Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB)

Proposed Changes to the Enzyme List

The entries below are proposed additions and amendments to the Enzyme Nomenclature list. They were prepared for the NC-IUBMB by Kristian Axelsen, Sinéad Boyce, Richard Cammack, Ron Caspi, Minoru Kanehisa, Andrew McDonald, Gerry Moss, Dietmar Schomburg, Ida Schomburg and Keith Tipton. Comments and suggestions on these draft entries should be sent to Dr Andrew McDonald (Department of Biochemistry, Trinity College Dublin, Dublin 2, Ireland). The entries were added on the date indicated and fully approved after four weeks.

An asterisk before 'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.


Contents

*EC 1.1.1.14 L-iditol 2-dehydrogenase (28 March 2011)
EC 1.1.1.310 (S)-sulfolactate dehydrogenase (28 March 2011)
EC 1.1.1.311 (S)-1-phenylethanol dehydrogenase (28 March 2011)
EC 1.1.98.2 glucose-6-phosphate dehydrogenase (coenzyme-F420) (28 March 2011)
EC 1.1.99.34 transferred now EC 1.1.98.2 (28 March 2011)
*EC 1.2.1.8 betaine-aldehyde dehydrogenase (28 March 2011)
*EC 1.2.1.10 acetaldehyde dehydrogenase (acetylating) (28 March 2011)
EC 1.3.7.7 ferredoxin:protochlorophyllide reductase (ATP-dependent) (28 March 2011)
EC 1.5.3.18 L-saccharopine oxidase (28 March 2011)
EC 1.6.5.8 NADH:ubiquinone reductase (Na+-transporting) (28 March 2011)
*EC 1.11.1.7 peroxidase (28 March 2011)
*EC 1.11.1.10 chloride peroxidase (28 March 2011)
EC 1.11.1.20 prostamide/prostaglandin F synthase (28 March 2011)
EC 1.11.2.2 myeloperoxidase (28 March 2011)
EC 1.11.2.3 plant seed peroxygenase (28 March 2011)
EC 1.11.2.4 fatty-acid peroxygenase (28 March 2011)
*EC 1.13.12.16 nitronate monooxygenase (28 March 2011)
EC 1.13.12.18 dinoflagellate luciferase (28 March 2011)
*EC 1.14.13.7 phenol 2-monooxygenase (28 March 2011)
EC 1.14.13.119 5-epiaristolochene 1,3-dihydroxylase (28 March 2011)
EC 1.14.13.120 costunolide synthase (28 March 2011)
EC 1.14.13.121 premnaspirodiene oxygenase (28 March 2011)
*EC 1.14.15.7 choline monooxygenase (28 March 2011)
EC 1.14.21.8 pseudobaptigenin synthase (28 March 2011)
*EC 1.17.99.1 4-methylphenol dehydrogenase (hydroxylating) (28 March 2011)
EC 2.1.1.29 transferred now EC 2.1.1.202, EC 2.1.1.203 and EC 2.1.1.204 (28 March 2011)
EC 2.1.1.200 tRNA (cytidine32/uridine32-2'-O)-methyltransferase (28 March 2011)
EC 2.1.1.201 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase (28 March 2011)
EC 2.1.1.202 multisite-specific tRNA:(cytosine-C5)-methyltransferase (28 March 2011)
EC 2.1.1.203 tRNA (cytosine34-C5)-methyltransferase (28 March 2011)
EC 2.1.1.204 RNA (cytosine38-C5)-methyltransferase (28 March 2011)
EC 2.1.1.205 tRNA (cytidine32/guanosine34-2'-O)-methyltransferase (28 March 2011)
EC 2.1.1.206 tRNA (cytidine56-2'-O)-methyltransferase (28 March 2011)
EC 2.3.1.193 tRNAMet cytidine acetyltransferase (28 March 2011)
EC 2.3.1.194 acetoacetyl-CoA synthase (28 March 2011)
EC 2.3.1.195 (Z)-3-hexen-1-ol acetyltransferase (28 March 2011)
EC 2.4.1.254 cyanidin-3-O-glucoside 2-O-glucuronosyltransferase (28 March 2011)
EC 2.4.1.255 protein O-GlcNAc transferase (28 March 2011)
EC 2.7.7.73 sulfur carrier protein ThiS adenylyltransferase (28 March 2011)
EC 2.7.8.32 3-O-α-D-mannopyranosyl-α-D-mannopyranose xylosylphosphotransferase (28 March 2011)
EC 3.1.7.7 drimenol cyclase (28 March 2011)
EC 3.2.1.169 protein O-GlcNAcase (28 March 2011)
*EC 4.1.99.5 octadecanal decarbonylase (28 March 2011)
*EC 4.2.1.83 4-oxalmesaconate hydratase (28 March 2011)
EC 4.2.3.55 (S)-β-bisabolene synthase (28 March 2011)
EC 4.2.3.56 γ-humulene synthase (28 March 2011)
EC 4.2.3.57 β-caryophyllene synthase (28 March 2011)
EC 4.2.3.58 longifolene synthase (28 March 2011)
EC 4.2.3.59 (E)-γ-bisabolene synthase (28 March 2011)
EC 4.2.3.60 germacrene C synthase (28 March 2011)
*EC 5.4.99.12 tRNA pseudouridine38-40 synthase (28 March 2011)
EC 5.4.99.19 16S rRNA pseudouridine516 synthase (28 March 2011)
EC 5.4.99.20 23S rRNA pseudouridine2457 synthase (28 March 2011)
EC 5.4.99.21 23S rRNA pseudouridine2604 synthase (28 March 2011)
EC 5.4.99.22 23S rRNA pseudouridine2605 synthase (28 March 2011)
EC 5.4.99.23 23S rRNA pseudouridine1911/1915/1917 synthase (28 March 2011)
EC 5.4.99.24 23S rRNA pseudouridine955/2504/2580 synthase (28 March 2011)
EC 5.4.99.25 tRNA pseudouridine55 synthase (28 March 2011)
EC 5.4.99.26 tRNA pseudouridine65 synthase (28 March 2011)
EC 5.4.99.27 tRNA pseudouridine13 synthase (28 March 2011)
EC 5.4.99.28 tRNA pseudouridine32 synthase (28 March 2011)
EC 5.4.99.29 23S rRNA pseudouridine746 synthase (28 March 2011)
EC 5.4.99.30 UDP-arabinopyranose mutase (28 March 2011)
EC 5.5.1.17 (S)-β-macrocarpene synthase (28 March 2011)

*EC 1.1.1.14

Accepted name: L-iditol 2-dehydrogenase

Reaction: L-iditol + NAD+ = L-sorbose + NADH + H+

Other name(s): polyol dehydrogenase; sorbitol dehydrogenase; L-iditol:NAD+ 5-oxidoreductase; L-iditol (sorbitol) dehydrogenase; glucitol dehydrogenase; L-iditol:NAD+ oxidoreductase; NAD+-dependent sorbitol dehydrogenase; NAD+-sorbitol dehydrogenase

Systematic name: L-iditol:NAD+ 2-oxidoreductase

Comments: This enzyme is widely distributed and has been described in archaea, bacteria, yeast, plants and animals. It acts on a number of sugar alcohols, including (but not limited to) L-iditol, D-glucitol, D-xylitol, and D-galactitol. Enzymes from different organisms or tissues display different substrate specificity. The enzyme is specific to NAD+ and can not use NADP+.

Links to other databases: BRENDA, EXPASY, GTD, KEGG, PDB, CAS registry number: 9028-21-1

References:

1. Bailey, J.P., Renz, C. and McGuinness, E.T. Sorbitol dehydrogenase from horse liver: purification, characterization and comparative properties. Comp. Biochem. Physiol. 69B (1981) 909-914.

2. Burnell, J.N. and Holmes, R.S. Purification and properties of sorbitol dehydrogenase from mouse liver. Int. J. Biochem. 15 (1983) 507-511. [PMID: 6852349]

3. Leissing, N. and McGuinness, E.T. Rapid affinity purification and properties of rat liver sorbitol dehydrogenase. Biochim. Biophys. Acta 524 (1978) 254-261. [PMID: 667078]

4. Negm, F.B. and Loescher, W.H. Detection and characterization of sorbitol dehydrogenase from apple callus tissue. Plant Physiol. 64 (1979) 69-73. [PMID: 16660917]

5. O'Brien, M.M., Schofield, P.J. and Edwards, M.R. Polyol-pathway enzymes of human brain. Partial purification and properties of sorbitol dehydrogenase. Biochem. J. 211 (1983) 81-90. [PMID: 6870831]

6. Ng, K., Ye, R., Wu, X.C. and Wong, S.L. Sorbitol dehydrogenase from Bacillus subtilis. Purification, characterization, and gene cloning. J. Biol. Chem. 267 (1992) 24989-24994. [PMID: 1460002]

[EC 1.1.1.14 created 1961, modified 2011]

EC 1.1.1.310

Accepted name: (S)-sulfolactate dehydrogenase

Reaction: (2S)-3-sulfolactate + NAD+ = 3-sulfopyruvate + NADH + H+

Other name(s): (2S)-3-sulfolactate dehydrogenase; SlcC

Systematic name: (2S)-sulfolactate:NAD+ oxidoreductase

Comments: This enzyme, isolated from the bacterium Chromohalobacter salexigens DSM 3043, acts only on the (S)-enantiomer of 3-sulfolactate. Combined with EC 1.1.1.272 [(R)-2-hydroxyacid dehydrogenase], it provides a racemase system that converts (2S)-3-sulfolactate to (2R)-3-sulfolactate, which is degraded further by EC 4.4.1.24 [(2R)-sulfolactate sulfo-lyase]. Specific for NAD+.

References:

1. Denger, K. and Cook, A.M. Racemase activity effected by two dehydrogenases in sulfolactate degradation by Chromohalobacter salexigens: purification of (S)-sulfolactate dehydrogenase. Microbiology 156 (2010) 967-974. [PMID: 20007648]

[EC 1.1.1.310 created 2011]

EC 1.1.1.311

Accepted name: (S)-1-phenylethanol dehydrogenase

Reaction: (S)-1-phenylethanol + NAD+ = acetophenone + NADH + H+

Other name(s): PED

Systematic name: (S)-1-phenylethanol:NAD+ oxidoreductase

Comments: The enzyme is involved in degradation of ethylbenzene.

References:

1. Kniemeyer, O. and Heider, J. (S)-1-phenylethanol dehydrogenase of Azoarcus sp. strain EbN1, an enzyme of anaerobic ethylbenzene catabolism. Arch. Microbiol. 176 (2001) 129-135. [PMID: 11479712]

2. Hoffken, H.W., Duong, M., Friedrich, T., Breuer, M., Hauer, B., Reinhardt, R., Rabus, R. and Heider, J. Crystal structure and enzyme kinetics of the (S)-specific 1-phenylethanol dehydrogenase of the denitrifying bacterium strain EbN1. Biochemistry 45 (2006) 82-93. [PMID: 16388583]

[EC 1.1.1.311 created 2011]

EC 1.1.98.2

Accepted name: glucose-6-phosphate dehydrogenase (coenzyme-F420)

Reaction: D-glucose 6-phosphate + oxidized coenzyme F420 = 6-phospho-D-glucono-1,5-lactone + reduced coenzyme F420

Other name(s): coenzyme F420-dependent glucose-6-phosphate dehydrogenase; F420-dependent glucose-6-phosphate dehydrogenase; FGD1; Rv0407; F420-dependent glucose-6-phosphate dehydrogenase 1

Systematic name: D-glucose-6-phosphate:F420 1-oxidoreductase

Comments: The enzyme is very specific for D-glucose 6-phosphate. No activity with NAD+, NADP+, flavin adenine dinucleotide and flavin mononucleotide [1].

References:

1. Purwantini, E. and Daniels, L. Purification of a novel coenzyme F420-dependent glucose-6-phosphate dehydrogenase from Mycobacterium smegmatis. J. Bacteriol. 178 (1996) 2861-2866. [PMID: 8631674]

2. Bashiri, G., Squire, C.J., Baker, E.N. and Moreland, N.J. Expression, purification and crystallization of native and selenomethionine labeled Mycobacterium tuberculosis FGD1 (Rv0407) using a Mycobacterium smegmatis expression system. Protein Expr. Purif. 54 (2007) 38-44. [PMID: 17376702]

3. Purwantini, E., Gillis, T.P. and Daniels, L. Presence of F420-dependent glucose-6-phosphate dehydrogenase in Mycobacterium and Nocardia species, but absence from Streptomyces and Corynebacterium species and methanogenic Archaea. FEMS Microbiol. Lett. 146 (1997) 129-134. [PMID: 8997717]

[EC 1.1.98.2 created 2010 as EC 1.1.99.34, transferred 2011 to EC 1.1.98.2]

[EC 1.1.99.34 Transferred entry: glucose-6-phosphate dehydrogenase (coenzyme-F420). As the acceptor is now known, the enzyme has been transferred to EC 1.1.98.2, glucose-6-phosphate dehydrogenase (coenzyme-F420) (EC 1.1.99.34 created 2010, deleted 2011)]

*EC 1.2.1.8

Accepted name: betaine-aldehyde dehydrogenase

Reaction: betaine aldehyde + NAD+ + H2O = betaine + NADH + 2 H+

Glossary: betaine = glycine betaine = N,N,N-trimethylglycine

betaine aldehyde = N,N,N-trimethyl-2-oxoethylammonium

Other name(s): betaine aldehyde oxidase; BADH; betaine aldehyde dehydrogenase; BetB

Systematic name: betaine-aldehyde:NAD+ oxidoreductase

Comments: In many bacteria, plants and animals, the osmoprotectant betaine is synthesized in two steps: (1) choline to betaine aldehyde and (2) betaine aldehyde to betaine. This enzyme is involved in the second step and appears to be the same in plants, animals and bacteria. In contrast, different enzymes are involved in the first reaction. In plants, this reaction is catalysed by EC 1.14.15.7 (choline monooxygenase), whereas in animals and many bacteria it is catalysed by either membrane-bound EC 1.1.99.1 (choline dehydrogenase) or soluble EC 1.1.3.17 (choline oxidase) [5]. In some bacteria, betaine is synthesized from glycine through the actions of EC 2.1.1.156 (glycine/sarcosine N-methyltransferase) and EC 2.1.1.157 (sarcosine/dimethylglycine N-methyltransferase).

Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 9028-90-4

References:

1. Rothschild, H.A. and Barron, E.S.G. The oxidation of betaine aldehyde by betaine aldehyde dehydrogenase. J. Biol. Chem. 209 (1954) 511-523. [PMID: 13192104]

2. Livingstone, J.R., Maruo, T., Yoshida, I., Tarui, Y., Hirooka, K., Yamamoto, Y., Tsutui, N. and Hirasawa, E. Purification and properties of betaine aldehyde dehydrogenase from Avena sativa. J. Plant Res. 116 (2003) 133-140. [PMID: 12736784]

3. Muñoz-Clares, R.A., González-Segura, L., Mújica-Jiménez, C. and Contreras-Diaz, L. Ligand-induced conformational changes of betaine aldehyde dehydrogenase from Pseudomonas aeruginosa and Amaranthus hypochondriacus L. leaves affecting the reactivity of the catalytic thiol. Chem. Biol. Interact. (2003) 129-137. [PMID: 12604197]

4. Johansson, K., El-Ahmad, M., Ramaswamy, S., Hjelmqvist, L., Jornvall, H. and Eklund, H. Structure of betaine aldehyde dehydrogenase at 2.1 Å resolution. Protein Sci. 7 (1998) 2106-2117. [PMID: 9792097]

5. Waditee, R., Tanaka, Y., Aoki, K., Hibino, T., Jikuya, H., Takano, J., Takabe, T. and Takabe, T. Isolation and functional characterization of N-methyltransferases that catalyze betaine synthesis from glycine in a halotolerant photosynthetic organism Aphanothece halophytica. J. Biol. Chem. 278 (2003) 4932-4942. [PMID: 12466265]

[EC 1.2.1.8 created 1961, modified 2005, modified 2011]

*EC 1.2.1.10

Accepted name: acetaldehyde dehydrogenase (acetylating)

Reaction: acetaldehyde + CoA + NAD+ = acetyl-CoA + NADH + H+

Other name(s): aldehyde dehydrogenase (acylating); ADA; acylating acetaldehyde dehyrogenase; DmpF

Systematic name: acetaldehyde:NAD+ oxidoreductase (CoA-acetylating)

Comments: Also acts, more slowly, on glycolaldehyde, propanal and butanal. In Pseudomonas species, this enzyme forms part of a bifunctional enzyme with EC 4.1.3.39, 4-hydroxy-2-oxovalerate aldolase. It is the final enzyme in the meta-cleavage pathway for the degradation of phenols, methylphenols and catechol, converting the acetaldehyde produced by EC 4.1.3.39 into acetyl-CoA [3]. NADP+ can replace NAD+ but the rate of reaction is much slower [3].

Links to other databases: BRENDA, EXPASY, GTD, KEGG, CAS registry number: 9028-91-5

References:

1. Burton, R.M. and Stadtman, E.R. The oxidation of acetaldehyde to acetyl coenzyme A. J. Biol. Chem. 202 (1953) 873-890. [PMID: 13061511]

2. Smith, L.T. and Kaplan, N.O. Purification, properties, and kinetic mechanism of coenzyme A-linked aldehyde dehydrogenase from Clostridium kluyveri. Arch. Biochem. Biophys. 203 (1980) 663-675. [PMID: 7458347]

3. Powlowski, J., Sahlman, L. and Shingler, V. Purification and properties of the physically associated meta-cleavage pathway enzymes 4-hydroxy-2-ketovalerate aldolase and aldehyde dehydrogenase (acylating) from Pseudomonas sp. strain CF600. J. Bacteriol. 175 (1993) 377-385. [PMID: 8419288]

[EC 1.2.1.10 created 1961, modified 2006, modified 2011]

EC 1.3.7.7

Accepted name: ferredoxin:protochlorophyllide reductase (ATP-dependent)

Reaction: chlorophyllide a + reduced ferredoxin + 2 ATP = protochlorophyllide + oxidized ferredoxin + 2 ADP + 2 phosphate

Other name(s): light-independent protochlorophyllide reductase

Systematic name: ATP-dependent ferredoxin:protochlorophyllide-a 7,8-oxidoreductase

Comments: Occurs in photosynthetic bacteria, cyanobacteria, green algae and gymnosperms. The enzyme catalyses trans-reduction of the D-ring of protochlorophyllide; the product has the (7S,8S)-configuration. Unlike EC 1.3.1.33 (protochlorophyllide reductase), light is not required. The enzyme contains a [4Fe-4S] cluster, and structurally resembles the Fe protein/MoFe protein complex of nitrogenase (EC 1.18.6.1), which catalyses an ATP-driven reduction.

References:

1. Fujita, Y., Matsumoto, H., Takahashi, Y. and Matsubara, H. Identification of a nifDK-like gene (ORF467) involved in the biosynthesis of chlorophyll in the cyanobacterium Plectonema boryanum. Plant Cell Physiol. 34 (1993) 305-314. [PMID: 8199775]

2. Nomata, J., Ogawa, T., Kitashima, M., Inoue, K. and Fujita, Y. NB-protein (BchN-BchB) of dark-operative protochlorophyllide reductase is the catalytic component containing oxygen-tolerant Fe-S clusters. FEBS Lett. 582 (2008) 1346-1350. [PMID: 18358835]

3. Muraki, N., Nomata, J., Ebata, K., Mizoguchi, T., Shiba, T., Tamiaki, H., Kurisu, G. and Fujita, Y. X-ray crystal structure of the light-independent protochlorophyllide reductase. Nature 465 (2010) 110-114. [PMID: 20400946]

[EC 1.3.7.7 created 2011]

EC 1.5.3.18

Accepted name: L-saccharopine oxidase

Reaction: L-saccharopine + H2O + O2 = (S)-2-amino-6-oxohexanoate + L-glutamate + H2O2

Glossary: (S)-2-amino-6-oxohexanoate = L-2-aminoadipate 6-semialdehyde = L-allysine

Other name(s): FAP2

Systematic name: L-saccharopine:oxygen oxidoreductase (L-glutamate forming)

Comments: The enzyme is involved in pipecolic acid biosynthesis. A flavoprotein (FAD).

References:

1. Yoshida, N., Akazawa, S., Katsuragi, T. and Tani, Y. Characterization of two fructosyl-amino acid oxidase homologs of Schizosaccharomyces pombe. J. Biosci. Bioeng. 97 (2004) 278-280. [PMID: 16233628]

2. Wickwire, B.M., Wagner, C. and Broquist, H.P. Pipecolic acid biosynthesis in Rhizoctonia leguminicola. II. Saccharopine oxidase: a unique flavin enzyme involved in pipecolic acid biosynthesis. J. Biol. Chem. 265 (1990) 14748-14753. [PMID: 2394693]

[EC 1.5.3.18 created 2011]

EC 1.6.5.8

Accepted name: NADH:ubiquinone reductase (Na+-transporting)

Reaction: NADH + H+ + ubiquinone + n Na+in = NAD+ + ubiquinol + n Na+out

Other name(s): Na+-translocating NADH-quinone reductase; (Na+-NQR)

Systematic name: NADH:ubiquinone oxidoreductase (Na+-translocating)

Comments: An iron-sulfur flavoprotein, containing two covalently bound molecules of FMN, one noncovalently bound FAD, one riboflavin, and one [2Fe-2S] cluster.

References:

1. Beattie, P., Tan, K., Bourne, R.M., Leach, D., Rich, P.R. and Ward, F.B. Cloning and sequencing of four structural genes for the Na+-translocating NADH-ubiquinone oxidoreductase of Vibrio alginolyticus. FEBS Lett. 356 (1994) 333-338. [PMID: 7805867]

2. Nakayama, Y., Hayashi, M. and Unemoto, T. Identification of six subunits constituting Na+-translocating NADH-quinone reductase from the marine Vibrio alginolyticus. FEBS Lett. 422 (1998) 240-242. [PMID: 9490015]

3. Bogachev, A.V., Bertsova, Y.V., Barquera, B. and Verkhovsky, M.I. Sodium-dependent steps in the redox reactions of the Na+-motive NADH:quinone oxidoreductase from Vibrio harveyi. Biochemistry 40 (2001) 7318-7323. [PMID: 11401580]

4. Barquera, B., Hellwig, P., Zhou, W., Morgan, J.E., Hase, C.C., Gosink, K.K., Nilges, M., Bruesehoff, P.J., Roth, A., Lancaster, C.R. and Gennis, R.B. Purification and characterization of the recombinant Na+-translocating NADH:quinone oxidoreductase from Vibrio cholerae. Biochemistry 41 (2002) 3781-3789. [PMID: 11888296]

5. Barquera, B., Nilges, M.J., Morgan, J.E., Ramirez-Silva, L., Zhou, W. and Gennis, R.B. Mutagenesis study of the 2Fe-2S center and the FAD binding site of the Na+-translocating NADH:ubiquinone oxidoreductase from Vibrio cholerae. Biochemistry 43 (2004) 12322-12330. [PMID: 15379571]

[EC 1.6.5.8 created 2011]

*EC 1.11.1.7

Accepted name: peroxidase

Reaction: 2 phenolic donor + H2O2 = 2 phenoxyl radical of the donor + 2 H2O

Other name(s): lactoperoxidase; guaiacol peroxidase; plant peroxidase; Japanese radish peroxidase; horseradish peroxidase (HRP); soybean peroxidase (SBP); extensin peroxidase; heme peroxidase; oxyperoxidase; protoheme peroxidase; pyrocatechol peroxidase; scopoletin peroxidase, Coprinus cinereus peroxidase, Arthromyces ramosus peroxidase

Systematic name: phenolic donor:hydrogen-peroxide oxidoreductase

Comments: Heme proteins with histidine as proximal ligand. The iron in the resting enzyme is Fe(III). They also peroxidize non-phenolic substrates such as 3,3',5,5'-tetramethylbenzidine (TMB) and 2,2'-azinobis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS). Certain peroxidases (e.g. lactoperoxidase, SBP) oxidize bromide, iodide and thiocyanate.

Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 9003-99-0

References:

1. Kenten, R.H. and Mann, P.J.G. Simple method for the preparation of horseradish peroxidase. Biochem. J. 57 (1954) 347-348. [PMID: 13172193]

2. Morrison, M., Hamilton, H.B. and Stotz, E. The isolation and purification of lactoperoxidase by ion exchange chromatography. J. Biol. Chem. 228 (1957) 767-776. [PMID: 13475358]

3. Paul, K.G. Peroxidases. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Eds), The Enzymes, 2nd edn, vol. 8, Academic Press, New York, 1963, pp. 227-274.

4. Tagawa, K., Shin, M. and Okunuki, K. Peroxidases from wheat germ. Nature (Lond.) 183 (1959) 111. [PMID: 13622706]

5. Theorell, H. The preparation and some properties of crystalline horse-radish peroxidase. Ark. Kemi Mineral. Geol. 16A No. 2 (1943) 1-11.

6. Farhangrazi, Z.S., Copeland, B.R., Nakayama, T., Amachi, T., Yamazaki, I. and Powers, L.S. Oxidation-reduction properties of compounds I and II of Arthromyces ramosus peroxidase. Biochemistry 33 (1994) 5647-5652. [PMID: 8180190]

7. Aitken, M.D. and Heck, P.E. Turnover capacity of coprinus cinereus peroxidase for phenol and monosubstituted phenol. Biotechnol. Prog. 14 (1998) 487-492. [PMID: 9622531]

8. Dunford, H.B. Heme peroxidases, Wiley-VCH, New York, 1999, pp. 33-218.

9. Torres, E and Ayala, M. Biocatalysis based on heme peroxidases, Springer, Berlin, 2010, pp. 7-110.

[EC 1.11.1.7 created 1961, modified 2010, modified 2011]

*EC 1.11.1.10

Accepted name: chloride peroxidase

Reaction: RH + chloride + H2O2 = RCl + 2 H2O

Other name(s): chloroperoxidase; CPO; vanadium haloperoxidase

Systematic name: chloride:hydrogen-peroxide oxidoreductase

Comments: Brings about the chlorination of a range of organic molecules, forming stable C-Cl bonds. Also oxidizes bromide and iodide. Enzymes of this type are either heme-thiolate proteins, or contain vanadate. A secreted enzyme produced by the ascomycetous fungus Caldariomyces fumago (Leptoxyphium fumago) is an example of the heme-thiolate type. It catalyses the production of hypochlorous acid by transferring one oxygen atom from H2O2 to chloride. At a separate site it catalyses the chlorination of activated aliphatic and aromatic substrates, via HClO and derived chlorine species. In the absence of halides, it shows peroxidase (e.g. phenol oxidation) and peroxygenase activities. The latter inserts oxygen from H2O2 into, for example, styrene (side chain epoxidation) and toluene (benzylic hydroxylation), however, these activities are less pronounced than its activity with halides. Has little activity with non-activated substrates such as aromatic rings, ethers or saturated alkanes. The chlorinating peroxidase produced by ascomycetous fungi (e.g. Curvularia inaequalis) is an example of a vanadium chloroperoxidase, and is related to bromide peroxidase (EC 1.11.1.18). It contains vanadate and oxidizes chloride, bromide and iodide into hypohalous acids. In the absence of halides, it peroxygenates organic sulfides and oxidizes ABTS [2,2'-azinobis(3-ethylbenzthiazoline-6-sulfonic acid)] but no phenols.

Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 9055-20-3

References:

1. Morris, D.R. and Hager, L.P. Chloroperoxidase. I. Isolation and properties of the crystalline glycoprotein. J. Biol. Chem. 241 (1966) 1763-1768. [PMID: 5949836]

2. Hager, L.P., Hollenberg, P.F., Rand-Meir, T., Chiang, R. and Doubek, D.L. Chemistry of peroxidase intermediates. Ann. N.Y. Acad. Sci. 244 (1975) 80-93. [PMID: 1056179]

3. Theiler, R., Cook, J.C., Hager, L.P. and Siuda, J.F. Halohydrocarbon synthesis by homoperoxidase. Science 202 (1978) 1094-1096.

