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Enzyme Classes

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Enzyme Classes Enzyme nomenclature: https://www.qmul.ac.uk/sbcs/iubmb/enzyme/ http://enzyme.expasy.org/ Name: Systematic: (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate,hydrogen-donor:oxygen oxidoreductase Accepted: prostaglandin-endoperoxidsynthasa Trivial: cyclooxygenase Enzyme classification code: EC 1.14.99.1 Enzyme classes: EC 1.x.x.x Oxidoreductases EC 2.x.x.x Transferases EC 3.x.x.x Hydrolases EC 4.x.x.x Lyases EC 5.x.x.x Isomerases EC 6.x.x.x Ligases EC 7.x.x.x Translocases Oxidoreductases: EC 1.x.x.x Systematic name: donor:acceptor oxidoreductase Accepted: xxx dehydrogenase (oxidation using a coenzyme), xxx oxidase (oxidation by O2, O2 not incorporated into the product), xxx monooxygenase (oxidation by O2, one O of O2 incorporated into the product), xxx dioxygenase (oxidation by O2, both O of O2 incorporated into the product/s), xxx reductase (can be anything), catalase (decomposes H2O2 to O2), peroxidases (oxidation of something by H2O2) Oxidoreductases: EC 1.1.1.1 Systematic: alcohol:NAD+ oxidoreductase Accepted: alcohol dehydrogenase Oxidoreductases: EC 1.1.3.4 = glucose oxidase EC 1.1.3.9 = galactose oxidase EC 1.6.1.1 = NAD(P)+ transhydrogenase EC 1.6.3.1 = NAD(P)H oxidase EC 1.9.3.1 = cytochrom-c oxidase EC 1.10.3.2 = laccase EC 1.11.1.6 = katalase EC 1.12.1.2 = hydrogen dehydrogenase EC 1.14.99.1 = cyclooxygenase EC 1.15.1.1 = superoxide dismutase EC 1.18.6.1 = nitrogenase Transferases: EC 2.x.x.x Systematic name: donor:acceptor grouptransferase Accepted: xxx kinase (phosphorylate by P from ATP), xxx transferase (usually take a group form activated substrates, such as UDP-glucose), xxx synthase (can be anything), xxx phosphorylase (cleavage by Pi), xxx transaminase (amino acid + oxo-acid <-> amino acid + oxo-acid) Transferases: EC 2.7.1.86 Systematic name: ATP:NADH 2'-phosphotransferase Accepted: NADH kinase Tranferases: EC 2.3.3.1 = citrate synthase EC 2.4.1.1 = phosphorylase EC 2.4.1.11 = glykogen synthase EC 2.4.2.4 = thymidine phosphorylase EC 2.6.1.1 = aspartate transaminase EC 2.7.1.1 = hexokinase EC 2.7.11.19 = phosphorylase kinase Hydrolases: EC 3.x.x.x Systematic name: substrate grouphydrolase Accepted: xxxase, exo-xxxase (cleave terminal residues), endo-xxxase (cleave in the middle) Proteases have special nomenclature! Hydrolases: EC 3.2.1.23 Systematic name: β-D-galactoside galactohydrolase Accepted: β-galactosidase Hydrolases: EC 3.1.1.7 = acetylcholineesterase EC 3.1.3.1 = alkaline phosphatase EC 3.1.3.2 = acid phosphatase EC 3.1.3.17 = [phosphorylase]-phosphatase EC 3.1.4.4 = phospholipase C EC 3.1.21.1 = DNase I EC 3.2.1.1 = α-amylase EC 3.2.1.2 = β-amylase EC 3.2.1.4 = cellulase EC 3.2.1.17 = lysozyme EC 3.4.21.1 = chymotrypsin EC 3.4.21.4 = trypsin EC 3.4.21.5 = thrombin EC 3.4.22.2 = papain EC 3.5.1.5 = urease EC 3.5.5.1 = nitrilase EC 3.6.1.1 = inorganic diphosphatase Lyases: EC 4.x.x.x Systematic name: substrate group-lyase Accepted: xxx decarboxylase, xxx dehydratase (water elimination), xxx hydratase (water addition), xxx aldolase (aldol condensation), xxx cyclase (e.g. cAMP production), xxx synthase (can be anything) Lyases: EC 4.1.1.1 Systematic name: pyruvate carboxy-lyase Accepted: pyruvate decarboxylase Lyases: EC 4.1.1.1 = pyruvate decarboxylase EC 4.1.2.13 = fructosebisphosphate aldolase EC 4.2.1.1 = carbonic anhydrase EC 4.2.1.22 = cystathionine-β synthase EC 4.3.2.1 = argininosuccinate lyase EC 4.6.1.1 = adenylate cyclase EC 4.99.1.1 = ferrochelatase Isomerases: EC 5.x.x.x Systematic name: depends on sub-class Sub-classes: racemases, epimerases, aldose-ketose-isomerases, keto-enol-isomerases, disulfide-isomerases, topoisomerases and others Isomerases: EC 5.1.1.1 Systematic and accepted name: alanine racemase Isomerases: EC 5.1.1.1 = alanine racemase EC 5.3.1.1 = triosaphosphate isomerase EC 5.99.1.2 = topoisomerase I EC 5.99.1.3 = topoisomerase II Ligases: EC 6.x.x.x Systematic name: substrate1:substrate2 ligase (product forming) (product is ADP, AMP, GMP...) Accepted: xxx-xxx ligase, xxx synthetase Ligases: EC 6.1.1.1 Systematic name: L-tyrosine:tRNATyr ligase (AMP forming) Accepted: tyrosin-tRNA ligase, tyrosyl-tRNA synthetase Ligases: EC 6.1.1.1 = tyrosin-tRNA ligase EC 6.2.1.3 = long-chain fatty acid-CoA ligase EC 6.3.1.1 = asparagine synthetase EC 6.4.1.2 = acetyl-CoA carboxylasa EC 6.5.1.1 = DNA-ligase (ATP) EC 6.5.1.2 = DNA-ligase (NAD+) Translocases (new in 2018): EC 7.x.x.x Systematic name: original from pre-2018 nomenclature Translocases (new in 2018): EC 7.1.2.1 Systematic name: ATP phosphohydrolase (H+-exporting) Accepted name: H+-exporting ATPase What can go wrong: More complicated reactions: Citrate synthase: acetyl-CoA + oxalacetate + H2O → citrate + HSCoA lyase? (addition), hydrolase? (hydrolysis of C-S bond), transferase? (acetate transfer) From 1962 to 2002: EC 4.1.3.7 Since 2002: EC 2.3.3.1 acetyl-CoA:oxaloacetate C-acetyltransferase [thioester-hydrolysing, (pro-S)-carboxymethyl forming] Broader substrate specificity: β-galactosidase (β-D-galactoside galactohydrolase, EC 3.2.1.23) lactase (lactose galactohydrolase, EC 3.2.1.108) More reactions possible: Xanthine dehydrogenase/oxidase + xanthin + NAD + H2O → uric acid + NADH + hypoxanthin + NAD + H2O → xanthin + NADH xanthin + O2 + H2O → uric acid + H2O2 change from dehydrogene to oxidase can be done by disulfide bridge reduction, partial proteolysis, heavy metals, thawing and freezing etc. What can go wrong: Polymeric substrates: α-Amylase (4-α-D-glucan glucanohydrolase) [isocitrate dehydrogenase (NADP+)] kinase (ATP:[isocitrate dehydrogenase (NADP+)] phosphotransferase) Direction of the reaction: Hexokinase (ATP:D-hexose 6-phosphotransferase, EC 2.7.1.1) Glc + ATP → Glc-6-P + ADP Pyruvate kinase (ATP:pyruvate 2-O-phosphotransferase, EC 2.7.1.40) phosphoenolpyruvate + ADP → pyruvate + ATP Enzyme or multi-enzyme complex? pyruvate dehydrogenasove complex: pyruvate dehydrogenase (E1, EC 1.2.4.1) dihydrolipoyl transacetylase (E2, EC 2.3.1.12) dihydrolipoyl dehydrogenase (E3, EC 1.8.1.4) Specials: Cyclophilin: 1984 – cyclophilin discovered as a receptor of cyclosporin Handschumacher R.E., Harding M.W., Rice J., Drugge R.J., Speicher D.W. (1984) Science 226, 544-547. 1984 – group of PPIases dicovered Fischer G., Bang H., Mech C. (1984) Biomed. Biochim. Acta. 43, 1101-1111. 1989 – cyclophilin is one of them Fischer G., Wittmann-Liebold B., Lang K., Kiefhaber T., Schmid F.X. (1989) Nature 337, 476-478. 1992 – both activities are more or less independent Zydowsky L.D., Etzkorn F.A., Chang H.Y., Ferguson S.B., Stolz L.A., Ho S.I., Walsh C.T. (1992) Prot. Sci. 1, 1092–1099. .
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