Ida Schomburg

BRENDA, the enzyme database: updates and major new developments

BRENDA (BRaunschweig ENzyme DAtabase) represents a comprehensive collection of enzyme and metabolic information, based on primary literature. The database contains data from at least 83,000 different enzymes from 9800 different organisms, classified in approximately 4200 EC numbers. BRENDA includes biochemical and molecular information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure, application, engineering, stability, disease, isolation and preparation, links and literature references. The data are extracted and evaluated from approximately 46,000 references, which are linked to PubMed as long as the reference is cited in PubMed. In the past year BRENDA has undergone major changes including a large increase in updating speed with >50% of all data updated in 2002 or in the first half of 2003, the development of a new EC-tree browser, a taxonomy-tree browser, a chemical substructure search engine for ligand structure, the development of controlled vocabulary, an ontology for some information fields and a thesaurus for ligand names. The database is accessible free of charge to the academic community at http://www.brenda. uni-koeln.de.

BRENDA, enzyme data and metabolic information

BRENDA is a comprehensive relational database on functional and molecular information of enzymes, based on primary literature. The database contains information extracted and evaluated from approximately 46 000 references, holding data of at least 40 000 different enzymes from more than 6900 different organisms, classified in approximately 3900 EC numbers. BRENDA is an important tool for biochemical and medical research covering information on properties of all classified enzymes, including data on the occurrence, catalyzed reaction, kinetics, substrates/products, inhibitors, cofactors, activators, structure and stability. All data are connected to literature references which in turn are linked to PubMed. The data and information provide a fundamental tool for research of enzyme mechanisms, metabolic pathways, the evolution of metabolism and, furthermore, for medicinal diagnostics and pharmaceutical research. The database is a resource for data of enzymes, classified according to the EC system of the IUBMB Enzyme Nomenclature Committee, and the entries are cross-referenced to other databases, i.e. organism classification, protein sequence, protein structure and literature references. BRENDA provides an academic web access at http://www.brenda.uni-koeln.de.

BRENDA, AMENDA and FRENDA: the enzyme information system in 2007

The BRENDA (BRaunschweig ENzyme DAtabase) enzyme information system () is the largest publicly available enzyme information system worldwide. The major parts of its contents are manually extracted from primary literature. It is not restricted to specific groups of enzymes, but includes information on all identified enzymes irrespective of the enzymes source. The range of data encompasses functional, structural, sequence, localisation, disease-related, isolation, stability information on enzyme and ligand-related data. Each single entry is linked to the enzyme source and to a literature reference. Recently the data repository was complemented by text-mining data in AMENDA (Automatic Mining of ENzyme DAta) and FRENDA (Full Reference ENzyme DAta). A genome browser, membrane protein prediction and full-text search capacities were added. The newly implemented web service provides instant access to the data for programmers via a SOAP (Simple Object Access Protocol) interface. The BRENDA data can be downloaded in the form of a text file from the beginning of 2007.

BRENDA: a resource for enzyme data and metabolic information.

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. Presently, the database holds data on more than 40 000 enzymes and 4460 different organisms, and includes information about enzyme-ligand relationships with numerous chemical compounds. The collection of molecular and biochemical information in BRENDA provides a fundamental resource for research in biotechnology, pharmacology, medicinal diagnostics, enzyme mechanics, and metabolism. BRENDA is accessible free of charge to the academic community at http://www.brenda.uni-koeln.de/; commercial users need a license available from http://www.science-factory.com/

Springer handbook of enzymes

The synonyms are arranged in alphabetical order and the respective recommended name as well as the EC number is stated in each of the 57,000 entries.

Enzyme data and metabolic information: BRENDA, a resource for research in biology, biochemistry, and medicine

The number of fully sequenced genomes available is rapidly increasing, and experiments are underway to get quantitative information of the transcription and expression of the different gene products. As this is progressing and projects on structural genomics are starting, the lack of readily accessible functional information about proteins is becoming more obvious. Here, we describe the comprehensive enzymatic and metabolic information system BRENDA (BRaunschweig ENzyme DAta base) which has been created - and is continuously updated - by manual extraction and evaluation of functional and molecular parameters on enzymes from the primary literature, presently containing parameters from approx. 35 000 literature references, holding data of at least 20 000 different enzymes from more than 4330 different organisms classified in the approx. 3 700 EC-numbers. More than 260 000 different enzyme/ligand relationships are given in the data repository. BRENDA is available via the world wide web (www.brenda.uni-koeln.de).

