Description of Datafields

Enzyme Nomenclature

Cas Registry Number

The Chemical Abstracts Service (CAS) number is a unique numerical identifier to chemical substances. Some have no number at all, some have two or more numbers. Sometimes two enzymes share a common number. Cross-references and sequence-specific information, if available are given in the commnentary.

EC Number

The Enzyme Commission number (EC Number) is given by the IUBMB (International Union of Biochemistry and Molecular Biology), classes of enzymes und subclasses based on the reaction they catalyze.

Every EC number is assigned to a 'Recommended Name' and a commentary (if necessary). If the enzyme was transferred, reclassified, or deleted by the IUBMB, the information is given here. Enzymes, which are not yet classified by the IUBMB, but are accepted in BRENDA are tagged 'preliminary BRENDA-supplied EC number', i.e. EC 1.1.1.B3

Enzyme Names

The general term 'Enzymes Names' comprises all EC numbers, the 'Accepted Name' (Recommended Name) of the IUBMB and 'Other Names', synonyms or gene names found in other databases or in the literature, abbreviations, names of commercially available products.

If identical names are frequently used for different enzymes, these will be mentioned here, cross references are given. If anouther EC number has been included into the entry, it is mentioned here. If an EC number was transferred and/or reclassified, the former EC number is given here.

Pathway

The data field specifies the pathways including the enzyme of interest with the source BRENDA, KEGG, or MetaCyc. The pathways are directly linked to the corresponding Pathway Maps.

Recommended Name

The 'Recommended Name' or 'Accepted Name' of an enzyme as given by the IUBMB (International Union of Biochemistry and Molecular Biology) a commonly used name. The name could be changed if it is misleading incorrect.

Synonyms

Synonyms comprise names by which an enzyme is known. The names are found found in other databases or in the literature, abbreviations, names of commercially available products or gene names. If identical names are frequently used for different enzymes, these will be mentioned here, cross references are given. If an EC number was transferred and/or re-classified, the former EC number is given here.

Systematic Name

Name as given by the IUBMB (International Union of Biochemistry and Molecular Biology) The systematic name fields provides a chemically more precise name and is usaually based on the substrate or, in the case of a bimolecular reaction, of the two substrates separated by a colon, and the nature of the reaction, i.e. oxidase. If there is more than one reaction listed, the systematic name is based on the first reaction.

Enzyme Structure

3D-Structure/ PDB Link

The 3D-structure search provides a search of all enzymes of the PDB database which are assigned to a complete EC number. BRENDA offfers an interactive 3D-view of the enzyme. The results are directly linked to the PDB via the PDB ID and to ProteinsPlus: 1. Protoss, a fully automated hydrogen prediction tool for protein-ligans complexes, 2. DoGSiteScorer, a grid-based method to detect potential binding pockets.

CATH

CATH is a tool for the classification of protein structures downloaded from the PDB. The protein domains are grouped into superfamilies if there is evidence of a common ancestor

Crystallization

Information on the X-ray structure of an enzyme and the procedure and conditions of the crystallization are described

Molecular Weight

This field gives the molecular weight of the holoenzyme. For monomeric enzymes the MW is identical to the value given for subunits. As the accuracy depends on the method of determination this is given in the commentary, if provided in the literature. Some enzyme are only active as multienzyme complexes for which the names and/or EC numbers of all participating enzymes are given in the commentary

Posttranslational Modification

This field describes covalent and general enzyme modifications following protein biosynthesis. The main entries in this field may be proteolytic modification, or glycoprotein, or phosphoprotein etc. The commentary gives details of the modifications.

Protein-Specific Search

All enzymes of the UniProt database (SwissProt, TrEMBL) assigned to a complete EC number can be searched in this data field. The respective results are directly linked to BRENDA entries and if available to more detailed manually annotated information from literature references.

Protein-Specific-Search

All enzymes of the UniProt database (SwissProt, TrEMBL) assigned to a complete EC number can be searched in this data field. The respective results are directly linked to BRENDA entries and if available to more detailed manually annotated information from literature references.

SCOPe

SCOPe (Structural Classification of Proteins - extended) is a tool for the classification of protein structural domains based on their simlarities and amino acid sequence.

