Proposed Changes to the Enzyme List

Accepted name: abieta-7,13-dien-18-al dehydrogenase

Other name(s): cholesterol- O₂ oxidoreductase; 3β-hydroxy steroid oxidoreductase; 3β-hydroxysteroid:oxygen oxidoreductase

Systematic name: cholesterol:oxygen oxidoreductase

Comments: Contains flavin adenine dinucleotide (FAD). Cholesterol oxidases are secreted bacterial bifunctional enzymes that catalyse the first two steps in the degradation of cholesterol. The enzyme catalyses the oxidation of the 3β-hydroxyl group to a keto group, and the isomerization of the double bond in the oxidized steroid ring system from the Δ⁵ position to Δ⁶ position (cf. EC 5.3.3.1, steroid Δ-isomerase).

Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 9028-76-6

References:

1. Richmond, W. Preparation and properties of a cholesterol oxidase from Nocardia sp. and its application to the enzymatic assay of total cholesterol in serum. Clin. Chem. 19 (1973) 1350-1356. [PMID: 4757363]

2. Stadtman, T.C., Cherkes, A. and Anfinsen, C.B. Studies on the microbiological degradation of cholesterol. J. Biol. Chem. 206 (1954) 511-523. [PMID: 13143010]

3. MacLachlan, J., Wotherspoon, A.T., Ansell, R.O. and Brooks, C.J. Cholesterol oxidase: sources, physical properties and analytical applications. J. Steroid Biochem. Mol. Biol. 72 (2000) 169-195. [PMID: 10822008]

4. Vrielink, A. Cholesterol oxidase: structure and function. Subcell. Biochem. 51 (2010) 137-158. [PMID: 20213543]

[EC 1.1.3.6 created 1961, modified 1982, modified 2012]

*EC 1.2.1.74

Reaction: abieta-7,13-diene-18-al + H₂O + NAD⁺ = abieta-7,13-diene-18-oate + NADH + H⁺

Accepted name: formaldehyde dismutase

Glossary: abieta-7,13-dien-18-al = (1R,4aR,4bR,10aR)-7-isopropyl-1,4a-dimethyl-1,2,3,4,4a,4b,5,6,10,10a-decahydrophenanthrene-1-carbaldehyde
abieta-7,13-diene-18-oate = (1R,4aR,4bR,10aR)-7-isopropyl-1,4a-dimethyl-1,2,3,4,4a,4b,5,6,10,10a-decahydrophenanthrene-1-carboxylate

Other name(s): abietadienal dehydrogenase (ambiguous)

Systematic name: abieta-7,13-dien-18-al:NAD⁺ oxidoreductase

Comments: Abietic acid is the principle component of conifer resin. This enzyme catalyses the last step of the pathway of abietic acid biosynthesis in Abies grandis (grand fir). The activity has been demonstrated in cell-free stem extracts of A. grandis, was present in the cytoplasm, and required NAD⁺ as cofactor [1]. The enzyme is expressed constitutively at a high level, and is not inducible by wounding of the plant tissue [2].

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

References:

1. Funk, C. and Croteau, R. Diterpenoid resin acid biosynthesis in conifers: characterization of two cytochrome P450-dependent monooxygenases and an aldehyde dehydrogenase involved in abietic acid biosynthesis. Arch. Biochem. Biophys. 308 (1994) 258-266. [PMID: 8311462]

2. Funk, C., Lewinsohn, E., Vogel, B.S., Steele, C.L. and Croteau, R. Regulation of oleoresinosis in grand fir (Abies grandis) (coordinate induction of monoterpene and diterpene cyclases and two cytochrome P450-dependent diterpenoid hydroxylases by stem wounding). Plant Physiol. 106 (1994) 999-1005. [PMID: 12232380]

[EC 1.2.1.74 created 2009, modified 2012]

*EC 1.2.99.4

Reaction: 2 formaldehyde + H₂O = formate + methanol

Other name(s): aldehyde dismutase; cannizzanase; nicotinoprotein aldehyde dismutase

Systematic name: formaldehyde:formaldehyde oxidoreductase

Comments: The enzyme contains a tightly but noncovalently bound NADP(H) cofactor, as well as Zn²⁺ and Mg²⁺. The enzyme from Mycobacterium sp. DSM 3803 also catalyses the reactions of EC 1.1.99.36, NDMA-dependent alcohol dehydrogenase and EC 1.1.99.37, NDMA-dependent methanol dehydrogenase [3]. Formaldehyde and acetaldehyde can act as donors; formaldehyde, acetaldehyde and propanal can act as acceptors [1,2].

Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 85204-94-0

References:

1. Kato, N., Shirakawa, K., Kobayashi, H. and Sakazawa, C. The dismutation of aldehydes by a bacterial enzyme. Agric. Biol. Chem. 47 (1983) 39-46.

2. Kato, N., Yamagami, T., Shimao, M. and Sakazawa, C. Formaldehyde dismutase, a novel NAD-binding oxidoreductase from Pseudomonas putida F61. Eur. J. Biochem. 156 (1986) 59-64. [PMID: 3514215]

3. Park, H., Lee, H., Ro, Y.T. and Kim, Y.M. Identification and functional characterization of a gene for the methanol : N,N'-dimethyl-4-nitrosoaniline oxidoreductase from Mycobacterium sp. strain JC1 (DSM 3803). Microbiology 156 (2010) 463-471. [PMID: 19875438]

[EC 1.2.99.4 created 1986, modified 2012]

*EC 1.4.1.13

Accepted name: glutamate synthase (NADPH)

Reaction: 2 L-glutamate + NADP⁺ = L-glutamine + 2-oxoglutarate + NADPH + H⁺ (overall reaction)
(1a) L-glutamate + NH₃ = L-glutamine + H₂O
(1b) L-glutamate + NADP⁺ + H₂O = NH₃ + 2-oxoglutarate + NADPH + H⁺

Other name(s): glutamate (reduced nicotinamide adenine dinucleotide phosphate) synthase; L-glutamate synthase; L-glutamate synthetase; glutamate synthetase (NADP); NADPH-dependent glutamate synthase; glutamine-ketoglutaric aminotransferase; NADPH-glutamate synthase; NADPH-linked glutamate synthase; glutamine amide-2-oxoglutarate aminotransferase (oxidoreductase, NADP); L-glutamine:2-oxoglutarate aminotransferase, NADPH oxidizing; GOGAT

Systematic name: L-glutamate:NADP⁺ oxidoreductase (transaminating)

Comments: Binds FMN, FAD, 2 4Fe-4S clusters and 1 3Fe-4S cluster. The reaction takes place in the opposite direction. The protein is composed of two subunits, α and β. The α subunit is composed of two domains, one hydrolysing L-glutamine to NH₃ and L-glutamate (cf. EC 3.5.1.2, glutaminase), the other combining the produced NH₃ with 2-oxoglutarate to produce a second molecule of L-glutamate (cf. EC 1.4.1.4, glutamate dehydrogenase [NADP⁺]). The β subunit transfers electrons to the cosubstrate. The NH₃ is channeled through a 31 Å channel in the active protein. In the absence of the β subunit, coupling between the two domains of the α subunit is compromised and some ammonium can be produced. In the intact αβ complex, ammonia production only takes place as part of the overall reaction.

Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 37213-53-9

References:

1. Miller, R.E. and Stadtman, E.R. Glutamate synthase from Escherichia coli. An iron-sulfide flavoprotein. J. Biol. Chem. 247 (1972) 7407-7419. [PMID: 4565085]

2. Tempest, D.W., Meers, J.L. and Brown, C.M. Synthesis of glutamate in Aerobacter aerogenes by a hitherto unknown route. Biochem. J. 117 (1970) 405-407. [PMID: 5420057]

3. Vanoni, M.A. and Curti, B. Glutamate synthase: a complex iron-sulfur flavoprotein. Cell. Mol. Life Sci. 55 (1999) 617-638. [PMID: 10357231]

4. Ravasio, S., Curti, B. and Vanoni, M.A. Determination of the midpoint potential of the FAD and FMN flavin cofactors and of the 3Fe-4S cluster of glutamate synthase. Biochemistry 40 (2001) 5533-5541. [PMID: 11331018]

[EC 1.4.1.13 created 1972 as EC 2.6.1.53, transferred 1976 to EC 1.4.1.13, modified 2001, modified 2012]

*EC 1.4.7.1

Accepted name: glutamate synthase (ferredoxin)

Reaction: 2 L-glutamate + 2 oxidized ferredoxin = L-glutamine + 2-oxoglutarate + 2 reduced ferredoxin + 2 H⁺ (overall reaction)
(1a) L-glutamate + NH₃ = L-glutamine + H₂O
(1b) L-glutamate + 2 oxidized ferredoxin + H₂O = NH₃ + 2-oxoglutarate + 2 reduced ferredoxin + 2 H⁺

Other name(s): ferredoxin-dependent glutamate synthase; ferredoxin-glutamate synthase; glutamate synthase (ferredoxin-dependent)

Systematic name: L-glutamate:ferredoxin oxidoreductase (transaminating)

Comments: Binds a 3Fe-4S cluster as well as FAD and FMN. The protein is composed of two domains, one hydrolysing L-glutamine to NH₃ and L-glutamate (cf. EC 3.5.1.2, glutaminase), the other combining the produced NH₃ with 2-oxoglutarate to produce a second molecule of L-glutamate. The NH₃ is channeled through a 24 Å channel in the active protein. No hydrolysis of glutamine takes place without ferredoxin and 2-oxoglutarate being bound to the protein [5,6].

Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 62213-56-3

References:

1. Galván, F., Márquez, A.J. and Vega, J.M. Purification and molecular properties of ferredoxin-glutamate synthase from Chlamydomonas reinhardii. Planta 162 (1984) 180-187.

2. Lea, P.J. and Miflin, B.J. Alternative route for nitrogen assimilation in higher plants. Nature (Lond.) 251 (1974) 614-616. [PMID: 4423889]

3. Ravasio, S., Dossena, L., Martin-Figueroa, E., Florencio, F.J., Mattevi, A., Morandi, P., Curti, B. and Vanoni, M.A. Properties of the recombinant ferredoxin-dependent glutamate synthase of Synechocystis PCC6803. Comparison with the Azospirillum brasilense NADPH-dependent enzyme and its isolated α subunit. Biochemistry 41 (2002) 8120-8133. [PMID: 12069605]

4. Navarro, F., Martin-Figueroa, E., Candau, P. and Florencio, F.J. Ferredoxin-dependent iron-sulfur flavoprotein glutamate synthase (GlsF) from the cyanobacterium Synechocystis sp. PCC 6803: expression and assembly in Escherichia coli. Arch. Biochem. Biophys. 379 (2000) 267-276. [PMID: 10898944]

5. van den Heuvel, R.H., Ferrari, D., Bossi, R.T., Ravasio, S., Curti, B., Vanoni, M.A., Florencio, F.J. and Mattevi, A. Structural studies on the synchronization of catalytic centers in glutamate synthase. J. Biol. Chem. 277 (2002) 24579-24583. [PMID: 11967268]

6. van den Heuvel, R.H., Svergun, D.I., Petoukhov, M.V., Coda, A., Curti, B., Ravasio, S., Vanoni, M.A. and Mattevi, A. The active conformation of glutamate synthase and its binding to ferredoxin. J. Mol. Biol. 330 (2003) 113-128. [PMID: 12818206]

[EC 1.4.7.1 created 1976, modified 2012]

EC 1.5.8.3

Accepted name: sarcosine dehydrogenase

Reaction: sarcosine + H₂O + electron-transfer flavoprotein = glycine + formaldehyde + reduced electron-transfer flavoprotein

Other name(s): sarcosine N-demethylase; monomethylglycine dehydrogenase; sarcosine:(acceptor) oxidoreductase (demethylating)

Systematic name: sarcosine:electron-transfer flavoprotein oxidoreductase (demethylating)

Comments: A flavoprotein (FMN). Tetrahydrofolate is also a substrate, being converted to N⁵,N¹⁰-methylenetetrahydrofolate.