3,4-Dihydroxy-2-butanone-4-phosphate synthase

The formation of the riboflavin precursor, 6,7-dimethyl-8-ribityllumazine, from 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione requires a phosphorylated 4-carbon intermediate which has been designated as Compound X (Neuberger, G., and Bacher, A. (1985) Biochem. Biophys. Res. Commun. 127, 175-181). The enzyme catalyzing the formation of Compound X has been purified about 600-fold from the cell extract of the flavinogenic yeast Candida guilliermondii by chromatographic procedures. The purified protein appeared homogeneous as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and consisted of a single polypeptide of 24 kDa. The committed substrate of the enzyme was identified as D-ribulose 5-phosphate. The enzyme yields two products which were identified as L-3,4-dihydroxy-2-butanone 4-phosphate and formate by NMR and CD spectroscopy. Mg2+ is required for activity.

Class 4-6 : lyases, isomerases, ligases

Acetylenedicarboxylate decarboxylase.- Sulfopyruvate decarboxylase.- 4-Hydroxyphenylpyruvate decarboxylase.- Threonine-phosphate decarboxylase.- Phosphonopyruvate decarboxylase.- 4-Hydroxyphenylacetate decarboxylase.- D-Dopachrome decarboxylase.- 3-Dehydro-L-gulonate-6-phosphate decarboxylase.- Diaminobutyrate decarboxylase.- Vanillin synthase.- D-Threonine aldolase.- 1-Deoxy-D-xylulose 5-phosphate synthase.- Aminodeoxychorismate lyase.- 4-Hydroxy-2-oxovalerate aldolase.- Chorismate lyase.- Aristolochene synthase.- Pinene synthase.- Myrcene synthase.- (?)-(4S)-Limonene synthase.- Benzylsuccinate synthase.- 3,4-Dihydroxy-2-butanone-4-phosphate synthase.- Cyclohexa-1,5-dienecarbonyl-CoA hydratase.- trans-Feruloyl-CoA hydratase.- Cyclohexa-1,5-dienecarbonyl-CoA hydratase.- Cyclohexyl-isocyanide hydratase.- Cyanase.- 2-Hydroxyisoflavanone dehydratase.- Bile-acid 7?-dehydratase.- 3?,7?,12?-Trihydroxy-5?-cholest-24-enoyl-CoA hydratase.- Ectoine synthase.- Methylthioribulose 1-phosphate dehydratase.- Aldos-2-ulose dehydratase.- 1,5-Anhydro-D-fructose dehydratase.- Acetylene hydratase.- o-succinylbenzoate synthase.- Glucuronan lyase.- Anhydrosialidase.- Levan fructotransferase (DFA-IV-forming).- Inulin fructotransferase (DFA-I-forming).- Inulin fructotransferase (DFA-III-forming).- Chondroitin B lyase.- Chondroitin-sulfate-ABC endolyase.- Chondroitin-sulfate-ABC exolyase.- Pectate trisaccharide-lyase.- Threonine synthase.- Ethanolamine-phosphate phospho-lyase.- Methylglyoxal synthase.- 3-Dehydroquinate synthase.- Chorismate synthase.- Pentalenene synthase.- Casbene synthase.- Aristolochene synthase.- (?)-Endo-fenchol synthase.- Sabinene-hydrate synthase.- 6-Pyruvoyltetrahydropterin synthase.- (+)-?-Cadinene synthase.- Pinene synthase.- Myrcene synthase.- (4S)-Limonene synthase.- Taxadiene synthase.- Abietadiene synthase.- ent-Kaurene synthase.- (R)-Limonene synthase.- Vetispiradiene synthase.- Germacradienol synthase.- Germacrene-A synthase.- Amorpha-4,11-diene synthase.- S-Linalool synthase.- R-Linalool synthase.- Isoprene synthase.- 2-Hydroxypropyl-CoM lyase.- threo-3-Hydroxyaspartate ammonia-lyase.- L-Serine ammonia-lyase.- D-Serine ammonia-lyase.- Threonine ammonia-lyase.- erythro-3-Hydroxyaspartate ammonia-lyase.- Aminodeoxygluconate ammonia-lyase.- 3,4-Dihydroxyphenylalanine reductive deaminase.- Deacetylisoipecoside synthase.- Deacetylipecoside synthase.- Prenylcysteine lyase.- Phosphosulfolactate synthase.- Leukotriene-C4 synthase.- S-Ribosylhomocysteine lyase.- S-(Hydroxymethyl)glutathione synthase.- 2-Hydroxypropyl-CoM lyase.- Sulfolactate sulfo-lyase.- L-Cysteate sulfo-lyase.- 2-C-Methyl-D-erythritol 2,4-cyclodiphosphate synthase.- Phosphatidylinositol diacylglycerol-lyase.- Glycosylphosphatidylinositol diacylglycerollyase.- FAD-AMP lyase (cyclizing).- Sirohydrochlorin cobaltochelatase.- Sirohydrochlorin ferrochelatase.- Aliphatic aldoxime dehydratase.- Indoleacetaldoxime dehydratase.- Phenylacetaldoxime dehydratase.- Isopenicillin-N epimerase.- Serine racemase.- Maltose epimerase.- L-Ribulose-5-phosphate 3-epimerase.- UDP-2,3-Diacetamido-2,3-dideoxyglucuronic acid 2-epimerase.- Polyenoic fatty acid isomerase.- trans-2-Decenoyl-[acyl-carrier protein] isomerase.- Ascopyrone tautomerase.- Capsanthin/capsorubin synthase.- Neoxanthin synthase.- Phosphoglucosamine mutase.- (Hydroxyamino)benzene mutase.- Isochorismate synthase.- 3-(Hydroxyamino)phenol mutase.- Squalene-hopene cyclase.- 5-(Carboxyamino)imidazole ribonucleotide mutase.- Copalyl diphosphate synthase.- Ent-copalyl diphosphate synthase.- Aspartate-tRNAAsn ligase.- Glutamate-tRNAGln ligase.- Lysine-tRNAPyl ligase.- Pyrrolysine-tRNAPyl ligase.- trans-Feruloyl-CoA synthase.- Adenosylcobinamide-phosphate synthase.- Glutamate-putrescine ligase.- D-Aspartate ligase.- N-(5-Amino-5-carboxypentanoyl)-L-cysteinyl-D-valine synthase.- Aerobactin synthase.- L-Amino-acid ?-ligase.- Cyanophycin synthase (L-aspartate-adding).- Cyanophycin synthase (L-arginine-adding).- (Carboxyethyl)arginine ?-lactam-synthase.- 5-(Carboxyamino)imidazole ribonucleotide synthase.- Asparaginyl-tRNA synthase (glutaminehydrolysing).- Glutaminyl-tRNA synthase (glutaminehydrolysing).- Aminodeoxychorismate synthase.- Hydrogenobyrinic acid a,c-diamide synthase (glutamine-hydrolysing).- Adenosylcobyric acid synthase (glutaminehydrolysing).- Acetone carboxylase.- 2-Oxoglutarate carboxylase.- Magnesium chelatase.- Cobaltochelatase.