4. Sundaramoorthy, M., Terner, J. and Poulos, T.L. The crystal structure of chloroperoxidase: a heme peroxidase—cytochrome P450 functional hybrid. Structure 3 (1995) 1367-1377. [PMID: 8747463]

5. ten Brink, H.B., Tuynman, A., Dekker, H.L., Hemrika, W., Izumi, Y., Oshiro, T., Schoemaker, H.E. and Wever, R. Enantioselective sulfoxidation catalyzed by vanadium haloperoxidases. Inorg. Chem. 37 (1998) 6780-6784. [PMID: 11670813]

6. ten Brink, H.B., Dekker, H.L., Schoemaker, H.E. and Wever, R. Oxidation reactions catalyzed by vanadium chloroperoxidase from Curvularia inaequalis. J. Inorg. Biochem. 80 (2000) 91-98. [PMID: 10885468]

7. Manoj, K.M. Chlorinations catalyzed by chloroperoxidase occur via diffusible intermediate(s) and the reaction components play multiple roles in the overall process. Biochim. Biophys. Acta 1764 (2006) 1325-1339. [PMID: 16870515]

8. Kuhnel, K., Blankenfeldt, W., Terner, J. and Schlichting, I. Crystal structures of chloroperoxidase with its bound substrates and complexed with formate, acetate, and nitrate. J. Biol. Chem. 281 (2006) 23990-23998. [PMID: 16790441]

9. Manoj, K.M. and Hager, L.P. Chloroperoxidase, a janus enzyme. Biochemistry 47 (2008) 2997-3003. [PMID: 18220360]

[EC 1.11.1.10 created 1972, modified 2011]

EC 1.11.1.20

Accepted name: prostamide/prostaglandin F synthase

Reaction: thioredoxin + (5Z,9α,11α,13E,15S)-9,11-epidioxy-15-hydroxy-prosta-5,13-dienoate = thioredoxin disulfide + (5Z,9α,11α,13E,15S)-9,11,15-trihydroxyprosta-5,13-dienoate

Glossary: prostamide H2 = (5Z)-N-(2-hydroxyethyl)-7-{(1R,4S,5R,6R)-6-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-2,3-dioxabicyclo[2.2.1]hept-5-yl}hept-5-enamide
prostamide F = (5Z,9α,11α,13E,15S)-9,11,15-trihydroxy-N-(2-hydroxyethyl)prosta-5,13-dien-1-amide
prostaglandin H2 = (5Z,9α,11α,13E,15S)-9,11-epidioxy-15-hydroxy-prosta-5,13-dienoate
prostaglandin F = (5Z,9α,11α,13E,15S)-9,11,15-trihydroxyprosta-5,13-dienoate

Other name(s): prostamide/PGF synthase; prostamide F synthase; prostamide/prostaglandin F synthase; tPGF synthase

Systematic name: thioredoxin:(5Z,9α,11α,13E,15S)-9,11-epidioxy-15-hydroxy-prosta-5,13-dienoate oxidoreductase

Comments: The enzyme contains a thioredoxin-type disulfide as a catalytic group. Prostamide H2 and prostaglandin H2 are the best substrates; the latter is converted to prostaglandin F. The enzyme also reduces tert-butyl hydroperoxide, cumene hydroperoxide and H2O2, but not prostaglandin D2 or prostaglandin E2.

References:

1. Moriuchi, H., Koda, N., Okuda-Ashitaka, E., Daiyasu, H., Ogasawara, K., Toh, H., Ito, S., Woodward, D.F. and Watanabe, K. Molecular characterization of a novel type of prostamide/prostaglandin F synthase, belonging to the thioredoxin-like superfamily. J. Biol. Chem. 283 (2008) 792-801. [PMID: 18006499]

2. Yoshikawa, K., Takei, S., Hasegawa-Ishii, S., Chiba, Y., Furukawa, A., Kawamura, N., Hosokawa, M., Woodward, D.F., Watanabe, K. and Shimada, A. Preferential localization of prostamide/prostaglandin F synthase in myelin sheaths of the central nervous system. Brain Res. 1367 (2011) 22-32. [PMID: 20950588]

[EC 1.11.1.20 created 2011]

EC 1.11.2.2

Accepted name: myeloperoxidase

Reaction: Cl + H2O2 + H+ = HClO + H2O

Other name(s): MPO; verdoperoxidase

Systematic name: chloride:hydrogen-peroxide oxidoreductase (hypochlorite-forming)

Comments: Contains calcium and covalently bound heme (proximal ligand histidine). It is present in phagosomes of neutrophils and monocytes, where the hypochlorite produced is strongly bactericidal. It differs from EC 1.11.1.10 chloride peroxidase in its preference for formation of hypochlorite over the chlorination of organic substrates under physiological conditions (pH 5-8). Hypochlorite in turn forms a number of antimicrobial products (Cl2, chloramines, hydroxyl radical, singlet oxygen). MPO also oxidizes bromide, iodide and thiocyanate. In the absence of halides, it oxidizes phenols and has a moderate peroxygenase activity toward styrene.

References:

1. Agner, K. Myeloperoxidase. Advances in Enzymology 3 (1943) 137-148.

2. Harrison, J.E. and Schultz, J. Studies on the chlorinating activity of myeloperoxidase. J. Biol. Chem. 251 (1976) 1371-1374. [PMID: 176150]

3. Furtmuller, P.G., Burner, U. and Obinger, C. Reaction of myeloperoxidase compound I with chloride, bromide, iodide, and thiocyanate. Biochemistry 37 (1998) 17923-17930. [PMID: 9922160]

4. Tuynman, A., Spelberg, J.L., Kooter, I.M., Schoemaker, H.E. and Wever, R. Enantioselective epoxidation and carbon-carbon bond cleavage catalyzed by Coprinus cinereus peroxidase and myeloperoxidase. J. Biol. Chem. 275 (2000) 3025-3030. [PMID: 10652281]

5. Klebanoff, S.J. Myeloperoxidase: friend and foe. J Leukoc Biol 77 (2005) 598-625. [PMID: 15689384]

6. Fiedler, T.J., Davey, C.A. and Fenna, R.E. X-ray crystal structure and characterization of halide-binding sites of human myeloperoxidase at 1.8 Å resolution. J. Biol. Chem. 275 (2000) 11964-11971. [PMID: 10766826]

7. Gaut, J.P., Yeh, G.C., Tran, H.D., Byun, J., Henderson, J.P., Richter, G.M., Brennan, M.L., Lusis, A.J., Belaaouaj, A., Hotchkiss, R.S. and Heinecke, J.W. Neutrophils employ the myeloperoxidase system to generate antimicrobial brominating and chlorinating oxidants during sepsis. Proc. Natl. Acad. Sci. USA 98 (2001) 11961-11966. [PMID: 11593004]

[EC 1.11.2.2 created 2011]

EC 1.11.2.3

Accepted name: plant seed peroxygenase

Reaction: R1H + R2OOH = R1OH + R2OH

Other name(s): plant peroxygenase, soybean peroxygenase

Systematic name: substrate:hydroperoxide oxidoreductase (RH-hydroxylating or epoxidising)

Comments: A heme protein with calcium binding motif (caleosin-type). Enzymes of this type include membrane-bound proteins found in seeds of different plants. They catalyse the direct transfer of one oxygen atom from an organic hydroperoxide, which is reduced into its corresponding alcohol to a substrate which will be oxidized. Reactions catalysed include hydroxylation, epoxidation and sulfoxidation. Preferred substrate and co-substrate are unsaturated fatty acids and fatty acid hydroperoxides, respectively. Plant seed peroxygenase is involved in the synthesis of cutin.

References:

1. Ishimaru, A. Purification and characterization of solubilized peroxygenase from microsomes of pea seeds. J. Biol. Chem. 254 (1979) 8427-8433. [PMID: 468835]

2. Blee, E., Wilcox, A.L., Marnett, L.J. and Schuber, F. Mechanism of reaction of fatty acid hydroperoxides with soybean peroxygenase. J. Biol. Chem. 268 (1993) 1708-1715. [PMID: 8420948]

3. Hamberg, M. and Hamberg, G. Peroxygenase-catalyzed fatty acid epoxidation in cereal seeds (sequential oxidation of linoleic acid into 9(S),12(S),13(S)-trihydroxy-10(E)-octadecenoic acid). Plant Physiol. 110 (1996) 807-815. [PMID: 12226220]

4. Lequeu, J., Fauconnier, M.L., Chammai, A., Bronner, R. and Blee, E. Formation of plant cuticle: evidence for the occurrence of the peroxygenase pathway. Plant J. 36 (2003) 155-164. [PMID: 14535881]

5. Hanano, A., Burcklen, M., Flenet, M., Ivancich, A., Louwagie, M., Garin, J. and Blee, E. Plant seed peroxygenase is an original heme-oxygenase with an EF-hand calcium binding motif. J. Biol. Chem. 281 (2006) 33140-33151. [PMID: 16956885]

[EC 1.11.2.3 created 2011]

EC 1.11.2.4

Accepted name: fatty-acid peroxygenase

Reaction: fatty acid + H2O2 = 3- or 2-hydroxy fatty acid + H2O

Other name(s): fatty acid hydroxylase; P450 peroxygenase; CYP152A1; P450BS; P450SPα

Systematic name: fatty acid:hydroperoxide oxidoreductase (RH-hydroxylating)

Comments: A cytosolic heme-thiolate protein with sequence homology to P450 monooxygenases. Unlike the latter, it needs neither NAD(P)H, dioxygen nor specific reductases for function. Enzymes of this type are produced by bacteria (e.g. Sphingomonas paucimobilis. Bacillus subtilis). Catalytic turnover rates are high compared with those of monooxygenation reactions as well as peroxide shunt reactions catalysed by the common P450s. A model substrate is myristate, but other saturated and unsaturated fatty acids are also hydroxylated. Oxidizes the peroxidase substrate 3,3',5,5'-tetramethylbenzidine (TMB) and peroxygenates aromatic substrates in a fatty-acid-dependent reaction.

References:

1. Matsunaga, I., Yamada, M., Kusunose, E., Nishiuchi, Y., Yano, I. and Ichihara, K. Direct involvement of hydrogen peroxide in bacterial α-hydroxylation of fatty acid. FEBS Lett. 386 (1996) 252-254. [PMID: 8647293]

2. Matsunaga, I., Yamada, M., Kusunose, E., Miki, T. and Ichihara, K. Further characterization of hydrogen peroxide-dependent fatty acid α-hydroxylase from Sphingomonas paucimobilis. J. Biochem. 124 (1998) 105-110. [PMID: 9644252]

3. Matsunaga, I., Ueda, A., Fujiwara, N., Sumimoto, T. and Ichihara, K. Characterization of the ybdT gene product of Bacillus subtilis: novel fatty acid β-hydroxylating cytochrome P450. Lipids 34 (1999) 841-846. [PMID: 10529095]

4. Imai, Y., Matsunaga, I., Kusunose, E. and Ichihara, K. Unique heme environment at the putative distal region of hydrogen peroxide-dependent fatty acid α-hydroxylase from Sphingomonas paucimobilis (peroxygenase P450SPα). J. Biochem. 128 (2000) 189-194. [PMID: 10920253]

5. Matsunaga, I., Yamada, A., Lee, D.S., Obayashi, E., Fujiwara, N., Kobayashi, K., Ogura, H. and Shiro, Y. Enzymatic reaction of hydrogen peroxide-dependent peroxygenase cytochrome P450s: kinetic deuterium isotope effects and analyses by resonance Raman spectroscopy. Biochemistry 41 (2002) 1886-1892. [PMID: 11827534]

6. Lee, D.S., Yamada, A., Sugimoto, H., Matsunaga, I., Ogura, H., Ichihara, K., Adachi, S., Park, S.Y. and Shiro, Y. Substrate recognition and molecular mechanism of fatty acid hydroxylation by cytochrome P450 from Bacillus subtilis. Crystallographic, spectroscopic, and mutational studies. J. Biol. Chem. 278 (2003) 9761-9767. [PMID: 12519760]

7. Matsunaga, I. and Shiro, Y. Peroxide-utilizing biocatalysts: structural and functional diversity of heme-containing enzymes. Curr. Opin. Chem. Biol. 8 (2004) 127-132. [PMID: 15062772]

8. Shoji, O., Wiese, C., Fujishiro, T., Shirataki, C., Wunsch, B. and Watanabe, Y. Aromatic C-H bond hydroxylation by P450 peroxygenases: a facile colorimetric assay for monooxygenation activities of enzymes based on Russig’s blue formation. J. Biol. Inorg. Chem. 15 (2010) 1109-1115. [PMID: 20490877]

[EC 1.11.2.4 created 2011]

*EC 1.13.12.16

Accepted name: nitronate monooxygenase

Reaction: ethylnitronate + O2 = acetaldehyde + nitrite + other products

Other name(s): NMO; 2-nitropropane dioxygenase (incorrect)

Systematic name: nitronate:oxygen 2-oxidoreductase (nitrite-forming)

Comments: Previously classified as 2-nitropropane dioxygenase (EC 1.13.11.32), but it is now recognized that this was the result of the slow ionization of nitroalkanes to their nitronate (anionic) forms. The enzymes from the fungus Neurospora crassa and the yeast Williopsis saturnus var. mrakii (formerly classified as Hansenula mrakii) contain non-covalently bound FMN as the cofactor. Neither hydrogen peroxide nor superoxide were detected during enzyme turnover. Active towards linear alkyl nitronates of lengths between 2 and 6 carbon atoms and, with lower activity, towards propyl-2-nitronate. The enzyme from N. crassa can also utilize neutral nitroalkanes, but with lower activity.

Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number:

References:

1. Francis, K., Russell, B. and Gadda, G. Involvement of a flavosemiquinone in the enzymatic oxidation of nitroalkanes catalyzed by 2-nitropropane dioxygenase. J. Biol. Chem. 280 (2005) 5195-5204. [PMID: 15582992]

2. Ha, J.Y., Min, J.Y., Lee, S.K., Kim, H.S., Kim do, J., Kim, K.H., Lee, H.H., Kim, H.K., Yoon, H.J. and Suh, S.W. Crystal structure of 2-nitropropane dioxygenase complexed with FMN and substrate. Identification of the catalytic base. J. Biol. Chem. 281 (2006) 18660-18667. [PMID: 16682407]

3. Gadda, G. and Francis, K. Nitronate monooxygenase, a model for anionic flavin semiquinone intermediates in oxidative catalysis. Arch. Biochem. Biophys. 493 (2010) 53-61. [PMID: 19577534]

4. Francis, K. and Gadda, G. Kinetic evidence for an anion binding pocket in the active site of nitronate monooxygenase. Bioorg. Chem. 37 (2009) 167-172. [PMID: 19683782]

[EC 1.13.12.16 created 1984 as EC 1.13.11.32, transferred 2009 to EC 1.13.12.16, modified 2011]

EC 1.13.12.18

Accepted name: dinoflagellate luciferase

Reaction: dinoflagellate luciferin + O2 = oxidized dinoflagellate luciferin + H2O +

For diagram of reaction, click here

Glossary: dinoflagellate luciferin = (1S,2S,3S)-1-carboxy-3-(2-carboxyethyl)-12-ethyl-2,8,13,18-tetramethyl-17-vinyl-1,2,3,21-tetrahydro-5,7-ethanobilene-a-19(16H),52-dione

Other name(s): (dinoflagellate luciferin) luciferase; Gonyaulax luciferase

Systematic name: dinoflagellate-luciferin:oxygen 132-oxidoreductase

Comments: A luciferase from dinoflagelates such as Gonyaulax polyedra, Lingulodinium polyedrum, Noctiluca scintillans, and Pyrocystis lunula. It is a single protein with three luciferase domains. The luciferin is strongly bound by a luciferin binding protein above a pH of 7.

References:

1. Dunlap, J.C. and Hastings, J.W. The biological clock in Gonyaulax controls luciferase activity by regulating turnover. J. Biol. Chem. 256 (1981) 10509-10518. [PMID: 7197271]

2. Morse, D., Pappenheimer, A.M., Jr. and Hastings, J.W. Role of a luciferin-binding protein in the circadian bioluminescent reaction of Gonyaulax polyedra. J. Biol. Chem. 264 (1989) 11822-11826. [PMID: 2745419]

3. Bae, Y.M. and Hastings, J.W. Cloning, sequencing and expression of dinoflagellate luciferase DNA from a marine alga, Gonyaulax polyedra. Biochim. Biophys. Acta 1219 (1994) 449-456. [PMID: 7918642]

4. Li, L. Gonyaulax luciferase: gene structure, protein expression, and purification from recombinant sources. Methods Enzymol. 305 (2000) 249-258. [PMID: 10812605]

5. Morse, D. and Mittag, M. Dinoflagellate luciferin-binding protein. Methods Enzymol. 305 (2000) 258-276. [PMID: 10812606]

6. Schultz, L.W., Liu, L., Cegielski, M. and Hastings, J.W. Crystal structure of a pH-regulated luciferase catalyzing the bioluminescent oxidation of an open tetrapyrrole. Proc. Natl. Acad. Sci. USA 102 (2005) 1378-1383. [PMID: 15665092]

[EC 1.13.12.18 created 2011]

*EC 1.14.13.7

Accepted name: phenol 2-monooxygenase

Reaction: phenol + NADPH + H+ + O2 = catechol + NADP+ + H2O

Other name(s): phenol hydroxylase; phenol o-hydroxylase

Systematic name: phenol,NADPH:oxygen oxidoreductase (2-hydroxylating)

Comments: A flavoprotein (FAD). Also active with resorcinol and 2-methylphenol.

Links to other databases: BRENDA, EXPASY, KEGG, PDB, UM-BBD, CAS registry number: 37256-84-1

References:

1. Nakagawa, H. and Takeda, Y. Phenol hydroxylase. Biochim. Biophys. Acta 62 (1962) 423-426. [PMID: 14478080]

2. Neujahr, H.Y. and Gaal, A. Phenol hydroxylase from yeast. Purification and properties of the enzyme from Trichosporon cutaneum. Eur. J. Biochem. 35 (1973) 386-400. [PMID: 4146224]

3. Neujahr, H.Y. and Gaal, A. Phenol hydroxylase from yeast. Sulfhydryl groups in phenol hydroxylase from Trichosporon cutaneum. Eur. J. Biochem. 58 (1975) 351-357. [PMID: 810352]

[EC 1.14.13.7 created 1972, modified 2011]

EC 1.14.13.119

Accepted name: 5-epiaristolochene 1,3-dihydroxylase

Reaction: 5-epiaristolochene + 2 NADPH + 2 H+ + 2 O2 = capsidiol + 2 NADP+ + 2 H2O

Other name(s): 5-epi-aristolochene 1,3-dihydroxylase; EAH

Systematic name: 5-epiaristolochene,NADPH:oxygen oxidoreductase (1- and 3-hydroxylating)

Comments: A heme-thiolate protein (P-450). Kinetic studies suggest that 1β-hydroxyepiaristolochene is mainly formed first followed by hydroxylation at C-3. However the reverse order via 3α-hydroxyepiaristolochene does occur.

References:

1. Ralston, L., Kwon, S.T., Schoenbeck, M., Ralston, J., Schenk, D.J., Coates, R.M. and Chappell, J. Cloning, heterologous expression, and functional characterization of 5-epi-aristolochene-1,3-dihydroxylase from tobacco (Nicotiana tabacum). Arch. Biochem. Biophys. 393 (2001) 222-235. [PMID: 11556809]

2. Takahashi, S., Zhao, Y., O'Maille, P.E., Greenhagen, B.T., Noel, J.P., Coates, R.M. and Chappell, J. Kinetic and molecular analysis of 5-epiaristolochene 1,3-dihydroxylase, a cytochrome P450 enzyme catalyzing successive hydroxylations of sesquiterpenes. J. Biol. Chem. 280 (2005) 3686-3696. [PMID: 15522862]

[EC 1.14.13.119 created 2011]

EC 1.14.13.120

Accepted name: costunolide synthase

Reaction: germacra-1(10),4,11(13)-trien-12-oate + NADPH + H+ + O2 = (+)-costunolide + NADP+ + 2 H2O

Systematic name: germacra-1(10),4,11(13)-trien-12-oate,NADPH:oxygen oxidoreductase (6α-hydroxylating)

Comments: A heme-thiolate protein (P-450). The enzyme hydroxylates carbon C-6 of germacra-1(10),4,11(13)-trien-12-oate to give 6α-hydroxygermacra-1(10),4,11(13)-trien-12-oate, which probably spontaneously cyclises to form the lactone ring.

References:

1. de Kraker, J.W., Franssen, M.C., Joerink, M., de Groot, A. and Bouwmeester, H.J. Biosynthesis of costunolide, dihydrocostunolide, and leucodin. Demonstration of cytochrome p450-catalyzed formation of the lactone ring present in sesquiterpene lactones of chicory. Plant Physiol. 129 (2002) 257-268. [PMID: 12011356]

[EC 1.14.13.120 created 2011]

EC 1.14.13.121

Accepted name: premnaspirodiene oxygenase

Reaction: (1) (–)-vetispiradiene + NADPH + H+ + O2 = solavetivol + NADP+ + H2O
(2) solavetivol + NADPH + H+ + O2 = solavetivone + NADP+ + 2 H2O

Glossary: (–)-premnaspirodiene = (–)-vetispiradiene

Other name(s): HPO; Hyoscymus muticus premnaspirodiene oxygenase

Systematic name: (–)-vetispiradiene,NADPH:oxygen 2α-oxidoreductase

Comments: A heme-thiolate protein (P-450). The enzyme from the plant Hyoscymus muticus also hydroxylates valencene at C-2 to give the α-hydroxy compound, nootkatol, and this is converted into nootkatone. 5-Epiaristolochene and epieremophilene are hydroxylated at C-2 to give a 2β-hydroxy derivative which is not further oxidized.

References:

1. Takahashi, S., Yeo, Y.S., Zhao, Y., O'Maille, P.E., Greenhagen, B.T., Noel, J.P., Coates, R.M. and Chappell, J. Functional characterization of premnaspirodiene oxygenase, a cytochrome P450 catalyzing regio- and stereo-specific hydroxylations of diverse sesquiterpene substrates. J. Biol. Chem. 282 (2007) 31744-31754. [PMID: 17715131]

[EC 1.14.13.121 created 2011]

*EC 1.14.15.7

Accepted name: choline monooxygenase

Reaction: choline + O2 + 2 reduced ferredoxin + 2 H+ = betaine aldehyde hydrate + H2O + 2 oxidized ferredoxin

Glossary: betaine = glycine betaine = N,N,N-trimethylammonioacetate
betaine aldehyde = N,N,N-trimethyl-2-oxoethylammonium
choline = (2-hydroxyethyl)trimethylammonium

Systematic name: choline,reduced-ferredoxin:oxygen oxidoreductase

Comments: The spinach enzyme, which is located in the chloroplast, contains a Rieske-type [2Fe-2S] cluster, and probably also a mononuclear Fe centre. Requires Mg2+. Catalyses the first step of glycine betaine synthesis. In many bacteria, plants and animals, betaine is synthesized in two steps: (1) choline to betaine aldehyde and (2) betaine aldehyde to betaine. Different enzymes are involved in the first reaction. In plants, the reaction is catalysed by this enzyme whereas in animals and many bacteria it is catalysed by either membrane-bound EC 1.1.99.1 (choline dehydrogenase) or soluble EC 1.1.3.17 (choline oxidase) [7]. The enzyme involved in the second step, EC 1.2.1.8 (betaine-aldehyde dehydrogenase), appears to be the same in plants, animals and bacteria. In some bacteria, betaine is synthesized from glycine through the actions of EC 2.1.1.156 (glycine/sarcosine N-methyltransferase) and EC 2.1.1.157 (sarcosine/dimethylglycine N-methyltransferase).

Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 118390-76-4

References:

1. Brouquisse, R., Weigel, P., Rhodes, D., Yocum, C.F. and Hanson, A.D. Evidence for a ferredoxin-dependent choline monooxygenase from spinach chloroplast stroma. Plant Physiol. 90 (1989) 322-329. [PMID: 16666757]

2. Burnet, M., Lafontaine, P.J. and Hanson, A.D. Assay, purification, and partial characterization of choline monooxygenase from spinach. Plant Physiol. 108 (1995) 581-588. [PMID: 12228495]

3. Rathinasabapathi, B., Burnet, M., Russell, B.L., Gage, D.A., Liao, P., Nye, G.J., Scott, P., Golbeck, J.H. and Hanson, A.D. Choline monooxygenase, an unusual iron-sulfur enzyme catalyzing the first step of glycine betaine synthesis in plants: Prosthetic group characterization and cDNA cloning. Proc. Natl. Acad. Sci. USA 94 (1997) 3454-3458. [PMID: 9096415]

4. Russell, B.L., Rathinasabapathi, B. and Hanson, A.D. Osmotic stress induces expression of choline monooxygenase in sugar beet and amaranth. Plant Physiol. 116 (1998) 859-865. [PMID: 9489025]

5. Nuccio, M.L., Russell, B.L., Nolte, K.D., Rathinasabapathi, B., Gage, D.A. and Hanson, A.D. Glycine betaine synthesis in transgenic tobacco expressing choline monooxygenase is limited by the endogenous choline supply. Plant J. 16 (1998) 101-110.

6. Nuccio, M.L., Russell, B.L., Nolte, K.D., Rathinasabapathi, B., Gage, D.A. and Hanson, A.D. The endogenous choline supply limits glycine betaine synthesis in transgenic tobacco expressing choline. Plant J. 16 (1998) 487-496. [PMID: 9881168]

7. Waditee, R., Tanaka, Y., Aoki, K., Hibino, T., Jikuya, H., Takano, J., Takabe, T. and Takabe, T. Isolation and functional characterization of N-methyltransferases that catalyze betaine synthesis from glycine in a halotolerant photosynthetic organism Aphanothece halophytica. J. Biol. Chem. 278 (2003) 4932-4942. [PMID: 12466265]

[EC 1.14.15.7 created 2001, modified 2002 (EC 1.14.14.4 created 2000, incorporated 2002), modified 2005, modified 2011]

EC 1.14.21.8

Accepted name: pseudobaptigenin synthase

Reaction: (1) calycosin + NADPH + H+ + O2 = pseudobaptigenin + NADP+ + 2 H2O
(2) pratensein + NADPH + H+ + O2 = 5-hydroxypseudobaptigenin + NADP+ + 2 H2O

Glossary: calycosin = 3'-hydroxyformononetin
pratensein = 3'-hydroxybiochanin A

Systematic name: calycosin,NADPH:oxygen oxidoreductase (methylenedioxy-bridge-forming)

Comments: A heme-thiolate enzyme (P450) catalysing an oxidative reaction that does not incorporate oxygen into the product. Catalyses a step in the biosynthesis of (–)-maackiain, the main pterocarpan phytoalexin in chickpea (Cicer arietinum).

References:

1. Clemens S., Barz W. Cytochrome P450-dependent methylenedioxy bridge formation in Cicer arietinum. Phytochemistry 41 (1996) 457-460.

[EC 1.14.21.8 created 2011]

*EC 1.17.99.1

Accepted name: 4-methylphenol dehydrogenase (hydroxylating)

Reaction: 4-methylphenol + acceptor + H2O = 4-hydroxybenzaldehyde + reduced acceptor

Glossary: 4-methylphenol = 4-cresol = p-cresol

Other name(s): p-cresol-(acceptor) oxidoreductase (hydroxylating); p-cresol methylhydroxylase; 4-cresol dehydrogenase (hydroxylating)

Systematic name: 4-methylphenol:acceptor oxidoreductase (methyl-hydroxylating)

Comments: A flavocytochrome c (FAD). Phenazine methosulfate can act as acceptor. A quinone methide is probably formed as intermediate. The first hydroxylation forms 4-hydroxybenzyl alcohol; a second hydroxylation converts this into 4-hydroxybenzaldehyde.