1. Hoskins, D.D. and MacKenzie, C.G. Solubilization and electron transfer flavoprotein requirement of mitochondrial sarcosine dehydrogenase and dimethylglycine dehydrogenase. J. Biol. Chem. 236 (1961) 177-183. [PMID: 13716069]

2. Frisell, W.R. and MacKenzie, C.G. Separation and purification of sarcosine dehydrogenase and dimethylglycine dehydrogenase. J. Biol. Chem. 237 (1962) 94-98. [PMID: 13895406]

3. Steenkamp, D.J. and Husain, M. The effect of tetrahydrofolate on the reduction of electron transfer flavoprotein by sarcosine and dimethylglycine dehydrogenases. Biochem. J. 203 (1982) 707-715. [PMID: 6180732]

[EC 1.5.8.3 created 1972 as EC 1.5.99.1, transferred 2012 to EC 1.5.8.3]

EC 1.5.8.4

Accepted name: dimethylglycine dehydrogenase

Reaction: N,N-dimethylglycine + electron-transfer flavoprotein + H₂O = sarcosine + formaldehyde + reduced electron-transfer flavoprotein

Other name(s): N,N-dimethylglycine oxidase; N,N-dimethylglycine:(acceptor) oxidoreductase (demethylating); Me2GlyDH

Systematic name: N,N-dimethylglycine:electron-transfer flavoprotein oxidoreductase (demethylating)

Comments: A flavoprotein, containing a histidyl(N³)-(8α)FAD linkage

1. Frisell, W.R. and MacKenzie, C.G. Separation and purification of sarcosine dehydrogenase and dimethylglycine dehydrogenase. J. Biol. Chem. 237 (1962) 94-98. [PMID: 13895406]

2. Hoskins, D.D. and MacKenzie, C.G. Solubilization and electron transfer flavoprotein requirement of mitochondrial sarcosine dehydrogenase and dimethylglycine dehydrogenase. J. Biol. Chem. 236 (1961) 177-183. [PMID: 13716069]

3. Brizio, C., Brandsch, R., Bufano, D., Pochini, L., Indiveri, C. and Barile, M. Over-expression in Escherichia coli, functional characterization and refolding of rat dimethylglycine dehydrogenase. Protein Expr. Purif. 37 (2004) 434-442. [PMID: 15358367]

4. Brizio, C., Brandsch, R., Douka, M., Wait, R. and Barile, M. The purified recombinant precursor of rat mitochondrial dimethylglycine dehydrogenase binds FAD via an autocatalytic reaction. Int. J. Biol. Macromol. 42 (2008) 455-462. [PMID: 18423846]

[EC 1.5.8.4 created 1972 as EC 1.5.99.2, transferred 2012 to EC 1.5.8.4]

[EC 1.5.99.1 Transferred entry: sarcosine dehydrogenase. Now EC 1.5.8.3, sarcosine dehydrogenase (EC 1.5.99.1 created 1972, deleted 2012)]

[EC 1.5.99.2 Transferred entry: dimethylglycine dehydrogenase. Now EC 1.5.8.4, dimethylglycine dehydrogenase (EC 1.5.99.2 created 1972, deleted 2012)]

[EC 1.13.11.13 Deleted entry: ascorbate 2,3-dioxygenase. The activity is the sum of several enzymatic and spontaneous reactions (EC 1.13.11.13 created 1972, deleted 2012)]

*EC 1.14.13.108

Accepted name: abieta-7,13-diene hydroxylase

Reaction: abieta-7,13-diene + NADPH + H⁺ + O₂ = abieta-7,13-dien-18-ol + NADP⁺ + H₂O

Accepted name: abieta-7,13-dien-18-ol hydroxylase

Glossary: abieta-7,13-diene = (4aS,4bR,10aS)-7-isopropyl-1,1,4a-trimethyl-1,2,3,4,4a,4b,5,6,10,10a-decahydrophenanthrene
abieta-7,13-dien-18-ol = ((1R,4aR,4bR,10aR)-7-isopropyl-1,4a-dimethyl-1,2,3,4,4a,4b,5,6,10,10a-decahydrophenanthren-1-yl)methanol

Other name(s): abietadiene hydroxylase (ambiguous)

Systematic name: abieta-7,13-diene,NADPH:oxygen oxidoreductase (18-hydroxylating)

Comments: A heme-thiolate protein (P-450). This enzyme catalyses a step in the pathway of abietic acid biosynthesis. The activity has been demonstrated in cell-free stem extracts of Abies grandis (grand fir) and Pinus contorta (lodgepole pine). The enzyme is localized in the microsomal fraction and requires both oxygen and NADPH. Inhibition by carbon monoxide and several substituted N-heterocyclic inhibitors suggests that the enzyme is a cytochrome P-450-dependent monooxygenase [1]. Activity is induced by wounding of the plant tissue [2].

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

References:

[EC 1.14.13.108 created 2009, modified 2012]

*EC 1.14.13.109

Reaction: abieta-7,13-dien-18-ol + NADPH + H⁺ + O₂ = abieta-7,13-dien-18-al + NADP⁺ + 2 H₂O (overall reaction)
(1a) abieta-7,13-dien-18-ol + NADPH + H⁺ + O₂ = abieta-7,13-dien-18,18-diol + + NADP⁺ + H₂O
(1b) abieta-7,13-dien-18,18-diol = abieta-7,13-dien-18-al + H₂O (spontaneous)

Accepted name: indole-2-monooxygenase

Glossary: abieta-7,13-dien-18-ol = ((1R,4aR,4bR,10aR)-7-isopropyl-1,4a-dimethyl-1,2,3,4,4a,4b,5,6,10,10a-decahydrophenanthren-1-yl)methanol
abieta-7,13-dien-18-al = (1R,4aR,4bR,10aR)-7-isopropyl-1,4a-dimethyl-1,2,3,4,4a,4b,5,6,10,10a-decahydrophenanthrene-1-carbaldehyde

Other name(s): CYP720B1; PtAO; abietadienol hydroxylase (ambiguous)

Systematic name: abieta-7,13-dien-18-ol,NADPH:oxygen oxidoreductase (18-hydroxylating)

Comments: A heme-thiolate protein (P-450). This enzyme catalyses a step in the pathway of abietic acid biosynthesis. The activity has been demonstrated in cell-free stem extracts of Abies grandis (grand fir) and Pinus contorta (lodgepole pine) [1], and the gene encoding the enzyme has been identified in Pinus taeda (loblolly pine) [3]. The recombinant enzyme catalyses the oxidation of multiple diterpene alcohol and aldehydes, including levopimaradienol, isopimara-7,15-dienol, isopimara-7,15-dienal, dehydroabietadienol and dehydroabietadienal. It is not able to oxidize abietadiene.

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

References:

3. Ro, D.K., Arimura, G., Lau, S.Y., Piers, E. and Bohlmann, J. Loblolly pine abietadienol/abietadienal oxidase PtAO (CYP720B1) is a multifunctional, multisubstrate cytochrome P450 monooxygenase. Proc. Natl. Acad. Sci. USA 102 (2005) 8060-8065. [PMID: 15911762]

[EC 1.14.13.109 created 2009, modified 2012]

EC 1.14.13.137

Reaction: indole + NAD(P)H + H⁺ + O₂ = indolin-2-one + NAD(P)⁺ + H₂O

Accepted name: indolin-2-one monooxygenase

Other name(s): BX2 (gene name); CYP71C4 (gene name)

Systematic name: indole,NAD(P)H:oxygen oxidoreductase (2-hydroxylating)

Comments: The enzyme is involved in the biosynthesis of protective and allelophatic benzoxazinoids in some plants, most commonly from the family of Poaceae (grasses). It is a member of the cytochrome P₄₅₀ dependent monooxygenases.