Violaxanthin de-epoxidase

Violaxanthin de-epoxidase catalyzes the de-epoxidation of violaxanthin to antheraxanthin and zeaxanthin in the xanthophyll cycle. Its activity is optimal at approximately pH 5.2 and requires ascorbate. In conjunction with the transthylakoid pH gradient, the formation of antheraxanthin and zeaxanthin reduces the photochemical efficiency of photosystem II by increasing the nonradiative (heat) dissipation of energy in the antennae. Previously, violaxanthin de-epoxidase had been partially purified. Here we report its purification from lettuce (Lactuca sativa var Romaine) to one major polypeptide fraction, detectable by two-dimensional isoelectic focusing/sodium dodecyl sulfate-polyacrylamide gel electrophoresis, using anion-exchange chromatography on Mono Q and a novel lipid-affinity precipitation step with monogalactosyldiacylglyceride. The association of violaxanthin de-epoxidase and monogalactosyldiacyglyceride at pH 5.2 is apparently specific, since little enzyme was precipitated by eight other lipids tested. Violaxanthin de-epoxidase has an isoelectric point of 5.4 and an apparent molecular mass of 43 kD. Partial amino acid sequences of the N terminus and tryptic fragments are reported. The peptide sequences are unique in the GenBank data base and suggest that violaxanthin de-epoxidase is nuclear encoded, similar to other chloroplast proteins localized in the lumen.