Sequence/ Swissprot Link

The 'Sequence Search' provides a search of all enzymes of the UniProt database (SwissProt, TrEMBL) which are assigned to a complete EC number. As a result the protein sequence can be dislayed and further search options are offered, i.e. A BLAST search of the prediction of transmembrane helices.

Subunits

The tertiary structure of the active enzyme is described. It can be active as a monomer, dimer, trimer etc. The stoichiometry of the subunits is given.

Enzyme-Ligand Interactions

Activating Compounds

All compounds are given that have positive effects on the activity except metal ions or cofactors The enzyme may be inactive in the absence of certain compounds or require activating molecules like sulfhydryl compounds, chelating agents, or lipids. If a substance is activating at a specific concentration but inhibiting at a highr or lower value, it will be explained in the commentary.

Cofactors, Prosthetic Groups

All compounds which participate in the reaction, which are loosely-bound to the protein and are required for the enzyme activity, whereas prosthetic groups are tightly-bound to the enzyme. The commentary gives, if available, information on the function of the cofactor, on specific assay conditions, the concentration of the cofactor, the cofactor specificity, or the influence of isozymes, wild-type or mutant enzymes, or detailed binding mechanisms or binding sites of the cofactor to the enzyme molecule.

Inhibitors

All compounds found to be inhibitory are listed. The commentary gives, if available, information on the function of the inhibitor, or on specific assay conditions, the concentration yielding a specific degree of inhibition, or the mechanisms of inhibition. If a compound is activating at a specific concentration but inihibiting at a higher or lower value, the commentary will explain this.

Ligands

The term 'Ligands' comprises all metabolites and substances interacting with enzymes, i.e. substrates, products, inhibitors etc. in enzyme-catalyzed reactions. The specific role is given in the results.

Detailed information: The result page provides a direct link to the 'Enzyme Summary Page' displaying all information of a particular enzyme. The 'Ligand Summary Page' provides a detailed view on the basic information, i.e. nomenclature and structural information and further specific information on the ligand-enzyme interaction, the molecular structure, kinetic parameters, and links to the PubMed and PubChem databases.

Metals And Ions

All ions or salts that have activating effects, or are closely bound to the enzyme.The commentary explains the role of each of the cited metals has, being either bound, e.g. as Fe-S centres or being required in solution. If an ion plays a dual role, activating at a certain concentration but inhibiting at a higher or lower concentration, this will be given in den commentary.

Natural Substrates And Products

The term 'Natural Substrates and Products' specifies the substrates and products in the metabolism of the cell in vivo, under physiological conditions. A natural substrate and/or product is only given if it is specified in the literature reference.

The commentary gives information on the pathways in which this enzyme plays an important role. The reversibilty of the reaction is given here. Information on enzyme induction or growth conditions is included in the commentary. In ADDITIONAL INFORMATION you will find further comments on the metabolic roles or assumptions of the authors are included if the natural substrate is unkown.

Substrates And Products

All natural or synthetic substrates and products are listed here (not in stoichiometric quantities). The reversibility of the reaction is given here. The commentary contains isomers accepted as substrates and on the efficiency of substrates. If a substrate is accepted by only one of several isozymes etc., this is stated here. In cases with unclear product formation only a '?' as a dummy is given. The ADDITIONAL INFORMATION summarizes compounds that are not accepted as substrates or general comments which are valid for all substrates.

Functional Parameters

IC50 Value [mM]

The IC50 value specifies the half maximal inhibitory concentration of a compund and the unit is mM.

The commentary gives, if available, information on specific assay conditions, or if the reaction is carried out by a wild-type, recombinant, or mutant enzyme. Values which cannot be expressed in the defined unit (e.g. for macromolecular, not precisely defined inhibitors) or information on detailed description of detailed inhibition kinetics are summarized in ADDITIONAL INFORMATION.

kcat/KM Value [mM/s]

The unit of this value is mM/s. Each value is connected to a substrate name.

The commentary gives, if available, information on specific reaction conditions, isoenzymes or the presence of activators. kcat/KM-values which cannot be expressed in the defined unit mM/s (e.g. for macromolecular, not precisely defined substrates) are given in ADDITIONAL INFORMATION. If a literature reference deals with detailed kinetic analyses the information is also cited here.