References:

1. Frey, M., Chomet, P., Glawischnig, E., Stettner, C., Grün, S., Winklmair, A., Eisenreich, W., Bacher, A., Meeley, R.B., Briggs, S.P., Simcox, K. and Gierl, A. Analysis of a chemical plant defense mechanism in grasses. Science 277 (1997) 696-699. [PMID: 9235894]

2. Glawischnig, E., Grun, S., Frey, M. and Gierl, A. Cytochrome P450 monooxygenases of DIBOA biosynthesis: specificity and conservation among grasses. Phytochemistry 50 (1999) 925-930. [PMID: 10385992]

[EC 1.14.13.137 created 2012]

EC 1.14.13.138

Reaction: indolin-2-one + NAD(P)H + H⁺ + O₂ = 3-hydroxyindolin-2-one + NAD(P)⁺ + H₂O

Accepted name: 3-hydroxyindolin-2-one monooxygenase

Other name(s): BX3 (gene name); CYP71C2 (gene name)

Systematic name: indolin-2-one,NAD(P)H:oxygen oxidoreductase (3-hydroxylating)

References:

[EC 1.14.13.138 created 2012]

EC 1.14.13.139

Reaction: 3-hydroxyindolin-2-one + NAD(P)H + H⁺ + O₂ = 2-hydroxy-2H-1,4-benzoxazin-3(4H)-one + NAD(P)⁺ + H₂O

Accepted name: 2-hydroxy-1,4-benzoxazin-3-one monooxygenase

Glossary: 2-hydroxy-2H-1,4-benzoxazin-3(4H)-one = HBOA

Other name(s): BX4 (gene name); CYP71C1 (gene name)

Systematic name: 3-hydroxyindolin-2-one,NAD(P)H:oxygen oxidoreductase (2-hydroxy-2H-1,4-benzoxazin-3(4H)-one-forming)

References:

1. Glawischnig, E., Grun, S., Frey, M. and Gierl, A. Cytochrome P450 monooxygenases of DIBOA biosynthesis: specificity and conservation among grasses. Phytochemistry 50 (1999) 925-930. [PMID: 10385992]

2. Frey, M., Chomet, P., Glawischnig, E., Stettner, C., Grün, S., Winklmair, A., Eisenreich, W., Bacher, A., Meeley, R.B., Briggs, S.P., Simcox, K. and Gierl, A. Analysis of a chemical plant defense mechanism in grasses. Science 277 (1997) 696-699. [PMID: 9235894]

3. Spiteller, P., Glawischnig, E., Gierl, A. and Steglich, W. Studies on the biosynthesis of 2-hydroxy-1,4-benzoxazin-3-one (HBOA) from 3-hydroxyindolin-2-one in Zea mays. Phytochemistry 57 (2001) 373-376. [PMID: 11393516]

[EC 1.14.13.139 created 2012]

EC 1.14.13.140

Reaction: 2-hydroxy-2H-1,4-benzoxazin-3(4H)-one + NAD(P)H + H⁺ + O₂ = 2,4-dihydroxy-2H-1,4-benzoxazin-3(4H)-one + NAD(P)⁺ + H₂O

Accepted name: cholest-4-en-3-one 26-monooxygenase

Glossary: 2,4-dihydroxy-2H-1,4-benzoxazin-3(4H)-one = DIBOA
2-hydroxy-2H-1,4-benzoxazin-3(4H)-one = HBOA

Other name(s): BX5 (gene name); CYP71C3 (gene name)

Systematic name: 2-hydroxy-2H-1,4-benzoxazin-3(4H)-one,NAD(P)H:oxygen oxidoreductase (N-hydroxylating)

References:

1. Bailey, B.A. and Larson, R.L. Maize microsomal benzoxazinone N-monooxygenase. Plant Physiol. 95 (1991) 792-796. [PMID: 16668055]

[EC 1.14.13.140 created 2012]

EC 1.14.13.141

Reaction: cholest-4-en-3-one + NADH + H⁺ + O₂ = 26-hydroxycholest-4-en-3-one + NAD⁺ + H₂O

Other name(s): CYP125; CYP125A1; cholest-4-en-3-one 27-monooxygenase

Systematic name: cholest-4-en-3-one,NADH:oxygen oxidoreductase (26-hydroxylating)

Comments: This heme thiolate (P₄₅₀) enzyme, found in several bacterial pathogens, is involved in degradation of the host cholesterol. It catalyses the hydroxylation of the C-26 carbon, followed by oxidation of the alcohol to the carboxylic acid via the aldehyde intermediate [4]. These activities are required to initiate the degradation of the alkyl side-chain of cholesterol. The enzyme also accepts cholesterol as a substrate, but unlike EC 1.14.13.15, cholestanetriol 26-monooxygenase, this enzyme is specific for C-26 and prefers cholest-4-en-3-one.

References:

1. Rosloniec, K.Z., Wilbrink, M.H., Capyk, J.K., Mohn, W.W., Ostendorf, M., van der Geize, R., Dijkhuizen, L. and Eltis, L.D. Cytochrome P450 125 (CYP125) catalyses C²⁶-hydroxylation to initiate sterol side-chain degradation in Rhodococcus jostii RHA1. Mol. Microbiol. 74 (2009) 1031-1043. [PMID: 19843222]

2. McLean, K.J., Lafite, P., Levy, C., Cheesman, M.R., Mast, N., Pikuleva, I.A., Leys, D. and Munro, A.W. The Structure of Mycobacterium tuberculosis CYP125: molecular basis for cholesterol binding in a P450 needed for host infection. J. Biol. Chem. 284 (2009) 35524-35533. [PMID: 19846552]

3. Capyk, J.K., Kalscheuer, R., Stewart, G.R., Liu, J., Kwon, H., Zhao, R., Okamoto, S., Jacobs, W.R., Jr., Eltis, L.D. and Mohn, W.W. Mycobacterial cytochrome P450 125 (Cyp125) catalyzes the terminal hydroxylation of C₂₇ steroids. J. Biol. Chem. 284 (2009) 35534-35542. [PMID: 19846551]

