With a specific entry code for the pdb 4, swissprotexpasy 7,11 and kegg database 8, the enzyme data related to the database entries can be retrieved. Kegg enzyme is based on the explorenz database at trinity college dublin, and is maintained in the kegg ligand relational database with additional annotation of reaction hierarchy and sequence data links. The enzyme section is based on the nomenclature of enzymes by iubmb international union of biochemistry and molecular biology and the. The kegg resource for deciphering the genome pedagogix. The total number of compounds with chemical structures is 9383, roughly classified, according to the source, into 977 drugrelated compounds, 2649 phytochemical compounds secondary. Each constituent database has its own entry point as shown below. Enzyme is taken from the enzyme nomenclature database explorenz 6 and given additional annotation of. Computation with the kegg pathway database sciencedirect. Ligand enzyme are compiled from the original enzyme database and linked to lots of databases kegg databases and other databases. Pdul is an evolutionarily distinct phosphotransacylase involved in b12dependent 1,2propanediol degradation by salmonella enterica serovar typhimurium lt2. Here we present an expanded coverage of our original.
The enzyme is membranebound, and the 2electron acceptor is a component of the respiratory chain. Enzyme for the information of enzyme molecules and enzymatic reactions, compound for the information of metabolites and other chemical. The substrate analogues phosphopantetheine and coa are not substrates. It is primarily based on the recommendations of the nomenclature committee of the international union of biochemistry and molecular biology iubmb, and it contains the following data for each type of characterized enzyme for which an ec enzyme commission number. Enzyme, ec number, enzyme nomenclature, kegg enzyme. The current version of compound includes xenobiotic chemicals such as environmental pollutants and toxins, because kegg has an agreement with umbbd 9 to include. Presently, the database holds data on more than 40 000 enzymes and 4460 different organisms, and includes information about enzymeligand relationships with numerous chemical compounds.
Finally, the usefulness of those regions to classify reactions is evaluated. Kegg reaction is a database of chemical reactions, mostly enzymatic reactions, containing all reactions that appear in the kegg metabolic pathway maps and additional reactions that appear only in the enzyme nomenclature. Enzyme the enzyme database is a repository of information relative to the nomenclature of enzymes. Kegg ligand is a composite database name for chemical. Kegg pathway database contains the information of how molecules or. Presently, the database holds data on more than 40 000 enzymes and 4460 different organisms, and includes information about enzymeligand. Acts on aromatic amines and, more slowly, on some longchain aliphatic amines, but not on methylamine or ethylamine. A reaction appearing as a chemical equation format in the enzyme section andor a reaction in the kegg pathway database is given a unique accession number and stored in this section. Enzyme for the information of enzyme molecules and enzymatic reactions, compound for the information of metabolites and other chemical compounds, and reaction for the collection of substrateproduct relations. We are planning to use data from kegg database because it contains kegg rpair database 22, kegg ligand database will be used to find universal index for each item in each compound 23. Use of this online version of brenda is free under the cc by 4. The protein network, which is the most unique data object in kegg, is stored as a collection of pathway maps in the pathway database, representing wiring diagrams of proteins and other gene products responsible for various cellular functions. The class line lists the hierarchical classification of this gene as listed in the gene.
The current release includes 3390 enzymes, 5645 compounds. Moreover, types of activesite residues can be specified along with ligand names or types that are related to enzymes as cofactors. An initial list of reactions, corresponding to related genes and enzymes, were generated from uniprot and kegg ligand database goto et al. For instance lets say that ive two compounds ie glycine and glucose. Extract enzyme information for a list of compound names in. Enzyme commission numbers link to the kegg brite hierachy pages outlining how they define each enzyme. After compiling the database, we computed matched and other regions of pairs using the graph theoretical method 1. Brenda braunschweig enzyme database, founded in 1987 by dietmar schomburg, is a comprehensive protein function database, containing enzymatic and metabolic information extracted from the primary literature. Return to the kegg disease page and click on the classification of human. Another important aspect in the overall architecture of kegg is network hierarchy.
A mechanism kegg orthology system is developed for linking genes in the genome to nodes of the molecular network. Development of a chemical structure comparison method for. A third database in kegg is ligand for the information about chemical compounds, enzyme. The enzyme hydrolyses only one of the amide bonds of pantetheine. Kegg genes and kegg enzyme are derived from refseq pruitt et al. Because the kegg pathway database consists of graphical diagrams representing known. Ligand is part of the kegg 6 metabolic pathway database. Each reaction is identified by the r number, such as r00259 for the acetylation of lglutamate. The enzyme recycles pantothenate vitamin b5 and produces 2aminoethanethiol cysteamine, a potent antioxidant 5.