KI Value [mM]

The unit of the inhibition constant is mM. Each value is connected to a inhibitor name.

The commentary gives, if available, information on specific assay conditions, or if the reaction is carried out by a wild-type, recombinant, or mutant enzyme. Values which cannot be expressed in the defined unit (e.g. for macromolecular, not precisely defined inhibitors) or information on detailed description of detailed inhibition kinetics are summarized in ADDITIONAL INFORMATION.

KM Value [mM]

The unit of the Michalis-Menten value is mM. Each value is connected to a substrate name.

The commentary gives, if available, information on specific reaction conditions, isoenzymes or the presence of activators, or if the reaction is carried out by a wild-type, recombinant, or mutant enzyme. KM-values which cannot be expressed in the defined unit mM (e.g. for macromolecular, not precisely definded substrates) are given in ADDITIONAL INFORMATION. If a literature reference deals with detailed kinetic analyses the information is also cited here.

pH Optimum

The pH optimum is the value of maximal activity, given with one decimal place.

The commentary gives, if available, information on specific assay conditions, or if this value is valid for isozymes, wild-type or mutant enzymes. If the enzyme has a second optimum, this will be mentioned here. If the optimal pH is not mentioned in the literature, the pH of the assay is given instead.

pH Range

This data field describes the pH range in which the enzyme is active, mostly given in a range, e.g. 4.0-7.0

The commentary gives detailed information of the enzyme activity in this range and if available, information on specific assay conditions, or if this value is valid for isozymes, wild-type or mutant enzymes. If not a range but a single value indicates the upper and lower limit of the activity, the commentary is obligatory.

pI Value

Isoelectric point of the enzyme, the pH value at which the protein carries no net electrical charge. The commentary gives, if available, information on the method which was used, i.e. Isoelectric focusing or if the value was calculated.

Specific Activity [micromol/min/mg]

The unit of this value is micromol/min/mg of protein. The commentary gives, if available, information on specific assay conditions or if another than the natural substrate was used in the assay, or if the reaction is carried out by a wild-type, recombinant, or mutant enzyme. Values which cannot be expressed in the defined unit micromol/min/mg or information on detailed description of the assay method are included in ADDITIONAL INFORMATION.

Temperature Optimum

Temperature optimum of reaction in °C

The commentary gives, if available, information on specific assay conditions, or if this value is valid for isozymes, wild-type or mutant enzymes. If the enzyme has a second optimum, this will be mentioned here. If the optimal temperature is not mentioned in the literature, the temperature of the assay is given instead.

Temperature Range

Temperature range in which the enzyme is active

The commentary gives detailed information of the enzyme activity in this range and if available, information on specific assay conditions, or if this value is valid for isozymes, wild-type or mutant enzymes. If not a range but a single value indicates the upper and lower limit of the activity, the commentary is obligatory.

Turnover Number [1/s]

The turnover number (kcat) is given in the unit 1/s. Each value is connected to a substrate name.

The commentary gives information on the reaction conditions, if available, or the type of reaction, or if the enzyme is capable of catalyzing different reactions with a single substrate, or if the reaction is carried out by a wild-type, recombinant, or mutant enzyme. In the case of turnover numbers without the default defined unit (e.g. substrates without a defined molecular weight, or an defined amount of protein) the values and information is summarized in ADDITIONAL INFORMATION.

General

Application

Actual or possible application in the fields of i.e. pharmacology, medicine, biofuel production, analysis, biotechnology etc. are described.

General Information

This field contains more general information on the role of an enzyme in the metabolism, the physiological function, a possible malfunction, or evolutionary aspects.

References

This information field contains all manually annotated references, consisting of the bibliographical information (authors, title, journal, volume, pages, and year, and if known the PubMed-ID. The searches can be supplemented using the automatic text mining approach 'AMENDA' or 'FRENDA' (for more details, see link)

Isolation & Preparation

Expression

This information field describes the effect of compounds and/or conditions on the expression of enzymes leading to an up- or downregulation.

Purification

This data field contains information on the enzyme purification methods and the purity of an enzyme.

Renatured

This data field contains information on the renaturation, refolding and reactivation procedures of enzymes after denaturation processes.

Isolation& Preparation

Cloned

Information on expresssion and cloning procedures and systems are given and in which organism or cell culture an enzyme is expressed in.

