction, a catalyst is not consumed by the reaction itself. A catalyst may participate in multiple chemical transformations....
biochemical
Biochemistry
Biochemistry, sometimes called biological chemistry, is the study of chemical processes in living organisms, including, but not limited to, living matter. Biochemistry governs all living organisms and living processes...
reaction
Chemical reaction
A chemical reaction is a process that leads to the transformation of one set of chemical substances to another. Chemical reactions can be either spontaneous, requiring no input of energy, or non-spontaneous, typically following the input of some type of energy, such as heat, light or electricity...
. Kinetic properties of the corresponding reactants; i.e., substrates
Substrate (biochemistry)
In biochemistry, a substrate is a molecule upon which an enzyme acts. Enzymes catalyze chemical reactions involving the substrate. In the case of a single substrate, the substrate binds with the enzyme active site, and an enzyme-substrate complex is formed. The substrate is transformed into one or...
and products
Product (chemistry)
Product are formed during chemical reactions as reagents are consumed. Products have lower energy than the reagents and are produced during the reaction according to the second law of thermodynamics. The released energy comes from changes in chemical bonds between atoms in reagent molecules and...
are described in detail.
BRENDA provides a web-based user interface
User interface
The user interface, in the industrial design field of human–machine interaction, is the space where interaction between humans and machines occurs. The goal of interaction between a human and a machine at the user interface is effective operation and control of the machine, and feedback from the...
that allows a convenient and sophisticated access to the data.
BRENDA was founded in 1987 at the former German National Research Centre for Biotechnology (now: Helmholtz Centre for Infection Research) in Braunschweig
Braunschweig
Braunschweig , is a city of 247,400 people, located in the federal-state of Lower Saxony, Germany. It is located north of the Harz mountains at the farthest navigable point of the Oker river, which connects to the North Sea via the rivers Aller and Weser....
and was originally published as a series of books. From 1996 to 2007, BRENDA was located at the University of Cologne
University of Cologne
The University of Cologne is one of the oldest universities in Europe and, with over 44,000 students, one of the largest universities in Germany. The university is part of the Deutsche Forschungsgemeinschaft, an association of Germany's leading research universities...
. There, BRENDA developed into a publicly accessible enzyme information system. In 2007, BRENDA returned to Braunschweig
Braunschweig
Braunschweig , is a city of 247,400 people, located in the federal-state of Lower Saxony, Germany. It is located north of the Harz mountains at the farthest navigable point of the Oker river, which connects to the North Sea via the rivers Aller and Weser....
. Currently, BRENDA is maintained and further developed at the Department of Bioinformatics and Biochemistry at the TU Braunschweig.
BRENDA contains enzyme-specific data manually extracted from primary scientific literature
Scientific literature
Scientific literature comprises scientific publications that report original empirical and theoretical work in the natural and social sciences, and within a scientific field is often abbreviated as the literature. Academic publishing is the process of placing the results of one's research into the...
and additional data derived from automatic information retrieval
Information retrieval
Information retrieval is the area of study concerned with searching for documents, for information within documents, and for metadata about documents, as well as that of searching structured storage, relational databases, and the World Wide Web...
methods such as text mining
Text mining
Text mining, sometimes alternately referred to as text data mining, roughly equivalent to text analytics, refers to the process of deriving high-quality information from text. High-quality information is typically derived through the devising of patterns and trends through means such as...
.
A major update of the data in BRENDA is performed twice a year. Besides the upgrade of its content, improvements of the user interface are also incorporated into the BRENDA database.
The latest update was performed .
Content and Features
Database:The database contains more than 40 data fields with enzyme-specific information on more than 4800 EC number
EC number
The Enzyme Commission number is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze....
s that are classified according to the IUBMB
International Union of Biochemistry and Molecular Biology
The International Union of Biochemistry and Molecular Biology is an international non-governmental organisation concerned with biochemistry and molecular biology...
.
The different data fields cover information on the enzyme's nomenclature, reaction and specificity, enzyme structure
Protein structure
Proteins are an important class of biological macromolecules present in all organisms. Proteins are polymers of amino acids. Classified by their physical size, proteins are nanoparticles . Each protein polymer – also known as a polypeptide – consists of a sequence formed from 20 possible L-α-amino...
, isolation and preparation, enzyme stability, kinetic parameters such as Km value
Michaelis-Menten kinetics
In biochemistry, Michaelis–Menten kinetics is one of the simplest and best-known models of enzyme kinetics. It is named after German biochemist Leonor Michaelis and Canadian physician Maud Menten. The model takes the form of an equation describing the rate of enzymatic reactions, by relating...
and turnover number, occurrence and localization, mutants and engineered enzymes, application of enzymes and ligand-related data. The data originates from almost 85,000 different scientific articles
Scientific literature
Scientific literature comprises scientific publications that report original empirical and theoretical work in the natural and social sciences, and within a scientific field is often abbreviated as the literature. Academic publishing is the process of placing the results of one's research into the...
. Each enzyme entry is clearly linked to at least one literature reference, to its source organism
Organism
In biology, an organism is any contiguous living system . In at least some form, all organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homoeostasis as a stable whole.An organism may either be unicellular or, as in the case of humans, comprise...