Links to other databases: BRENDA, EXPASY, KEGG, PDB, UM-BBD, CAS registry number: 66772-07-4

References:

1. Hopper, D.J. and Taylor, D.G. The purification and properties of p-cresol-(acceptor) oxidoreductase (hydroxylating), a flavocytochrome from Pseudomonas putida. Biochem. J. 167 (1977) 155-162. [PMID: 588247]

2. McIntire, W., Edmondson, D.E. and Singer, T.P. 8α-O-Tyrosyl-FAD: a new form of covalently bound flavin from p-cresol methylhydroxylase. J. Biol. Chem. 255 (1980) 6553-6555. [PMID: 7391034]

[EC 1.17.99.1 created 1983, modified 2001, modified 2011]

[EC 2.1.1.29 Transferred entry: tRNA (cytosine-5-)-methyltransferase. Now covered by EC 2.1.1.202 [multisite-specific tRNA:(cytosine-C5)-methyltransferase], EC 2.1.1.203 [tRNA (cytosine34-C5)-methyltransferase] and EC 2.1.1.204 [RNA (cytosine38-C5)-methyltransferase]. (EC 2.1.1.29 created 1972, deleted 2011)]

EC 2.1.1.200

Accepted name: tRNA (cytidine32/uridine32-2'-O)-methyltransferase

Reaction: (1) S-adenosyl-L-methionine + cytidine32 in tRNA = S-adenosyl-L-homocysteine + 2'-O-methylcytidine32 in tRNA
(2) S-adenosyl-L-methionine + uridine32 in tRNA = S-adenosyl-L-homocysteine + 2'-O-methyluridine32 in tRNA

Other name(s): YfhQ; tRNA:Cm32/Um32 methyltransferase; TrMet(Xm32); TrmJ

Systematic name: S-adenosyl-L-methionine:tRNA (cytidine32/uridine32-2'-O)-methyltransferase

Comments: In Escherichia coli YfhQ is the only methyltransferase responsible for the formation of 2'-O-methylcytidine32 in tRNA. No methylation of cytosine34 in tRNALeu(CAA). In vitro the enzyme 2-O-methylates cytidine32 of tRNASer1 and uridine32 of tRNAGln2.

References:

1. Purta, E., van Vliet, F., Tkaczuk, K.L., Dunin-Horkawicz, S., Mori, H., Droogmans, L. and Bujnicki, J.M. The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase. BMC Mol Biol 7 (2006) 23. [PMID: 16848900]

[EC 2.1.1.200 created 2011]

EC 2.1.1.201

Accepted name: 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase

Reaction: S-adenosyl-L-methionine + 2-methoxy-6-all-trans-polyprenyl-1,4-benzoquinol = S-adenosyl-L-homocysteine + 6-methoxy-3-methyl-2-all-trans-polyprenyl-1,4-benzoquinol

Other name(s): ubiE (gene name, ambiguous)

Systematic name: S-adenosyl-L-methionine:2-methoxy-6-all-trans-polyprenyl-1,4-benzoquinol 5-C-methyltransferase

Comments: This enzyme is involved in ubiquinone biosynthesis. Ubiquinones from different organisms have a different number of prenyl units (for example, ubiquinone-6 in Saccharomyces, ubiquinone-9 in rat and ubiquinone-10 in human), and thus the natural substrate for the enzymes from different organisms has a different number of prenyl units. However, the enzyme usually shows a low degree of specificity regarding the number of prenyl units. For example, when the COQ5 gene from Saccharomyces cerevisiae is introduced into Escherichia coli, it complements the respiratory deficiency of an ubiE mutant [3]. The bifunctional enzyme from Escherichia coli also catalyses the methylation of demethylmenaquinol-8 (this activity is classified as EC 2.1.1.163) [1].

References:

1. Lee, P.T., Hsu, A.Y., Ha, H.T. and Clarke, C.F. A C-methyltransferase involved in both ubiquinone and menaquinone biosynthesis: isolation and identification of the Escherichia coli ubiE gene. J. Bacteriol. 179 (1997) 1748-1754. [PMID: 9045837]

2. Young, I.G., McCann, L.M., Stroobant, P. and Gibson, F. Characterization and genetic analysis of mutant strains of Escherichia coli K-12 accumulating the biquinone precursors 2-octaprenyl-6-methoxy-1,4-benzoquinone and 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinone. J. Bacteriol. 105 (1971) 769-778. [PMID: 4323297]

3. Dibrov, E., Robinson, K.M. and Lemire, B.D. The COQ5 gene encodes a yeast mitochondrial protein necessary for ubiquinone biosynthesis and the assembly of the respiratory chain. J. Biol. Chem. 272 (1997) 9175-9181. [PMID: 9083048]

4. Barkovich, R.J., Shtanko, A., Shepherd, J.A., Lee, P.T., Myles, D.C., Tzagoloff, A. and Clarke, C.F. Characterization of the COQ5 gene from Saccharomyces cerevisiae. Evidence for a C-methyltransferase in ubiquinone biosynthesis. J. Biol. Chem. 272 (1997) 9182-9188. [PMID: 9083049]

[EC 2.1.1.201 created 2011]

EC 2.1.1.202

Accepted name: multisite-specific tRNA:(cytosine-C5)-methyltransferase

Reaction: (1) S-adenosyl-L-methionine + cytosine34 in tRNA precursor = S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
(2) S-adenosyl-L-methionine + cytosine40 in tRNA precursor = S-adenosyl-L-homocysteine + 5-methylcytosine40 in tRNA precursor
(3) S-adenosyl-L-methionine + cytosine48 in tRNA = S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNA
(4) S-adenosyl-L-methionine + cytosine49 in tRNA = S-adenosyl-L-homocysteine + 5-methylcytosine49 in tRNA

Other name(s): multisite-specific tRNA:m5C-methyltransferase; TRM4 (gene name, gene corresponding to ORF YBL024w)

Systematic name: S-adenosyl-L-methionine:tRNA (cytosine-C5)-methyltransferase

Comments: The enzyme from Saccharomyces cerevisiae is responsible for complete 5-methylcytosine methylations of yeast tRNA. The incidence of modification depends on the cytosine position in tRNA. At positions 34 and 40, 5-methylcytosine is found only in two yeast tRNAs (tRNALeu(CUA) and tRNAPhe(GAA), respectively), whereas most other elongator yeast tRNAs bear either 5-methylcytosine48 or 5-methylcytosine49, but never both in the same tRNA molecule [1]. The formation of 5-methylcytosine34 and 5-methylcytosine40 is a strictly intron-dependent process, whereas the formation of 5-methylcytosine48 and 5-methylcytosine49 is an intron-independent process [2,3].

References:

1. Motorin, Y. and Grosjean, H. Multisite-specific tRNA:m5C-methyltransferase (Trm4) in yeast Saccharomyces cerevisiae: identification of the gene and substrate specificity of the enzyme. RNA 5 (1999) 1105-1118. [PMID: 10445884]

2. Jiang, H.Q., Motorin, Y., Jin, Y.X. and Grosjean, H. Pleiotropic effects of intron removal on base modification pattern of yeast tRNAPhe: an in vitro study. Nucleic Acids Res. 25 (1997) 2694-2701. [PMID: 9207014]

3. Strobel, M.C. and Abelson, J. Effect of intron mutations on processing and function of Saccharomyces cerevisiae SUP53 tRNA in vitro and in vivo. Mol. Cell Biol. 6 (1986) 2663-2673. [PMID: 3537724]

4. Walbott, H., Husson, C., Auxilien, S. and Golinelli-Pimpaneau, B. Cysteine of sequence motif VI is essential for nucleophilic catalysis by yeast tRNA m5C methyltransferase. RNA 13 (2007) 967-973. [PMID: 17475914]

[EC 2.1.1.202 created 1976 as EC 2.1.1.29, part-transferred 2011 to EC 2.1.1.202]

EC 2.1.1.203

Accepted name: tRNA (cytosine34-C5)-methyltransferase

Reaction: S-adenosyl-L-methionine + cytosine34 in tRNA precursor = S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor

Other name(s): hTrm4 Mtase; hTrm4 methyltransferase; hTrm4 (gene name); tRNA:m5C-methyltransferase (ambiguous)

Systematic name: S-adenosyl-L-methionine:tRNA (cytosine34-C5)-methyltransferase

Comments: The human enzyme is specific for C5-methylation of cytosine34 in tRNA precursors. The intron in the human pre-tRNALeu(CAA) is indispensable for the C5-methylation of cytosine in the first position of the anticodon. It is not able to form 5-methylcytosine at positions 48 and 49 of human and yeast tRNA precursors [1].

References:

1. Brzezicha, B., Schmidt, M., Makalowska, I., Jarmolowski, A., Pienkowska, J. and Szweykowska-Kulinska, Z. Identification of human tRNA:m5C methyltransferase catalysing intron-dependent m5C formation in the first position of the anticodon of the pre-tRNA Leu (CAA). Nucleic Acids Res. 34 (2006) 6034-6043. [PMID: 17071714]

[EC 2.1.1.203 created 1976 as EC 2.1.1.29, part-transferred 2011 to EC 2.1.1.203]

EC 2.1.1.204

Accepted name: RNA (cytosine38-C5)-methyltransferase

Reaction: S-adenosyl-L-methionine + cytosine38 in tRNA = S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNA

Other name(s): hDNMT2 (gene name); DNMT2 (gene name); TRDMT1 (gene name)

Systematic name: S-adenosyl-L-methionine:tRNA (cytosine38-C5)-methyltransferase

Comments: The eukaryotic enzyme catalyses methylation of cytosine38 in the anti-codon loop of tRNAAsp(GTC), tRNAVal(AAC) and tRNAGly(GCC). Methylation by Dnmt2 protects tRNAs against stress-induced cleavage by ribonuclease [3].

References:

1. Goll, M.G., Kirpekar, F., Maggert, K.A., Yoder, J.A., Hsieh, C.L., Zhang, X., Golic, K.G., Jacobsen, S.E. and Bestor, T.H. Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2. Science 311 (2006) 395-398. [PMID: 16424344]

2. Jurkowski, T.P., Meusburger, M., Phalke, S., Helm, M., Nellen, W., Reuter, G. and Jeltsch, A. Human DNMT2 methylates tRNA(Asp) molecules using a DNA methyltransferase-like catalytic mechanism. RNA 14 (2008) 1663-1670. [PMID: 18567810]

3. Schaefer, M., Pollex, T., Hanna, K., Tuorto, F., Meusburger, M., Helm, M. and Lyko, F. RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage. Genes Dev. 24 (2010) 1590-1595. [PMID: 20679393]

[EC 2.1.1.204 created 1976 as EC 2.1.1.29, part-transferred 2011 to EC 2.1.1.204]

EC 2.1.1.205

Accepted name: tRNA (cytidine32/guanosine34-2'-O)-methyltransferase

Reaction: S-adenosyl-L-methionine + cytidine32/guanosine34 in tRNA = S-adenosyl-L-homocysteine + 2'-O-methylcytidine32/2'-O-methylguanosine34 in tRNA

Other name(s): Trm7p

Systematic name: S-adenosyl-L-methionine:tRNA (cytidine32/guanosine34-2'-O)-methyltransferase

Comments: The enzyme from Saccharomyces cerevisiae catalyses the formation of 2'-O-methylnucleotides at positions 32 and 34 of the yeast tRNAPhe, tRNATrp and, possibly, tRNALeu.

References:

1. Pintard, L., Lecointe, F., Bujnicki, J.M., Bonnerot, C., Grosjean, H. and Lapeyre, B. Trm7p catalyses the formation of two 2'-O-methylriboses in yeast tRNA anticodon loop. EMBO J. 21 (2002) 1811-1820. [PMID: 11927565]

[EC 2.1.1.205 created 2011]

EC 2.1.1.206

Accepted name: tRNA (cytidine56-2'-O)-methyltransferase

Reaction: S-adenosyl-L-methionine + cytidine56 in tRNA = S-adenosyl-L-homocysteine + 2'-O-methylcytidine56 in tRNA

Other name(s): aTrm56; tRNA ribose 2'-O-methyltransferase aTrm56; PAB1040 (gene name)

Systematic name: S-adenosyl-L-methionine:tRNA (cytidine56-2'-O)-methyltransferase

Comments: The archaeal enzyme specifically catalyses the S-adenosyl-L-methionine dependent 2'-O-ribose methylation of cytidine at position 56 in tRNA transcripts.

References:

1. Renalier, M.H., Joseph, N., Gaspin, C., Thebault, P. and Mougin, A. The Cm56 tRNA modification in archaea is catalyzed either by a specific 2'-O-methylase, or a C/D sRNP. RNA 11 (2005) 1051-1063. [PMID: 15987815]

2. Kuratani, M., Bessho, Y., Nishimoto, M., Grosjean, H. and Yokoyama, S. Crystal structure and mutational study of a unique SpoU family archaeal methylase that forms 2'-O-methylcytidine at position 56 of tRNA. J. Mol. Biol. 375 (2008) 1064-1075. [PMID: 18068186]

[EC 2.1.1.206 created 2011]

EC 2.3.1.193

Accepted name: tRNAMet cytidine acetyltransferase

Reaction: [elongator tRNAMet]-cytidine34 + ATP + acetyl-CoA = [elongator tRNAMet]-N4-acetylcytidine34 + ADP + phosphate + CoA

Other name(s): YpfI; TmcA

Systematic name: acetyl-CoA: [elongator tRNAMet]-cytidine34 N4-acetyltransferase (ATP-hydrolysing)

Comments: The enzyme acetylates the wobble base C34 of the CAU anticodon of elongation-specific tRNAMet. Escherichia coli TmcA strictly discriminates elongator tRNAMet from tRNAIle, which is structurally similar and has the same anticodon loop, mainly by recognizing the C27G43 pair in the anticodon stem. The enzyme can use GTP in place of ATP for formation of N4-acetylcytidine [1].

References:

1. Ikeuchi, Y., Kitahara, K. and Suzuki, T. The RNA acetyltransferase driven by ATP hydrolysis synthesizes N4-acetylcytidine of tRNA anticodon. EMBO J. 27 (2008) 2194-2203. [PMID: 18668122]

2. Chimnaronk, S., Suzuki, T., Manita, T., Ikeuchi, Y., Yao, M., Suzuki, T. and Tanaka, I. RNA helicase module in an acetyltransferase that modifies a specific tRNA anticodon. EMBO J. 28 (2009) 1362-1373. [PMID: 19322199]

[EC 2.3.1.193 created 2011]

EC 2.3.1.194

Accepted name: acetoacetyl-CoA synthase

Reaction: acetyl-CoA + malonyl-CoA = acetoacetyl-CoA + CoA + CO2

Other name(s): NphT7

Systematic name: acetyl-CoA:malonyl-CoA C-acetyltransferase (decarboxylating)

Comments: The enzyme from the soil bacterium Streptomyces sp. CL190 produces acetoacetyl-CoA to be used for mevalonate production via the mevalonate pathway. Unlike the homologous EC 2.3.1.180 (β-ketoacyl-[acyl-carrier-protein] synthase III), this enzyme does not accept malonyl-[acyl-carrier-protein] as a substrate.