Brenda the comprehensive enzyme information system. Kegg is tightly integrated with the ligand chemical database for enzyme. The docked cognateligand enzyme structures obtained would have the potential to enhance and supplement virtual screening datasets and facilitate the further study of ligandenzyme interactions. The enzyme database contains enzyme nomenclature with. The ligand database 1 has been organized to fill in the gap between genomic information and chemical information and applied to actual reconstruction of metabolic pathways in the completely sequenced organisms in kegg 2,3. Keggpathway database, as well as the enzyme section. Ligand database for enzymes, compounds and reactions. Enzyme is derived from the iubmbiupac enzyme nomenclature, but the others are internally developed and maintained. Kegg kyoto encyclopedia of genes and genomes is a database resource that integrates genomic, chemical and systemic functional information. Kegg enzyme is an implementation of the enzyme nomenclature ec number system produced by the iubmbiupac biochemical nomenclature committee. The product, 6deoxyerythronolide b, contains a 14membered lactone ring and is an intermediate in the biosynthesis of erythromycin antibiotics.
Enzyme nomenclature enzymes are classified into six different groups according to the reaction being catalyzed. Classi cation and analysis of keggreaction database. The compound section was originally created by extracting chemical compounds from the metabolic pathways of the keggpathway database, as well as the enzyme section of ligand. Information regarding nomenclature by iubmb is also available from the. Kegg reaction, chemical structure transformation patterns derived from them kegg rpair and supplementary information on enzyme nomenclature kegg enzyme. The ligand database is a composite database comprising three sections. View entry in original enzyme format view entry in raw text format no links all uniprotkbswissprot entries referenced in this entry, with possibility to download in different formats, align etc. The enzyme object is hyperlinked to the enzyme section of the ligand database containing, among others, the enzyme nomenclature, the reaction scheme, the chemical compounds involved, and additional links to molecular and biological information suyama et al. Reactions are linked to enzyme kos as defined by the ko database, enabling. The kegg database experimental knowledge on systemic functions of the cell, the organism and the ecosystem is represented in terms of molecular networks kegg pathway maps, brite functional hierarchies and kegg modules. In particular, gene catalogs from completely sequenced genomes are linked to higherlevel systemic functions of the cell, the organism and the ecosystem. The nomenclature was determined by the enzyme commission in 1961 with the latest update having occurred in 1992, hence all enzymes are assigned an ec number. The different data fields cover information on the enzymes 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.
Using the kegg database resource tanabe 2012 current. Enzyme and ligand nomenclature organism reaction and specificity kinetic properties structure and role of the ligands stability information ligandenzyme information enzyme sequence and structure mutants and disease occurrence, isolation, and preparation pathways. A reaction appearing as a chemical equation format in the enzyme section andor a reaction in the keggpathway database is given a unique accession number and stored in this section. The enzyme can act with various artificial electron acceptors, including phenazine methosulfate. Each enzyme has recorded at the end details of when first published in enzyme nomenclature or when added to the database and its subsequent history. Database of chemical compounds and reactions in biological pathways article pdf available in nucleic acids research 301. Ligand is constructed as a flatfile database and the data format of each section is similar to those of genbank and pir flatfiles, a fixed number of columns are assigned to specify each field of entry. The databases in the chemical information category are compound, glycan, reaction, rclass and enzyme, which are collectively called kegg ligand. We aim to generate a dataset of docked cognateligand enzyme structures to be released alongside the similarity scores in an online database. The data, which are stored in a mysql database, preserve the formatting of chemical names according to iupac standards. Kegg ligand is a composite database name for compound, glycan, reaction, rclass, and enzyme databases, whose entries are identified by c, g, r, rc, and ec numbers, respectively.
Ranking enzyme structures in the pdb by bound ligand. Kegg reaction database kegg rpair database rdm patterns reactant pair in the kegg atom type representation. Ligand is a composite database comprising three sections. Hi all, i have a list of compounds names and somehow i would like to retrieve the ec codes of its enzymes using kegg. Explorenz was developed at trinity college dublin in 2005 as a new way to access the data of the iubmb enzyme nomenclature list. Keggpathway database, as well as the enzyme section of ligand. The ligand database has been organized to fill in the gap between genomic information and chemical information and applied to actual reconstruction of metabolic pathways in the completely sequenced organisms in kegg 2,3. Web version of enzyme nomenclature the complete contents of enzyme nomenclature, 1992 plus subsequent supplements and other changes are listed below in enzyme number order giving just the. Kegg for representation and analysis of molecular networks. The reaction section is newly added in the latest release release 17. Recommendations of the nomenclature committee of the international union of biochemistry and molecular biology on the nomenclature and classification of enzymes by the reactions. The collection of molecular and biochemical information in brenda provides a fundamental resource for research in biotechnology, pharmacology, medicinal. It is a composite database consisting of three sections. This protocol provides an introduction to the kegg pathway database.
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