, and, where available, to the protein sequence of the enzyme. Furthermore, cross-references to external information resources such as sequence and 3D-structure
Protein structure
Proteins are an important class of biological macromolecules present in all organisms. Proteins are polymers of amino acids. Classified by their physical size, proteins are nanoparticles . Each protein polymer – also known as a polypeptide – consists of a sequence formed from 20 possible L-α-amino...
databases, as well as biomedical ontologies
Open Biomedical Ontologies
Open Biomedical Ontologies is an effort to create controlled vocabularies for shared use across different biological and medical domains. As of 2006, OBO forms part of the resources of the U.S...
, 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
Biomedical text mining
Biomedical text mining refers to text mining applied to texts and literature of the biomedical and molecular biology domain...
approach. For this purpose, two text-mining repositories FRENDA (Full Reference ENzyme DAta) and AMENDA (Automatic Mining of ENzyme DAta) were introduced. These text-mining results were derived from the titles and abstracts of all articles in the literature database PubMed
PubMed
PubMed is a free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez information retrieval system...
.
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)
- ECEC numberThe Enzyme Commission number is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze....
tree browser - TaxonomyAlpha taxonomyAlpha taxonomy is the discipline concerned with finding, describing and naming species of living or fossil organisms. This field is supported by institutions holding collections of these organisms, with relevant data, carefully curated: such institutes include natural history museums, herbaria and...
tree browser - OntologiesOpen Biomedical OntologiesOpen Biomedical Ontologies is an effort to create controlled vocabularies for shared use across different biological and medical domains. As of 2006, OBO forms part of the resources of the U.S...
for different biological domains (e.g., BRENDA tissue ontologyBRENDA tissue ontologyBTO, the BRENDA Tissue Ontology is an ontology of anatomical structures, cell types, tissues and cell lines. The ontology is a sub-project of the BRENDA database....
, Gene OntologyGene OntologyThe Gene Ontology, or GO, is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species...
) - ThesaurusThesaurusA thesaurus is a reference work that lists words grouped together according to similarity of meaning , in contrast to a dictionary, which contains definitions and pronunciations...
for ligandChemical substanceIn chemistry, a chemical substance is a form of matter that has constant chemical composition and characteristic properties. It cannot be separated into components by physical separation methods, i.e. without breaking chemical bonds. They can be solids, liquids or gases.Chemical substances are...
names - Chemical substructure search engine for ligand structures
- SOAPSOAPSOAP, originally defined as Simple Object Access Protocol, is a protocol specification for exchanging structured information in the implementation of Web Services in computer networks...
interface
Availability
The usage of BRENDA is free of charge. In addition, FRENDA and AMENDA are free for non-profit users. Commercial users are in need of a license for these databases.Other databases
BRENDA provides links to several other databases with a different focus on the enzymeEnzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
, e.g., metabolic
Metabolism
Metabolism is the set of chemical reactions that happen in the cells of living organisms to sustain life. These processes allow organisms to grow and reproduce, maintain their structures, and respond to their environments. Metabolism is usually divided into two categories...
function or enzyme structure
Protein structure
Proteins are an important class of biological macromolecules present in all organisms. Proteins are polymers of amino acids. Classified by their physical size, proteins are nanoparticles . Each protein polymer – also known as a polypeptide – consists of a sequence formed from 20 possible L-α-amino...
. Other links lead to ontological information on the corresponding gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
of the enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
in question. Links to the literature are established with PubMed
PubMed
PubMed is a free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez information retrieval system...
.
BRENDA links to some further databases and repositories such as:
- BRENDA tissue ontologyBRENDA tissue ontologyBTO, the BRENDA Tissue Ontology is an ontology of anatomical structures, cell types, tissues and cell lines. The ontology is a sub-project of the BRENDA database....
- ExPASyExPASyExPASy is a bioinformatics resource portal operated by the Swiss Institute of Bioinformatics and in particular the SIB Web Team. It is an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences...
- NCBINational Center for Biotechnology InformationThe National Center for Biotechnology Information is part of the United States National Library of Medicine , a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper...
databases (Protein, nucleotide, structure, genome, OMIMMendelian Inheritance in ManOnline Mendelian Inheritance in Man is a database that catalogues all the known diseases with a genetic component, and—when possible—links them to the relevant genes in the human genome and provides references for further research and tools for genomic analysis of a catalogued gene. OMIM is one...
, Domains - IUBMB enzyme nomenclature
- KEGG
- PDBProtein Data BankThe Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
database (3D information) - PROSITEPROSITEPROSITE is a protein database. It consists of entries describing the protein families, domains and functional sites as well as amino acid patterns, signatures, and profiles in them. These are manually curated by a team of the Swiss Institute of Bioinformatics and tightly integrated into Swiss-Prot...
- SCOPStructural Classification of ProteinsThe Structural Classification of Proteins database is a largely manual classification of protein structural domains based on similarities of their structures and amino acid sequences. A motivation for this classification is to determine the evolutionary relationship between proteins...
- CATHCATHThe CATH Protein Structure Classification is a semi-automatic, hierarchical classification of protein domains published in 1997 by Christine Orengo, Janet Thornton and their colleagues....
- InterProInterProInterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences in order to functionally characterise them....
- ChEBIChEBIChemical Entities of Biological Interest, also known as ChEBI, is a database and ontology of molecular entities focused on 'small' chemical compounds, that is part of the Open Biomedical Ontologies effort...
- UniprotUniProtUniProt is a comprehensive, high-quality and freely accessible database of protein sequence and functional information, many of which are derived from genome sequencing projects...