4. Ouellet, H., Guan, S., Johnston, J.B., Chow, E.D., Kells, P.M., Burlingame, A.L., Cox, J.S., Podust, L.M. and de Montellano, P.R. Mycobacterium tuberculosis CYP125A1, a steroid C₂₇ monooxygenase that detoxifies intracellularly generated cholest-4-en-3-one. Mol. Microbiol. 77 (2010) 730-742. [PMID: 20545858]

[EC 1.14.13.141 created 2012]

EC 1.14.13.142

Accepted name: 3-ketosteroid 9α-monooxygenase

Reaction: androsta-1,4-diene-3,17-dione + NADH + H⁺ + O₂ = 9α-hydroxyandrosta-1,4-diene-3,17-dione + NAD⁺ + H₂O

Other name(s): KshAB; 3-ketosteroid 9α-hydroxylase

Systematic name: androsta-1,4-diene-3,17-dione,NADH:oxygen oxidoreductase (9α-hydroxylating)

Comments: The enzyme is involved in the cholesterol degradation pathway of several bacterial pathogens, such as Mycobacterium tuberculosis. It is a two-component system consisting of a terminal oxygenase (KshA) and a ferredoxin reductase (KshB). The oxygenase contains a Rieske-type iron-sulfur center and non-heme iron. The reductase component is a flavoprotein containing an NAD-binding domain and a plant-type iron-sulfur cluster. The product of the enzyme is unstable, and spontaneously converts to 3-hydroxy-9,10-seconandrost-1,3,5(10)-triene-9,17-dione.

1. Petrusma, M., Dijkhuizen, L. and van der Geize, R. Rhodococcus rhodochrous DSM 43269 3-ketosteroid 9α-hydroxylase, a two-component iron-sulfur-containing monooxygenase with subtle steroid substrate specificity. Appl. Environ. Microbiol. 75 (2009) 5300-5307. [PMID: 19561185]

2. Capyk, J.K., D'Angelo, I., Strynadka, N.C. and Eltis, L.D. Characterization of 3-ketosteroid 9α-hydroxylase, a Rieske oxygenase in the cholesterol degradation pathway of Mycobacterium tuberculosis. J. Biol. Chem. 284 (2009) 9937-9946. [PMID: 19234303]

3. Capyk, J.K., Casabon, I., Gruninger, R., Strynadka, N.C. and Eltis, L.D. Activity of 3-ketosteroid 9α-hydroxylase (KshAB) indicates cholesterol side chain and ring degradation occur simultaneously in Mycobacterium tuberculosis. J. Biol. Chem. (2011) . [PMID: 21987574]

[EC 1.14.13.142 created 2012]

EC 1.14.13.143

Accepted name: ent-isokaurene C2-hydroxylase

Reaction: ent-isokaurene + O₂ + NADPH + H⁺ = ent-2α-hydroxyisokaurene + H₂O + NADP⁺

Accepted name: 9β-pimara-7,15-diene oxidase

Other name(s): CYP71Z6

Systematic name: ent-isokaurene,NADPH:oxygen oxidoreductase (hydroxylating)

Comments: This is the initial step in the conversion of ent-isokaurene to the antibacterial oryzalides in rice, Oryza sativa.

References:

1. Wu, Y., Hillwig, M.L., Wang, Q. and Peters, R.J. Parsing a multifunctional biosynthetic gene cluster from rice: biochemical characterization of CYP71Z6 & 7. FEBS Lett. 585 (2011) 3446-3451. [PMID: 21985968]

[EC 1.14.13.143 created 2012]

EC 1.14.13.144

Reaction: 9β-pimara-7,15-diene + 3 O₂ + 3 NADPH + 3 H⁺ = 9β-pimara-7,15-dien-19-oate + 3 NADP⁺ + 4 H₂O (overall reaction)
(1a) 9β-pimara-7,15-diene + O₂ + NADPH + H⁺ = 9β-pimara-7,15-dien-19-ol + NADP⁺ + H₂O
(1b) 9β-pimara-7,15-dien-19-ol + O₂ + NADPH + H⁺ = 9β-pimara-7,15-dien-19-al + NADP⁺ + 2 H₂O
(1c) 9β-pimara-7,15-dien-19-al + O₂ + NADPH + H⁺ = 9β-pimara-7,15-dien-19-oate + NADP⁺ + H₂O

Accepted name: ent-cassa-12,15-diene 11-hydroxylase

Glossary: syn-pimara-7,15-diene = 9β-pimara-7,15-diene

Other name(s): CYP99A3

Systematic name: 9β-pimara-7,15-diene,NADPH:oxygen 19-oxidoreductase

Comments: Requires cytochrome P₄₅₀. A rice, Oryza sativa, enzyme involved in the phytoalexin momilactone biosynthesis. It also acts similarly on 9β-stemod-13(17)-ene.

References:

1. Wang, Q., Hillwig, M.L. and Peters, R.J. CYP99A3: functional identification of a diterpene oxidase from the momilactone biosynthetic gene cluster in rice. Plant J. 65 (2011) 87-95. [PMID: 21175892]

[EC 1.14.13.144 created 2012]

EC 1.14.13.145

Reaction: ent-cassa-12,15-diene + O₂ + NADPH + H⁺ = ent-11β-hydroxycassa-12,15-diene + NADP⁺ + H₂O

Accepted name: taxoid 14β-hydroxylase

Other name(s): ent-cassadiene C11α-hydroxylase; CYP76M7

Systematic name: ent-cassa-12,15-diene,NADPH:oxygen 11-oxidoreductase

Comments: Requires cytochrome P₄₅₀. A rice, Oryza sativa, enzyme involved in the biosynthesis of the antifungal phytocassanes.

References:

1. Swaminathan, S., Morrone, D., Wang, Q., Fulton, D.B. and Peters, R.J. CYP76M7 is an ent-cassadiene C11α-hydroxylase defining a second multifunctional diterpenoid biosynthetic gene cluster in rice. Plant Cell 21 (2009) 3315-3325. [PMID: 19825834]

[EC 1.14.13.145 created 2012]

EC 1.14.13.146

Reaction: 10β-hydroxytaxa-4(20),11-dien-5α-yl acetate + O₂ + NADPH + H⁺ = 10β,14β-dihydroxytaxa-4(20),11-dien-5α-yl acetate + NADP⁺ + H₂O

Systematic name: 10β-hydroxytaxa-4(20),11-dien-5α-yl-acetate,NADPH:oxygen 14-oxidoreductase

Comments: Requires cytochrome P₄₅₀. From the yew Taxus cuspidata. Also acts on taxa-4(20),11-dien-5α-yl acetate.