References:

1. Okamura, E., Tomita, T., Sawa, R., Nishiyama, M. and Kuzuyama, T. Unprecedented acetoacetyl-coenzyme A synthesizing enzyme of the thiolase superfamily involved in the mevalonate pathway. Proc. Natl. Acad. Sci. USA 107 (2010) 11265-11270. [PMID: 20534558]

[EC 2.3.1.194 created 2011]

EC 2.3.1.195

Accepted name: (Z)-3-hexen-1-ol acetyltransferase

Reaction: acetyl-CoA + (3Z)-hex-3-en-1-ol = (3Z)-hex-3-en-1-yl acetate + CoA

Other name(s): CHAT; At3g03480

Systematic name: acetyl-CoA:(3Z)-hex-3-en-1-ol acetyltransferase

Comments: The enzyme is resonsible for the production of (3Z)-hex-3-en-1-yl acetate, the major volatile compound released upon mechanical wounding of the leaves of Arabidopsis thaliana [1].

References:

1. D'Auria, J.C., Pichersky, E., Schaub, A., Hansel, A. and Gershenzon, J. Characterization of a BAHD acyltransferase responsible for producing the green leaf volatile (Z)-3-hexen-1-yl acetate in Arabidopsis thaliana. Plant J. 49 (2007) 194-207. [PMID: 17163881]

2. D'Auria, J.C., Chen, F. and Pichersky, E. Characterization of an acyltransferase capable of synthesizing benzylbenzoate and other volatile esters in flowers and damaged leaves of Clarkia breweri. Plant Physiol. 130 (2002) 466-476. [PMID: 12226525]

[EC 2.3.1.195 created 2011]

EC 2.4.1.254

Accepted name: cyanidin-3-O-glucoside 2-O-glucuronosyltransferase

Reaction: UDP-D-glucuronate + cyanidin 3-O-β-D-glucoside = UDP + cyanidin 3-O-(2-O-β-D-glucuronosyl)-β-D-glucoside

Other name(s): BpUGT94B1; UDP-glucuronic acid:anthocyanin glucuronosyltransferase; UDP-glucuronic acid:anthocyanidin 3-glucoside 2'-O-β-glucuronosyltransferase; BpUGAT

Systematic name: UDP-D-glucuronate:cyanidin-3-O-β-glucoside 2-O-β-glucuronosyltransferase

Comments: The enzyme is highly specific for cyanidin 3-O-glucosides and UDP-D-glucuronate. Involved in the production of glucuronosylated anthocyanins that are the origin of the red coloration of flowers of Bellis perennis [1].

References:

1. Sawada, S., Suzuki, H., Ichimaida, F., Yamaguchi, M.A., Iwashita, T., Fukui, Y., Hemmi, H., Nishino, T. and Nakayama, T. UDP-glucuronic acid:anthocyanin glucuronosyltransferase from red daisy (Bellis perennis) flowers. Enzymology and phylogenetics of a novel glucuronosyltransferase involved in flower pigment biosynthesis. J. Biol. Chem. 280 (2005) 899-906. [PMID: 15509561]

2. Osmani, S.A., Bak, S., Imberty, A., Olsen, C.E. and Møller, B.L. Catalytic key amino acids and UDP-sugar donor specificity of a plant glucuronosyltransferase, UGT94B1: molecular modeling substantiated by site-specific mutagenesis and biochemical analyses. Plant Physiol. 148 (2008) 1295-1308. [PMID: 18829982]

[EC 2.4.1.254 created 2011]

EC 2.4.1.255

Accepted name: protein O-GlcNAc transferase

Reaction: (1) UDP-N-acetyl-D-glucosamine + [protein]-L-serine = UDP + [protein]-3-O-(N-acetyl-β-D-glucosaminyl)-L-serine
(2) UDP-N-acetyl-D-glucosamine + [protein]-L-threonine = UDP + [protein]-3-O-(N-acetyl-β-D-glucosaminyl)-L-threonine

Other name(s): O-GlcNAc transferase; OGTase; O-linked N-acetylglucosaminyltransferase; uridine diphospho-N-acetylglucosamine:polypeptide β-N-acetylglucosaminyltransferase; protein O-linked β-N-acetylglucosamine transferase

Systematic name: UDP-N-acetyl-D-glucosamine:protein-O-β-N-acetyl-D-glucosaminyl transferase

Comments: Within higher eukaryotes post-translational modification of protein serines/threonines with N-acetylglucosamine (O-GlcNAc) is dynamic, inducible and abundant, regulating many cellular processes by interfering with protein phosphorylation. EC 2.4.1.255 (protein O-GlcNAc transferase) transfers GlcNAc onto substrate proteins and EC 3.2.1.169 (protein O-GlcNAcase) cleaves GlcNAc from the modified proteins.

References:

1. Banerjee, S., Robbins, P.W. and Samuelson, J. Molecular characterization of nucleocytosolic O-GlcNAc transferases of Giardia lamblia and Cryptosporidium parvum. Glycobiology 19 (2009) 331-336. [PMID: 18948359]

2. Clarke, A.J., Hurtado-Guerrero, R., Pathak, S., Schuttelkopf, A.W., Borodkin, V., Shepherd, S.M., Ibrahim, A.F. and van Aalten, D.M. Structural insights into mechanism and specificity of O-GlcNAc transferase. EMBO J. 27 (2008) 2780-2788. [PMID: 18818698]

3. Rao, F.V., Dorfmueller, H.C., Villa, F., Allwood, M., Eggleston, I.M. and van Aalten, D.M. Structural insights into the mechanism and inhibition of eukaryotic O-GlcNAc hydrolysis. EMBO J. 25 (2006) 1569-1578. [PMID: 16541109]

4. Haltiwanger, R.S., Blomberg, M.A. and Hart, G.W. Glycosylation of nuclear and cytoplasmic proteins. Purification and characterization of a uridine diphospho-N-acetylglucosamine:polypeptide β-N-acetylglucosaminyltransferase. J. Biol. Chem. 267 (1992) 9005-9013. [PMID: 1533623]

5. Lubas, W.A., Frank, D.W., Krause, M. and Hanover, J.A. O-Linked GlcNAc transferase is a conserved nucleocytoplasmic protein containing tetratricopeptide repeats. J. Biol. Chem. 272 (1997) 9316-9324. [PMID: 9083068]

6. Lazarus, M.B., Nam, Y., Jiang, J., Sliz, P. and Walker, S. Structure of human O-GlcNAc transferase and its complex with a peptide substrate. Nature 469 (2011) 564-567. [PMID: 21240259]

[EC 2.4.1.255 created 2011]

EC 2.7.7.73

Accepted name: sulfur carrier protein ThiS adenylyltransferase

Reaction: ATP + [ThiS] = diphosphate + adenylyl-[ThiS]

Other name(s): thiF (gene name)

Systematic name: ATP:[ThiS] adenylyltransferase

Comments: Binds Zn2+. The enzyme catalyses the adenylation of ThiS, a sulfur carrier protein involved in the biosynthesis of thiamine. The enzyme shows significant structural similarity to ubiquitin-activating enzyme [3,4]. In Escherichia coli, but not in Bacillus subtilis, the enzyme forms a cross link from Cys-184 to the ThiS carboxy terminus (the position that is also thiolated) via an acyldisulfide [2].

References:

1. Taylor, S.V., Kelleher, N.L., Kinsland, C., Chiu, H.J., Costello, C.A., Backstrom, A.D., McLafferty, F.W. and Begley, T.P. Thiamin biosynthesis in Escherichia coli. Identification of this thiocarboxylate as the immediate sulfur donor in the thiazole formation. J. Biol. Chem. 273 (1998) 16555-16560. [PMID: 9632726]

2. Xi, J., Ge, Y., Kinsland, C., McLafferty, F.W. and Begley, T.P. Biosynthesis of the thiazole moiety of thiamin in Escherichia coli: identification of an acyldisulfide-linked protein--protein conjugate that is functionally analogous to the ubiquitin/E1 complex. Proc. Natl. Acad. Sci. USA 98 (2001) 8513-8518. [PMID: 11438688]

3. Duda, D.M., Walden, H., Sfondouris, J. and Schulman, B.A. Structural analysis of Escherichia coli ThiF. J. Mol. Biol. 349 (2005) 774-786. [PMID: 15896804]

4. Lehmann, C., Begley, T.P. and Ealick, S.E. Structure of the Escherichia coli ThiS-ThiF complex, a key component of the sulfur transfer system in thiamin biosynthesis. Biochemistry 45 (2006) 11-19. [PMID: 16388576]

[EC 2.7.7.73 created 2011]

EC 2.7.8.32

Accepted name: 3-O-α-D-mannopyranosyl-α-D-mannopyranose xylosylphosphotransferase

Reaction: UDP-xylose + 3-O-α-D-mannopyranosyl-α-D-mannopyranose = UMP + 3-O-(6-O-α-D-xylosylphospho-α-D-mannopyranosyl)-α-D-mannopyranose

Glossary: O-α-D-xylosylphospho-α-D-mannopyranosyl)-α-D-mannopyranose = O-α-D-xylosylphosphono-α-D-mannopyranosyl)-α-D-mannopyranose

Other name(s): XPT1

Systematic name: UDP-D-xylose:3-O-α-D-mannopyranosyl-α-D-mannopyranose xylosylphosphotransferase

Comments: Mn2+ required for activity. The enzyme is specific for mannose as an acceptor but is flexible as to the structural context of the mannosyl disaccharide.

References:

1. Reilly, M.C., Levery, S.B., Castle, S.A., Klutts, J.S. and Doering, T.L. A novel xylosylphosphotransferase activity discovered in Cryptococcus neoformans. J. Biol. Chem. 284 (2009) 36118-36127. [PMID: 19864415]

[EC 2.7.8.32 created 2011]

EC 3.1.7.7

Accepted name: drimenol cyclase

Reaction: (2E,6E)-farnesyl diphosphate + H2O = drimenol + diphosphate

Other name(s): farnesyl pyrophosphate:drimenol cyclase

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphohydrolase (drimenol-forming)

References:

1. Banthorp, D.V., Brown, J.T. and Morris, G.S. Partial purification of farnesyl pyrophosphate:drimenol cyclase and geranylgerany pyrophosphate:sclareol cyclase, using cell culture as a source of material. Phytochemistry 31 (1992) 3391-3395.

[EC 3.1.7.7 created 2011]

EC 3.2.1.169

Accepted name: protein O-GlcNAcase

Reaction: (1) [protein]-3-O-(N-acetyl-β-D-glucosaminyl)-L-serine + H2O = [protein]-L-serine + N-acetyl-D-glucosamine
(2) [protein]-3-O-(N-acetyl-β-D-glucosaminyl)-L-theronine + H2O = [protein]-L-threonine + N-acetyl-D-glucosamine

Other name(s): OGA; glycoside hydrolase O-GlcNAcase; O-GlcNAcase; BtGH84; O-GlcNAc hydrolase

Systematic name: [protein]-3-O-(N-acetyl-β-D-glucosaminyl)-L-serine/threonine N-acetylglucosaminyl hydrolase

Comments: Within higher eukaryotes post-translational modification of protein serines/threonines with N-acetylglucosamine (O-GlcNAc) is dynamic, inducible and abundant, regulating many cellular processes by interfering with protein phosphorylation. EC 2.4.1.255 (protein O-GlcNAc transferase) transfers GlcNAc onto substrate proteins and EC 3.2.1.169 (protein O-GlcNAcase) cleaves GlcNAc from the modified proteins.

References:

1. Gao, Y., Wells, L., Comer, F.I., Parker, G.J. and Hart, G.W. Dynamic O-glycosylation of nuclear and cytosolic proteins: cloning and characterization of a neutral, cytosolic β-N-acetylglucosaminidase from human brain. J. Biol. Chem. 276 (2001) 9838-9845. [PMID: 11148210]

2. Wells, L., Gao, Y., Mahoney, J.A., Vosseller, K., Chen, C., Rosen, A. and Hart, G.W. Dynamic O-glycosylation of nuclear and cytosolic proteins: further characterization of the nucleocytoplasmic β-N-acetylglucosaminidase, O-GlcNAcase. J. Biol. Chem. 277 (2002) 1755-1761. [PMID: 11788610]

3. Cetinbas, N., Macauley, M.S., Stubbs, K.A., Drapala, R. and Vocadlo, D.J. Identification of Asp174 and Asp175 as the key catalytic residues of human O-GlcNAcase by functional analysis of site-directed mutants. Biochemistry 45 (2006) 3835-3844. [PMID: 16533067]

4. Dennis, R.J., Taylor, E.J., Macauley, M.S., Stubbs, K.A., Turkenburg, J.P., Hart, S.J., Black, G.N., Vocadlo, D.J. and Davies, G.J. Structure and mechanism of a bacterial β-glucosaminidase having O-GlcNAcase activity. Nat Struct Mol Biol 13 (2006) 365-371. [PMID: 16565725]

5. Kim, E.J., Kang, D.O., Love, D.C. and Hanover, J.A. Enzymatic characterization of O-GlcNAcase isoforms using a fluorogenic GlcNAc substrate. Carbohydr. Res. 341 (2006) 971-982. [PMID: 16584714]

6. Dong, D.L. and Hart, G.W. Purification and characterization of an O-GlcNAc selective N-acetyl-β-D-glucosaminidase from rat spleen cytosol. J. Biol. Chem. 269 (1994) 19321-19330. [PMID: 8034696]

[EC 3.2.1.169 created 2011]

*EC 4.1.99.5

Accepted name: octadecanal decarbonylase

Reaction: octadecanal = heptadecane + CO

Other name(s): decarbonylase; aldehyde decarbonylase

Systematic name: octadecanal alkane-lyase

Comments: Involved in the biosynthesis of alkanes. The enzyme from the cyanobacterium Nostoc punctiforme PCC 73102 is only active in vitro in the presence of ferredoxin, ferredoxin reductase and NADPH, and produces mostly C15 to C17 alkanes [2]. The enzyme from pea (Pisum sativum) produces alkanes of chain length C18 to C32 and is inhibited by metal-chelating agents [1]. The substrate for this enzyme is formed by EC 1.2.1.80, acyl-[acyl-carrier protein] reductase.

Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 94185-90-7

References:

1. Cheesbrough, T.M. and, K olattukudy, P.E. Alkane biosynthesis by decarbonylation of aldehydes catalyzed by a particulate preparation from Pisum sativum. Proc. Natl. Acad. Sci. USA 81 (1984) 6613-6617. [PMID: 6593720]

2. Schirmer, A., Rude, M.A., Li, X., Popova, E. and del Cardayre, S.B. Microbial biosynthesis of alkanes. Science 329 (2010) 559-562. [PMID: 20671186]

[EC 4.1.99.5 created 1989, modified 2011]

*EC 4.2.1.83

Accepted name: 4-oxalmesaconate hydratase

Reaction: 2-hydroxy-4-oxobutane-1,2,4-tricarboxylate = 2-hydroxy-4-carboxyhexa-2,4-dienedioate + H2O

Other name(s): 4-carboxy-2-oxohexenedioate hydratase; 4-carboxy-2-oxobutane-1,2,4-tricarboxylate 2,3-hydro-lyase; oxalmesaconate hydratase; γ-oxalmesaconate hydratase; 2-hydroxy-4-oxobutane-1,2,4-tricarboxylate 2,3-hydro-lyase; LigJ; GalB

Systematic name: 2-hydroxy-4-oxobutane-1,2,4-tricarboxylate 1,2-hydro-lyase (2-hydroxy-4-carboxyhexa-2,4-dienedioate-forming)

Comments: This enzyme participates in the degradation of protocatechuate (via the meta-cleavage pathway), syringate and gallate [1-3]. It accepts the enol-form of 4-oxalomesaconate, 2-hydroxy-4-carboxy-hexa-2,4-dienedioate [4].

Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 85204-95-1

References:

1. Maruyama, K. Enzymes responsible for degradation of 4-oxalmesaconic acid in Pseudomonas ochraceae. J. Biochem. 93 (1983) 567-574. [PMID: 6841354]

2. Maruyama, K. Purification and properties of γ-oxalomesaconate hydratase from Pseudomonas ochraceae grown with phthalate. Biochem. Biophys. Res. Commun. 128 (1985) 271-277. [PMID: 3985968]

3. Hara, H., Masai, E., Katayama, Y. and Fukuda, M. The 4-oxalomesaconate hydratase gene, involved in the protocatechuate 4,5-cleavage pathway, is essential to vanillate and syringate degradation in Sphingomonas paucimobilis SYK-6. J. Bacteriol. 182 (2000) 6950-6957. [PMID: 11092855]

4. Nogales, J., Canales, A., Jimenez-Barbero, J., Serra, B., Pingarron, J.M., Garcia, J.L. and Diaz, E. Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida. Mol. Microbiol. 79 (2011) 359-374. [PMID: 21219457]

[EC 4.2.1.83 created 1986, modified 2011]

EC 4.2.3.55

Accepted name: (S)-β-bisabolene synthase

Reaction: (2E,6E)-farnesyl diphosphate = (S)-β-bisabolene + diphosphate

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(S)-β-bisabolene-forming]

References:

1. Fujisawa, M., Harada, H., Kenmoku, H., Mizutani, S. and Misawa, N. Cloning and characterization of a novel gene that encodes (S)-β-bisabolene synthase from ginger, Zingiber officinale. Planta 232 (2010) 121-130. [PMID: 20229191]

[EC 4.2.3.55 created 2011]

EC 4.2.3.56

Accepted name: γ-humulene synthase

Reaction: (2E,6E)-farnesyl diphosphate = γ-humulene + diphosphate

Other name(s): humulene cyclase

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (γ-humulene-forming)

References:

1. Steele, C.L., Crock, J., Bohlmann, J. and Croteau, R. Sesquiterpene synthases from grand fir (Abies grandis). Comparison of constitutive and wound-induced activities, and cDNA isolation, characterization, and bacterial expression of δ-selinene synthase and γ-humulene synthase. J. Biol. Chem. 273 (1998) 2078-2089. [PMID: 9442047]

2. Little, D.B. and Croteau, R.B. Alteration of product formation by directed mutagenesis and truncation of the multiple-product sesquiterpene synthases δ-selinene synthase and γ-humulene synthase. Arch. Biochem. Biophys. 402 (2002) 120-135. [PMID: 12051690]

[EC 4.2.3.56 created 2011]

EC 4.2.3.57

Accepted name: β-caryophyllene synthase

Reaction: (2E,6E)-farnesyl diphosphate = β-caryophyllene + diphosphate

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (caryophyllene-forming)

References:

1. Cai, Y., Jia, J.W., Crock, J., Lin, Z.X., Chen, X.Y. and Croteau, R. A cDNA clone for β-caryophyllene synthase from Artemisia annua. Phytochemistry 61 (2002) 523-529. [PMID: 12409018]

[EC 4.2.3.57 created 2011]

EC 4.2.3.58

Accepted name: longifolene synthase

Reaction: (2E,6E)-farnesyl diphosphate = longifolene + diphosphate

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (longifolene-forming)

Comments: A well as 61% longifolene the enzyme gives 15% of α-longipinene, 6% longicyclene and traces of other sesquiterpenoids.

References:

1. Martin, D.M., Faldt, J. and Bohlmann, J. Functional characterization of nine Norway Spruce TPS genes and evolution of gymnosperm terpene synthases of the TPS-d subfamily. Plant Physiol. 135 (2004) 1908-1927. [PMID: 15310829]

[EC 4.2.3.58 created 2011]

EC 4.2.3.59

Accepted name: (E)-γ-bisabolene synthase

Reaction: (2E,6E)-farnesyl diphosphate = (E)-γ-bisabolene + diphosphate

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(E)-γ-bisabolene-forming]

References:

1. Huber, D.P.W., Philippe, R.N., Godard, K.-A., Sturrock, R.N. and Bohlmann, J. Characterization of four terpene synthase cDNAs from methyl jasmonate-induced Douglas-fir, Pseudotsuga menziesii. Phytochemistry 66 (2005) 1427-1439. [PMID: 15921711]

[EC 4.2.3.59 created 2011]

EC 4.2.3.60

Accepted name: germacrene C synthase

Reaction: (2E,6E)-farnesyl diphosphate = germacrene C + diphosphate

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (germacrene-C-forming)

References:

1. Colby, S.M., Crock, J., Dowdle-Rizzo, B., Lemaux, P.G. and Croteau, R. Germacrene C synthase from Lycopersicon esculentum cv. VFNT cherry tomato: cDNA isolation, characterization, and bacterial expression of the multiple product sesquiterpene cyclase. Proc. Natl. Acad. Sci. USA 95 (1998) 2216-2221. [PMID: 9482865]

[EC 4.2.3.60 created 2011]

*EC 5.4.99.12

Accepted name: tRNA pseudouridine38-40 synthase

Reaction: tRNA uridine38-40 = tRNA pseudouridine38-40

Other name(s): TruA; tRNA pseudouridine synthase I; PSUI; hisT (gene name)

Systematic name: tRNA-uridine38-40 uracil mutase

Comments: The uridylate residues at positions 38, 39 and 40 of nearly all tRNAs are isomerized to pseudouridine. TruA specifically modifies uridines at positions 38, 39, and/or 40 in the anticodon stem loop of tRNAs with highly divergent sequences and structures [1].

Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 61506-89-6

References:

1. Hur, S. and Stroud, R.M. How U38, 39, and 40 of many tRNAs become the targets for pseudouridylation by TruA. Mol. Cell 26 (2007) 189-203. [PMID: 17466622]

2. Huang, L., Pookanjanatavip, M., Gu, X. and Santi, D.V. A conserved aspartate of tRNA pseudouridine synthase is essential for activity and a probable nucleophilic catalyst. Biochemistry 37 (1998) 344-351. [PMID: 9425056]

3. Kammen, H.O., Marvel, C.C., Hardy, L. and Penhoet, E.E. Purification, structure, and properties of Escherichia coli tRNA pseudouridine synthase I. J. Biol. Chem. 263 (1988) 2255-2263. [PMID: 3276686]

4. Turnbough, C.L., Jr., Neill, R.J., Landsberg, R. and Ames, B.N. Pseudouridylation of tRNAs and its role in regulation in Salmonella typhimurium. J. Biol. Chem. 254 (1979) 5111-5119. [PMID: 376505]

5. Zhao, X. and Horne, D.A. The role of cysteine residues in the rearrangement of uridine to pseudouridine catalyzed by pseudouridine synthase I. J. Biol. Chem. 272 (1997) 1950-1955. [PMID: 8999885]

6. Foster, P.G., Huang, L., Santi, D.V. and Stroud, R.M. The structural basis for tRNA recognition and pseudouridine formation by pseudouridine synthase I. Nat. Struct. Biol. 7 (2000) 23-27. [PMID: 10625422]

7. Dong, X., Bessho, Y., Shibata, R., Nishimoto, M., Shirouzu, M., Kuramitsu, S. and Yokoyama, S. Crystal structure of tRNA pseudouridine synthase TruA from Thermus thermophilus HB8. RNA Biol 3 (2006) 115-122. [PMID: 17114947]

8. Arena, F., Ciliberto, G., Ciampi, S. and Cortese, R. Purification of pseudouridylate synthetase I from Salmonella typhimurium. Nucleic Acids Res. 5 (1978) 4523-4536. [PMID: 370771]

[EC 5.4.99.12 created 1990, modified 2011]

EC 5.4.99.19

Accepted name: 16S rRNA pseudouridine516 synthase

Reaction: 16S rRNA uridine516 = 16S rRNA pseudouridine516

Other name(s): 16S RNA pseudouridine516 synthase; 16S PsiI516 synthase; 16S RNA Ψ516 synthase; RNA pseudouridine synthase RsuA; RsuA; 16S RNA pseudouridine 516 synthase

Systematic name: 16S rRNA-uridine516 uracil mutase

Comments: The enzyme is specific for uridine516 in 16S rRNA. In vitro, the enzyme does not modify free 16S rRNA. The preferred substrate is a 5'-terminal fragment of 16S rRNA complexed with 30S ribosomal proteins [1].

References:

1. Wrzesinski, J., Bakin, A., Nurse, K., Lane, B.G. and Ofengand, J. Purification, cloning, and properties of the 16S RNA pseudouridine 516 synthase from Escherichia coli. Biochemistry 34 (1995) 8904-8913. [PMID: 7612632]

2. Conrad, J., Niu, L., Rudd, K., Lane, B.G. and Ofengand, J. 16S ribosomal RNA pseudouridine synthase RsuA of Escherichia coli: deletion, mutation of the conserved Asp102 residue, and sequence comparison among all other pseudouridine synthases. RNA 5 (1999) 751-763. [PMID: 10376875]

3. Sivaraman, J., Sauve, V., Larocque, R., Stura, E.A., Schrag, J.D., Cygler, M. and Matte, A. Structure of the 16S rRNA pseudouridine synthase RsuA bound to uracil and UMP. Nat. Struct. Biol. 9 (2002) 353-358. [PMID: 11953756]

[EC 5.4.99.19 created 2011]

EC 5.4.99.20

Accepted name: 23S rRNA pseudouridine2457 synthase

Reaction: 23S rRNA uridine2457 = 23S rRNA pseudouridine2457

Other name(s): RluE; YmfC

Systematic name: 23S rRNA-uridine2457 uracil mutase

Comments: The enzyme modifies uridine2457 in a stem of 23S RNA in Escherichia coli.

References:

1. Del Campo, M., Kaya, Y. and Ofengand, J. Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli. RNA 7 (2001) 1603-1615. [PMID: 11720289]

2. Pan, H., Ho, J.D., Stroud, R.M. and Finer-Moore, J. The crystal structure of E. coli rRNA pseudouridine synthase RluE. J. Mol. Biol. 367 (2007) 1459-1470. [PMID: 17320904]

[EC 5.4.99.20 created 2011]

EC 5.4.99.21

Accepted name: 23S rRNA pseudouridine2604 synthase

Reaction: 23S rRNA uridine2604 = 23S rRNA pseudouridine2604

Other name(s): RluF; YjbC

Systematic name: 23S rRNA-uridine2604 uracil mutase

Comments: The enzyme is not completely specific for uridine2604 and can, to a small extent, also react with uridine2605 [1].

References:

1. Del Campo, M., Kaya, Y. and Ofengand, J. Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli. RNA 7 (2001) 1603-1615. [PMID: 11720289]

2. Alian, A., DeGiovanni, A., Griner, S.L., Finer-Moore, J.S. and Stroud, R.M. Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome. J. Mol. Biol. 388 (2009) 785-800. [PMID: 19298824]

3. Sunita, S., Zhenxing, H., Swaathi, J., Cygler, M., Matte, A. and Sivaraman, J. Domain organization and crystal structure of the catalytic domain of E. coli RluF, a pseudouridine synthase that acts on 23S rRNA. J. Mol. Biol. 359 (2006) 998-1009. [PMID: 16712869]

[EC 5.4.99.21 created 2011]

EC 5.4.99.22

Accepted name: 23S rRNA pseudouridine2605 synthase

Reaction: 23S rRNA uridine2605 = 23S rRNA pseudouridine2605

Other name(s): RluB; YciL

Systematic name: 23S rRNA-uridine2605 uracil mutase

Comments: Pseudouridine synthase RluB converts uridine2605 of 23S rRNA to pseudouridine.

References:

1. Del Campo, M., Kaya, Y. and Ofengand, J. Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli. RNA 7 (2001) 1603-1615. [PMID: 11720289]

2. Jiang, M., Sullivan, S.M., Walker, A.K., Strahler, J.R., Andrews, P.C. and Maddock, J.R. Identification of novel Escherichia coli ribosome-associated proteins using isobaric tags and multidimensional protein identification techniques. J. Bacteriol. 189 (2007) 3434-3444. [PMID: 17337586]

[EC 5.4.99.22 created 2011]

EC 5.4.99.23

Accepted name: 23S rRNA pseudouridine1911/1915/1917 synthase

Reaction: 23S rRNA uridine1911/uridine1915/uridine1917 = 23S rRNA pseudouridine1911/pseudouridine1915/pseudouridine1917

Other name(s): RluD; pseudouridine synthase RluD

Systematic name: 23S rRNA-uridine1911/1915/1917 uracil mutase

Comments: Pseudouridine synthase RluD converts uridines at positions 1911, 1915, and 1917 of 23S rRNA to pseudouridines. These nucleotides are located in the functionally important helix-loop 69 of 23S rRNA [1].