Organism-related information

Localization

The intracellular localization of enzymes is described in this data field. Typical entries are cytoplasm, nucleus, mitochondrion, chloroplast, extracellular, membrane. The searches can be supplemented using the automatic textmining approach 'AMENDA' or 'FRENDA'

Organism

In this data field the organism used are listed The systematic names according to the NCBI Taxonomy are preferred. If the scientific name is missing the synonym or the names from the respective literature references are used.

If a taxonomic group is entered in the search field using the default 'exact' mode, all organism synonyms and the taxonomic descenden terms and their respective EC number are considered for the search, for example 'plants' or 'mammalia'. The searches can be supplemented using the automatic textmining approach 'AMENDA' or 'FRENDA'

Organism

In this data field the organism used are listed The systematic names according to the NCBI Taxonomy are preferred. If the scientific name is missing the synonym or the names from the respective literature references are used. If a taxonomic group is entered in the search field using the deafult 'exact' mode, all organism synonyms and the taxonomic descendent terms and their respective EC number are incorporated for the search, for example 'plants' or 'mammalia'. The searches can be supplemented using the automatic textmining approach 'AMENDA' or 'FRENDA'

Source Tissue

For multicellular organisms the tissues used for isolation of the enzyme or the tissue in which the enzyme is present. Cell-lines can also be a source of enzymes. The searches can be supplemented using the automatic textmining approach 'AMENDA' or 'FRENDA'

Reaction & Specificity

BKMS-react

BKMS-react is an integrated and non-redundant biochemical reaction database containing known enzyme-catalyzed and spontaneous reactions. Biochemical reactions collected from BRENDA, KEGG, MetaCyc, and SABIO-RK were matched and integrated by aligning substrates and products.BKMS-react reaction comparisons were done by an in silico approach in which two steps, first a comparison of reactant structures using InChIs (linearized chemical structure descriptors) and, second, a compound name comparison (incl. synonyms), were combined. After submitting an EC number or another attribute as substrate(s), product(s), or reaction ID of one of the databases, BKMS-react online will retrieve all results that match your query and display the aligned reactions for all databases in comparison.https://bkms.brenda-enzymes.org/

Catalysed Reaction

The reaction as defined by the IUBMB (International Union of Biochemistry and Molecular Biology). The commentary gives information on the mechanism, the stereochemistry, cross-references to other EC numbers, or on the thermodynamic data of the reaction.

Pathway

This field provides the search of enzymes involved in pathways listed in KEGG, MetaCyc, and in BRENDA. It is possible either to search for all enzymes of a specific pathway, or for a specific enzyme, or to search directly via the KEGG or MetaCyc link or within the BRENDA Pathway Maps.

Protein Variants

The properties of modified enzyme proteins are described. The modification could be i.e. natural occurring mutations, site-directed mutagenesis, deletions etc. In most cases the amino acid exchanges are given.

Reaction Type

According to the type of reaction, the enzymes catalyze, enzymes are classified into 7 main classes, oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases, and translocases with several subcategories, i.e. addition, elimination, carboxylation etc.

Stability

General Stability

This field summarizes general information on enzyme stability, e.g. the addition of stabilizing compounds.

Organic Solvent Stability

The enzyme stability in presence of organic solvents is described.

Oxidation Stability

The influence of oxidating agents on enzyme stability is described, e.g. O2, H2O2

pH Stability

This field can either give a range or a single value in which the enzyme has its optimal stability. The conditions are explained.

Storage Stability

In this data field the influence of the storage duration and the conditions such as temperature, pH, additives etc. on the enzyme stability and activity is described.

Temperature Stability

The temperature stability is given in °C. This field can either give a range or a single value in which the enzyme is stable. The conditions are explained.

Text Mining

DRENDA (Disease Related ENzyme information)

DRENDA is a supplement to BRENDA based on text mining methods providing disease-related enzyme information on the absence or malfunction of enzymes which have a major influence on the metabolism, regulation, and immunity etc. causing severe diseases.

KENDA (Kinetic ENzyme DAta)

KENDA is a supplement to the BRENDA database based on text mining methods, providing an additional overview on functional kinetic data of enzymes. (more details)