1. Jennewein, S., Rithner, C.D., Williams, R.M. and Croteau, R. Taxoid metabolism: taxoid 14β-hydroxylase is a cytochrome P450-dependent monooxygenase. Arch. Biochem. Biophys. 413 (2003) 262-270. [PMID: 12729625]

[EC 1.14.13.146 created 2012]

EC 1.14.13.147

Accepted name: taxoid 7β-hydroxylase

Reaction: taxusin + O₂ + NADPH + H⁺ = 7β-hydroxytaxusin + NADP⁺ + H₂O

Glossary: taxusin = taxa-4(20),11-diene-5α,9α,10β,13α-tetrayl tetraacetate

Systematic name: taxusin,NADPH:oxygen 7-oxidoreductase

Comments: Requires cytochrome P₄₅₀. From the yew tree Taxus cuspidata. Does not act on earlier intermediates in taxol biosynthesis.

1. Chau, M., Jennewein, S., Walker, K. and Croteau, R. Taxol biosynthesis: molecular cloning and characterization of a cytochrome P450 taxoid 7 β-hydroxylase. Chem. Biol. 11 (2004) 663-672. [PMID: 15157877]

[EC 1.14.13.147 created 2012]

EC 1.14.13.148

Accepted name: trimethylamine monooxygenase

Reaction: N,N,N-trimethylamine + NADPH + H⁺ + O₂ = N,N,N-trimethylamine N-oxide + NADP⁺ + H₂O

Other name(s): flavin-containing monooxygenase 3; FMO3; tmm (gene name)

Systematic name: N,N,N-trimethylamine,NADPH:oxygen oxidoreductase (N-oxide-forming)

Comments: A flavoprotein. The bacterial enzyme enables bacteria to use trimethylamine as the sole source of carbon and energy [1,4]. The mammalian enzyme is involved in detoxification of trimethylamine. Mutations in the human enzyme cause the inheritable disease known as trimethylaminuria (fish odor syndrome) [2,3].

1. Large, P.J., Boulton, C.A. and Crabbe, M.J. The reduced nicotinamide-adenine dinucleotide phosphate- and oxygen-dependent N-oxygenation of trimethylamine by Pseudomonas aminovorans. Biochem. J. 128 (1972) 137P-138P. [PMID: 4404764]

2. Dolphin, C.T., Riley, J.H., Smith, R.L., Shephard, E.A. and Phillips, I.R. Structural organization of the human flavin-containing monooxygenase 3 gene (FMO3), the favored candidate for fish-odor syndrome, determined directly from genomic DNA. Genomics 46 (1997) 260-267. [PMID: 9417913]

3. Treacy, E.P., Akerman, B.R., Chow, L.M., Youil, R., Bibeau, C., Lin, J., Bruce, A.G., Knight, M., Danks, D.M., Cashman, J.R. and Forrest, S.M. Mutations of the flavin-containing monooxygenase gene (FMO3) cause trimethylaminuria, a defect in detoxication. Hum. Mol. Genet. 7 (1998) 839-845. [PMID: 9536088]

4. Chen, Y., Patel, N.A., Crombie, A., Scrivens, J.H. and Murrell, J.C. Bacterial flavin-containing monooxygenase is trimethylamine monooxygenase. Proc. Natl. Acad. Sci. USA 108 (2011) 17791-17796. [PMID: 22006322]

[EC 1.14.13.148 created 2012]

EC 1.14.13.149

Accepted name: phenylacetyl-CoA 1,2-epoxidase

Reaction: phenylacetyl-CoA + NADPH + H⁺ + O₂ = 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA + NADP⁺ + H₂O

Accepted name: 2,4-dihydroxy-1,4-benzoxazin-3-one-glucoside dioxygenase

Glossary: 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA = 2-{7-oxabicyclo[4.1.0]hepta-2,4-dien-1-yl}acetyl-CoA

Other name(s): ring 1,2-phenylacetyl-CoA epoxidase; phenylacetyl-CoA monooxygenase; PaaAC; PaaABC(D)E

Systematic name: phenylacetyl-CoA:oxygen oxidoreductase (1,2-epoxidizing)

Comments: Part of the aerobic pathway of phenylacetate catabolism in Escherichia coli and Pseudomonas putida.

References:

1. Teufel, R., Mascaraque, V., Ismail, W., Voss, M., Perera, J., Eisenreich, W., Haehnel, W. and Fuchs, G. Bacterial phenylalanine and phenylacetate catabolic pathway revealed. Proc. Natl. Acad. Sci. USA 107 (2010) 14390-14395. [PMID: 20660314]

2. Grishin, A.M., Ajamian, E., Zhang, L. and Cygler, M. Crystallization and preliminary X-ray analysis of PaaAC, the main component of the hydroxylase of the Escherichia coli phenylacetyl-coenzyme A oxygenase complex. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 66 (2010) 1045-1049. [PMID: 20823522]

3. Grishin, A.M., Ajamian, E., Tao, L., Zhang, L., Menard, R. and Cygler, M. Structural and functional studies of the Escherichia coli phenylacetyl-CoA monooxygenase complex. J. Biol. Chem. 286 (2011) 10735-10743. [PMID: 21247899]

[EC 1.14.13.149 created 2012]

EC 1.14.20.2

Reaction: (2R)-4-hydroxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside + 2-oxoglutarate + O₂ = (2R)-4,7-dihydroxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside + succinate + CO₂ + H₂O

Accepted name: ferric-chelate reductase (NADPH)

Glossary: (2R)-4-hydroxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside = DIBOA β-D-glucoside
(2R)-4,7-dihydroxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside = TRIBOA β-D-glucoside

Other name(s): BX6 (gene name); DIBOA-Glc dioxygenase

Systematic name: (2R)-4-hydroxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside:oxygen oxidoreductase (7-hydroxylating)

Comments: The enzyme is involved in the biosynthesis of protective and allelophatic benzoxazinoids in some plants, most commonly from the family of Poaceae (grasses).

References:

1. Jonczyk, R., Schmidt, H., Osterrieder, A., Fiesselmann, A., Schullehner, K., Haslbeck, M., Sicker, D., Hofmann, D., Yalpani, N., Simmons, C., Frey, M. and Gierl, A. Elucidation of the final reactions of DIMBOA-glucoside biosynthesis in maize: characterization of Bx6 and Bx7. Plant Physiol. 146 (2008) 1053-1063. [PMID: 18192444]

[EC 1.14.20.2 created 2012]

*EC 1.16.1.9

Reaction: 2 Fe(II) + 2 an apo-siderophore + NADP⁺ + H⁺ = 2 an Fe(III)-siderophore + NADPH

Other name(s): ferric chelate reductase (ambigous); iron chelate reductase (ambigous); NADPH:Fe³⁺-EDTA reductase; NADPH-dependent ferric reductase; yqjH (gene name)

Systematic name: Fe(II):NADP⁺ oxidoreductase

Comments: Contains FAD. The reaction is catalysed in the reverse direction. The enzyme, which is widespread among bacteria, catalyses the reduction and release of iron from a variety of iron chelators (siderophores), including ferric triscatecholates and ferric dicitrate. The enzyme from Escherichia coli has the highest efficiency with the hydrolysed ferric enterobactin complex ferric N-(2,3-dihydroxybenzoyl)-L-serine [3].

Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 120720-17-4

References:

1. Bamford, V.A., Armour, M., Mitchell, S.A., Cartron, M., Andrews, S.C. and Watson, K.A. Preliminary X-ray diffraction analysis of YqjH from Escherichia coli: a putative cytoplasmic ferri-siderophore reductase. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64 (2008) 792-796. [PMID: 18765906]

2. Wang, S., Wu, Y. and Outten, F.W. Fur and the novel regulator YqjI control transcription of the ferric reductase gene yqjH in Escherichia coli. J. Bacteriol. 193 (2011) 563-574. [PMID: 21097627]

3. Miethke, M., Hou, J. and Marahiel, M.A. The Siderophore-Interacting Protein YqjH Acts as a Ferric Reductase in Different Iron Assimilation Pathways of Escherichia coli. Biochemistry (2011) . [PMID: 22098718]

[EC 1.16.1.9 created 1992 as EC 1.6.99.13, transferred 2002 to EC 1.16.1.7, transferred 2011 to EC 1.16.1.9, modified 2012]

EC 2.1.1.239

Accepted name: L-olivosyl-oleandolide 3-O-methyltransferase

Reaction: S-adenosyl-L-methionine + L-olivosyl-oleandolide = S-adenosyl-L-homocysteine + L-oleandrosyl-oleandolide

Other name(s): OleY

Systematic name: S-adenosyl-L-methionine:L-olivosyl-oleandolide B 3-O-methyltransferase

Comments: The enzyme is involved in the biosynthesis of the macrolide antibiotic oleandomycin in Streptomyces antibioticus. It can also act on other monoglycosylated macrolactones, including L-rhamnosyl-erythronolide B and L-mycarosyl-erythronolide B.

1. Rodriguez, L., Rodriguez, D., Olano, C., Brana, A.F., Mendez, C. and Salas, J.A. Functional analysis of OleY L-oleandrosyl 3-O-methyltransferase of the oleandomycin biosynthetic pathway in Streptomyces antibioticus. J. Bacteriol. 183 (2001) 5358-5363. [PMID: 11514520]

[EC 2.1.1.239 created 2012]

EC 2.1.1.240

Accepted name: trans-resveratrol di-O-methyltransferase

Reaction: 2 S-adenosyl-L-methionine + trans-resveratrol = 2 S-adenosyl-L-homocysteine + pterostilbene (overall reaction)
(1a) S-adenosyl-L-methionine + trans-resveratrol = S-adenosyl-L-homocysteine + 3-methoxy-4',5-dihydroxy-trans-stilbene
(1b) S-adenosyl-L-methionine + 3-methoxy-4',5-dihydroxy-trans-stilbene = S-adenosyl-L-homocysteine + pterostilbene

Accepted name: 2,4,7-trihydroxy-1,4-benzoxazin-3-one-glucoside 7-O-methyltransferase

Glossary: resveratrol monomethyl ether = 3-methoxy-4',5-dihydroxy-trans-stilbene
pterostilbene = 3,5-dimethoxy-4'-hydroxy-trans-stilbene

Other name(s): ROMT; resveratrol O-methyltransferase; pterostilbene synthase

Systematic name: S-adenosyl-L-methionine:trans-resveratrol 3,5-O-dimethyltransferase

Comments: The enzyme catalyses the biosynthesis of pterostilbene from resveratrol.

References:

1. Schmidlin, L., Poutaraud, A., Claudel, P., Mestre, P., Prado, E., Santos-Rosa, M., Wiedemann-Merdinoglu, S., Karst, F., Merdinoglu, D. and Hugueney, P. A stress-inducible resveratrol O-methyltransferase involved in the biosynthesis of pterostilbene in grapevine. Plant Physiol. 148 (2008) 1630-1639. [PMID: 18799660]

[EC 2.1.1.240 created 2012]

EC 2.1.1.241

Reaction: S-adenosyl-L-methionine + (2R)-4,7-dihydroxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside = S-adenosyl-L-homocysteine + (2R)-4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside

Accepted name: 16S rRNA (guanine¹⁵¹⁶-N²)-methyltransferase

Glossary: (2R)-4,7-dihydroxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside = TRIMBOA β-D-glucoside
(2R)-4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside = DIMBOA β-D-glucoside

Other name(s): BX7 (gene name); OMT BX7

Systematic name: S-adenosyl-L-methionine:(2R)-4,7-dihydroxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside 7-O-methyltransferase

Comments: The enzyme is involved in the biosynthesis of the protective and allelophatic benzoxazinoid DIMBOA [(2R)-4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin] in some plants, most commonly from the family of Poaceae (grasses).

References:

[EC 2.1.1.241 created 2012]

EC 2.1.1.242

Reaction: S-adenosyl-L-methionine + guanine¹⁵¹⁶ in 16S rRNA = S-adenosyl-L-homocysteine + N²-methylguanine¹⁵¹⁶ in 16S rRNA

Other name(s): yhiQ (gene name); rsmJ (gene name); m²G¹⁵¹⁶ methyltransferase

Systematic name: S-adenosyl-L-methionine:16S rRNA (guanine¹⁵¹⁶-N²)-methyltransferase

Comments: The enzyme specifically methylates guanine¹⁵¹⁶ at N² in 16S rRNA.