References:

1. Leppik, M., Peil, L., Kipper, K., Liiv, A. and Remme, J. Substrate specificity of the pseudouridine synthase RluD in Escherichia coli. FEBS J. 274 (2007) 5759-5766. [PMID: 17937767]

2. Ejby, M., Sorensen, M.A. and Pedersen, S. Pseudouridylation of helix 69 of 23S rRNA is necessary for an effective translation termination. Proc. Natl. Acad. Sci. USA 104 (2007) 19410-19415. [PMID: 18032607]

3. Sivaraman, J., Iannuzzi, P., Cygler, M. and Matte, A. Crystal structure of the RluD pseudouridine synthase catalytic module, an enzyme that modifies 23S rRNA and is essential for normal cell growth of Escherichia coli. J. Mol. Biol. 335 (2004) 87-101. [PMID: 14659742]

4. Wrzesinski, J., Bakin, A., Ofengand, J. and Lane, B.G. Isolation and properties of Escherichia coli 23S-RNA pseudouridine 1911, 1915, 1917 synthase (RluD). IUBMB Life 50 (2000) 33-37. [PMID: 11087118]

[EC 5.4.99.23 created 2011]

EC 5.4.99.24

Accepted name: 23S rRNA pseudouridine955/2504/2580 synthase

Reaction: 23S rRNA uridine955/uridine2504/uridine2580 = 23S rRNA pseudouridine955/pseudouridine2504/pseudouridine2580

Other name(s): RluC; pseudouridine synthase RluC

Systematic name: 23S rRNA-uridine955/2504/2580 uracil mutase

Comments: The enzyme converts uridines at position 955, 2504 and 2580 of 23S rRNA to pseudouridines.

References:

1. Jiang, M., Sullivan, S.M., Walker, A.K., Strahler, J.R., Andrews, P.C. and Maddock, J.R. Identification of novel Escherichia coli ribosome-associated proteins using isobaric tags and multidimensional protein identification techniques. J. Bacteriol. 189 (2007) 3434-3444. [PMID: 17337586]

2. Conrad, J., Sun, D., Englund, N. and Ofengand, J. The rluC gene of Escherichia coli codes for a pseudouridine synthase that is solely responsible for synthesis of pseudouridine at positions 955, 2504, and 2580 in 23 S ribosomal RNA. J. Biol. Chem. 273 (1998) 18562-18566. [PMID: 9660827]

3. Corollo, D., Blair-Johnson, M., Conrad, J., Fiedler, T., Sun, D., Wang, L., Ofengand, J. and Fenna, R. Crystallization and characterization of a fragment of pseudouridine synthase RluC from Escherichia coli. Acta Crystallogr. D Biol. Crystallogr. 55 (1999) 302-304. [PMID: 10089432]

4. Toh, S.M. and Mankin, A.S. An indigenous posttranscriptional modification in the ribosomal peptidyl transferase center confers resistance to an array of protein synthesis inhibitors. J. Mol. Biol. 380 (2008) 593-597. [PMID: 18554609]

[EC 5.4.99.24 created 2011]

EC 5.4.99.25

Accepted name: tRNA pseudouridine55 synthase

Reaction: tRNA uridine55 = tRNA pseudouridine55

Other name(s): TruB; aCbf5; Pus4; YNL292w (gene name); Ψ55 tRNA pseudouridine synthase; tRNA:Ψ55-synthase; tRNA pseudouridine 55 synthase; tRNA:pseudouridine-55 synthase; Ψ55 synthase; tRNA Ψ55 synthase; tRNA:Ψ55 synthase

Systematic name: tRNA-uridine55 uracil mutase

Comments: Pseudouridine synthase TruB from Escherichia coli specifically modifies uridine55 in tRNA molecules [1].

References:

1. Nurse, K., Wrzesinski, J., Bakin, A., Lane, B.G. and Ofengand, J. Purification, cloning, and properties of the tRNA psi 55 synthase from Escherichia coli. RNA 1 (1995) 102-112. [PMID: 7489483]

2. Becker, H.F., Motorin, Y., Planta, R.J. and Grosjean, H. The yeast gene YNL292w encodes a pseudouridine synthase (Pus4) catalyzing the formation of psi55 in both mitochondrial and cytoplasmic tRNAs. Nucleic Acids Res. 25 (1997) 4493-4499. [PMID: 9358157]

3. Pienkowska, J., Wrzesinski, J. and Szweykowska-Kulinska, Z. A cell-free yellow lupin extract containing activities of pseudouridine 35 and 55 synthases. Acta Biochim. Pol. 45 (1998) 745-754. [PMID: 9918501]

4. Chaudhuri, B.N., Chan, S., Perry, L.J. and Yeates, T.O. Crystal structure of the apo forms of Ψ55 tRNA pseudouridine synthase from Mycobacterium tuberculosis: a hinge at the base of the catalytic cleft. J. Biol. Chem. 279 (2004) 24585-24591. [PMID: 15028724]

5. Hoang, C., Hamilton, C.S., Mueller, E.G. and Ferre-D'Amare, A.R. Precursor complex structure of pseudouridine synthase TruB suggests coupling of active site perturbations to an RNA-sequestering peripheral protein domain. Protein Sci. 14 (2005) 2201-2206. [PMID: 15987897]

[EC 5.4.99.25 created 2011]

EC 5.4.99.26

Accepted name: tRNA pseudouridine65 synthase

Reaction: tRNA uridine65 = tRNA pseudouridine65

Other name(s): TruC; YqcB

Systematic name: tRNA-uridine65 uracil mutase

Comments: TruC specifically modifies uridines at positions 65 in tRNA.

References:

1. Del Campo, M., Kaya, Y. and Ofengand, J. Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli. RNA 7 (2001) 1603-1615. [PMID: 11720289]

[EC 5.4.99.26 created 2011]

EC 5.4.99.27

Accepted name: tRNA pseudouridine13 synthase

Reaction: tRNA uridine13 = tRNA pseudouridine13

Other name(s): TruD; YgbO; tRNA PSI13 synthase; RNA:PSI-synthase Pus7p; Pus7p; RNA:pseudouridine-synthase Pus7p; Pus7 protein

Systematic name: tRNA-uridine13 uracil mutase

Comments: Pseudouridine synthase TruD from Escherichia coli specifically acts on uridine13 in tRNA [2,3]. The Pus7 protein from Saccharomyces cerevisiae is a multisite-multisubstrate pseudouridine synthase that is able to modify uridine13 in several yeast tRNAs, uridine35 in the pre-tRNATyr, uridine35 in U2 small nuclear RNA, and uridine50 in 5S rRNA [5].

References:

1. Ericsson, U.B., Nordlund, P. and Hallberg, B.M. X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold. FEBS Lett. 565 (2004) 59-64. [PMID: 15135053]

2. Chan, C.M. and Huang, R.H. Enzymatic characterization and mutational studies of TruD—the fifth family of pseudouridine synthases. Arch. Biochem. Biophys. 489 (2009) 15-19. [PMID: 19664587]

3. Kaya, Y. and Ofengand, J. A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya. RNA 9 (2003) 711-721. [PMID: 12756329]

4. Behm-Ansmant, I., Urban, A., Ma, X., Yu, Y.T., Motorin, Y. and Branlant, C. The Saccharomyces cerevisiae U2 snRNA:pseudouridine-synthase Pus7p is a novel multisite-multisubstrate RNA:Ψ-synthase also acting on tRNAs. RNA 9 (2003) 1371-1382. [PMID: 14561887]

5. Urban, A., Behm-Ansmant, I., Branlant, C. and Motorin, Y. RNA sequence and two-dimensional structure features required for efficient substrate modification by the Saccharomyces cerevisiae RNA:Ψ-synthase Pus7p. J. Biol. Chem. 284 (2009) 5845-5858. [PMID: 19114708]

[EC 5.4.99.27 created 2011]

EC 5.4.99.28

Accepted name: tRNA pseudouridine32 synthase

Reaction: tRNA uridine32 = tRNA pseudouridine32

Other name(s): RluA (ambiguous); pseudouridine synthase RluA (ambiguous)

Systematic name: tRNA-uridine32 uracil mutase

Comments: The dual-specificity enzyme also catalyses the formation of pseudouridine746 in 23S rRNA [5]. cf. EC 5.4.99.29 (23S rRNA pseudouridine746 synthase).

References:

1. Hoang, C., Chen, J., Vizthum, C.A., Kandel, J.M., Hamilton, C.S., Mueller, E.G. and Ferre-D'Amare, A.R. Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure. Mol. Cell 24 (2006) 535-545. [PMID: 17188032]

2. Spedaliere, C.J., Hamilton, C.S. and Mueller, E.G. Functional importance of motif I of pseudouridine synthases: mutagenesis of aligned lysine and proline residues. Biochemistry 39 (2000) 9459-9465. [PMID: 10924141]

3. Raychaudhuri, S., Niu, L., Conrad, J., Lane, B.G. and Ofengand, J. Functional effect of deletion and mutation of the Escherichia coli ribosomal RNA and tRNA pseudouridine synthase RluA. J. Biol. Chem. 274 (1999) 18880-18886. [PMID: 10383384]

4. Ramamurthy, V., Swann, S.L., Spedaliere, C.J. and Mueller, E.G. Role of cysteine residues in pseudouridine synthases of different families. Biochemistry 38 (1999) 13106-13111. [PMID: 10529181]

5. Wrzesinski, J., Nurse, K., Bakin, A., Lane, B.G. and Ofengand, J. A dual-specificity pseudouridine synthase: an Escherichia coli synthase purified and cloned on the basis of its specificity for psi746 in 23S RNA is also specific for Ψ32 in tRNA(phe). RNA 1 (1995) 437-448. [PMID: 7493321]

[EC 5.4.99.28 created 2011]

EC 5.4.99.29

Accepted name: 23S rRNA pseudouridine746 synthase

Reaction: 23S rRNA uridine746 = 23S rRNA pseudouridine746

Other name(s): RluA (ambiguous); 23S RNA PSI746 synthase; 23S rRNA pseudouridine synthase; pseudouridine synthase RluA (ambiguous)

Systematic name: 23S rRNA-uridine746 uracil mutase

Comments: RluA is the sole protein responsible for the in vivo formation of 23S RNA pseudouridine746 [2]. The dual-specificity enzyme also catalyses the formation of uridine32 in tRNA [3]. cf. EC 5.4.99.28 (tRNA pseudouridine32 synthase).

References:

1. Hoang, C., Chen, J., Vizthum, C.A., Kandel, J.M., Hamilton, C.S., Mueller, E.G. and Ferre-D'Amare, A.R. Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure. Mol. Cell 24 (2006) 535-545. [PMID: 17188032]

2. Raychaudhuri, S., Niu, L., Conrad, J., Lane, B.G. and Ofengand, J. Functional effect of deletion and mutation of the Escherichia coli ribosomal RNA and tRNA pseudouridine synthase RluA. J. Biol. Chem. 274 (1999) 18880-18886. [PMID: 10383384]

3. Wrzesinski, J., Nurse, K., Bakin, A., Lane, B.G. and Ofengand, J. A dual-specificity pseudouridine synthase: an Escherichia coli synthase purified and cloned on the basis of its specificity for psi746 in 23S RNA is also specific for Ψ32 in tRNA(phe). RNA 1 (1995) 437-448. [PMID: 7493321]

[EC 5.4.99.29 created 2011]

EC 5.4.99.30

Accepted name: UDP-arabinopyranose mutase

Reaction: UDP-β-L-arabinofuranose = UDP-β-L-arabinopyranose

Other name(s): Os03g40270 protein; UAM1; UAM3; RGP1; RGP3; OsUAM1; OsUAM2; Os03g0599800 protein; Os07g41360 protein

Systematic name: UDP-arabinopyranose pyranomutase

Comments: The reaction is reversible and at thermodynamic equilibrium the pyranose form is favored over the furanose form (90:10) [1].

References:

1. Konishi, T., Takeda, T., Miyazaki, Y., Ohnishi-Kameyama, M., Hayashi, T., O'Neill, M.A. and Ishii, T. A plant mutase that interconverts UDP-arabinofuranose and UDP-arabinopyranose. Glycobiology 17 (2007) 345-354. [PMID: 17182701]

2. Konishi, T., Ohnishi-Kameyama, M., Funane, K., Miyazaki, Y., Konishi, T. and Ishii, T. An arginyl residue in rice UDP-arabinopyranose mutase is required for catalytic activity and autoglycosylation. Carbohydr. Res. 345 (2010) 787-791. [PMID: 20149347]

3. Konishi, T., Miyazaki, Y., Yamakawa, S., Iwai, H., Satoh, S. and Ishii, T. Purification and biochemical characterization of recombinant rice UDP-arabinopyranose mutase generated in insect cells. Biosci. Biotechnol. Biochem. 74 (2010) 191-194. [PMID: 20057139]

[EC 5.4.99.30 created 2011]

EC 5.5.1.17

Accepted name: (S)-β-macrocarpene synthase

Reaction: (S)-β-bisabolene = (S)-β-macrocarpene

Other name(s): TPS6; TPS11

Systematic name: (S)-β-macrocarpene lyase (decyclizing)

Comment:The synthesis of (S)-β-macrocarpene from (2E,6E)-farnesyl diphosphate proceeds in two steps. The first step is the cyclization to (S)-β-bisabolene (cf. EC 4.2.3.55, (S)-β-bisabolene synthase). The second step is the isomerization to (S)-β-macrocarpene. References:

1. Kollner, T.G., Schnee, C., Li, S., Svatos, A., Schneider, B., Gershenzon, J. and Degenhardt, J. Protonation of a neutral (S)-β-bisabolene intermediate is involved in (S)-β-macrocarpene formation by the maize sesquiterpene synthases TPS6 and TPS11. J. Biol. Chem. 283 (2008) 20779-20788. [PMID: 18524777]

[EC 5.5.1.17 created 2011]


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