1. Basturea, G.N., Dague, D.R., Deutscher, M.P. and Rudd, K.E. YhiQ Is RsmJ, the Methyltransferase Responsible for Methylation of G¹⁵¹⁶ in 16S rRNA of E. coli. J. Mol. Biol. 415 (2012) 16-21. [PMID: 22079366]

[EC 2.1.1.242 created 2012]

*EC 2.1.2.9

Accepted name: methionyl-tRNA formyltransferase

Reaction: 10-formyltetrahydrofolate + L-methionyl-tRNA^fMet = tetrahydrofolate + N-formylmethionyl-tRNA^fMet

Accepted name: dTDP-3-amino-3,6-dideoxy-α-D-galactopyranose 3-N-acetyltransferase

Other name(s): N¹⁰-formyltetrahydrofolic-methionyl-transfer ribonucleic transformylase; formylmethionyl-transfer ribonucleic synthetase; methionyl ribonucleic formyltransferase; methionyl-tRNA Met formyltransferase; methionyl-tRNA transformylase; methionyl-transfer RNA transformylase; methionyl-transfer ribonucleate methyltransferase; methionyl-transfer ribonucleic transformylase

Systematic name: 10-formyltetrahydrofolate:L-methionyl-tRNA N-formyltransferase

Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 9015-76-3

References:

1. Dickerman, H.W., Steers, E., Jr., Redfield, B.G. and Weissbach, H. Methionyl soluble ribonucleic acid transformylase. I. Purification and partial characterization. J. Biol. Chem. 242 (1967) 1522-1525. [PMID: 5337045]

[EC 2.1.2.9 created 1972, modified 2002, modified 2012]

EC 2.3.1.197

Reaction: acetyl-CoA + dTDP-3-amino-3,6-dideoxy-α-D-galactopyranose = CoA + dTDP-3-acetamido-3,6-dideoxy-α-D-galactopyranose

Other name(s): FdtC; dTDP-D-Fucp3N acetylase

Systematic name: acetyl-CoA:dTDP-3-amino-3,6-dideoxy-α-D-galactopyranose 3-N-acetyltransferase

Comments: The product, dTDP-3-acetamido-3,6-dideoxy-α-D-galactose, is a component of the glycan chain of the of the crystalline bacterial cell surface layer protein (S-layer glycoprotein) of Aneurinibacillus thermoaerophilus.

1. Pfoestl, A., Hofinger, A., Kosma, P. and Messner, P. Biosynthesis of dTDP-3-acetamido-3,6-dideoxy-α-D-galactose in Aneurinibacillus thermoaerophilus L420-91^T. J. Biol. Chem. 278 (2003) 26410-26417. [PMID: 12740380]

[EC 2.3.1.197 created 2012]

EC 2.4.1.278

Accepted name: desosaminyl transferase EryCIII

Reaction: dTDP-3-dimethylamino-4,6-dideoxy-α-D-glucopyranose + 3-α-mycarosylerythronolide B = dTDP + erythromycin D

Glossary: dTDP-3-dimethylamino-4,6-dideoxy-α-D-glucopyranose = dTDP-D-desosamine
erythromycin D =
(3R,4S,5S,6R,7R,9R,11R,12S,13R,14R)-4-(2,6-dideoxy-3-C-methyl-α-L-ribo-hexopyranosyloxy)-14-ethyl-7,12-dihydroxy-6-[3,4,6-trideoxy-3-(dimethylamino)-β-D-xylo-hexopyranosyloxy]-3,5,7,9,11,13-hexamethyloxacyclotetradecane-2,10-dione
3-O-α-mycarosylerythronolide B =
(3R,4S,5R,6R,7R,9R,11R,12S,13R,14R)-4-(2,6-dideoxy-3-C-methyl-α-L-ribo-hexopyranosyloxy)-14-ethyl-6,7,12-trihydroxy-3,5,7,9,11,13-hexamethyloxacyclotetradecane-2,10-dione

Other name(s): EryCIII

Systematic name: dTDP-3-dimethylamino-4,6-dideoxy-α-D-glucopyranose:3-α-mycarosylerythronolide B 3-dimethylamino-4,6-dideoxy-α-D-glucosyltransferase

Comments: The enzyme is involved in erythromycin biosynthesis.

1. Yuan, Y., Chung, H.S., Leimkuhler, C., Walsh, C.T., Kahne, D. and Walker, S. In vitro reconstitution of EryCIII activity for the preparation of unnatural macrolides. J. Am. Chem. Soc. 127 (2005) 14128-14129. [PMID: 16218575]

2. Lee, H.Y., Chung, H.S., Hang, C., Khosla, C., Walsh, C.T., Kahne, D. and Walker, S. Reconstitution and characterization of a new desosaminyl transferase, EryCIII, from the erythromycin biosynthetic pathway. J. Am. Chem. Soc. 126 (2004) 9924-9925. [PMID: 15303858]

3. Moncrieffe, M.C., Fernandez, M.J., Spiteller, D., Matsumura, H., Gay, N.J., Luisi, B.F. and Leadlay, P.F. Structure of the glycosyltransferase EryCIII in complex with its activating P450 homologue EryCII. J. Mol. Biol. 415 (2012) 92-101. [PMID: 22056329]

[EC 2.4.1.278 created 2012]

*EC 2.5.1.95

Accepted name: xanthan ketal pyruvate transferase

Reaction: phosphoenolpyruvate + D-Man-β-(1→4)-D-GlcA-β-(1→2)-D-Man-α-(1→3)-D-Glc-β-(1→4)-D-Glc-α-1-diphospho-ditrans,octacis-undecaprenol = 4,6-CH₃(COO^–)C-D-Man-β-(1→4)-D-GlcA-β-(1→2)-D-Man-α-(1→3)-D-Glc-β-(1→4)-D-Glc-α-1-diphospho-ditrans,octacis-undecaprenol + phosphate

Accepted name: Rhizobium leguminosarum exopolysaccharide glucosyl ketal-pyruvate-transferase

Other name(s): KPT

Systematic name: phosphoenolpyruvate:D-Man-β-(1→4)-GlcA-β-(1→2)-D-Man-α-(1→3)-D-Glc-β-(1→4)-D-Glc-α-1-diphospho-ditrans,octacis-undecaprenol 4,6-O-(1-carboxyethan-1,1-diyl)transferase

Comments: Involved in the biosynthesis of the polysaccharide xanthan. 30-40% of the terminal mannose residues of xanthan have a 4,6-O-(1-carboxyethan-1,1-diyl) ketal group. It also acts on the 6-O-acetyl derivative of the inner mannose unit.

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

References:

1. Marzocca, M.P., Harding, N.E., Petroni, E.A., Cleary, J.M. and Ielpi, L. Location and cloning of the ketal pyruvate transferase gene of Xanthomonas campestris. J. Bacteriol. 173 (1991) 7519-7524. [PMID: 1657892]

[EC 2.5.1.95 created 2011, modified 2012]

EC 2.5.1.98

Reaction: phosphoenolpyruvate + [D-GlcA-β-(1→4)-2-O-Ac-D-GlcA-β-(1→4)-D-Glc-β-(1→4)-[3-O-CH₃-CH₂CH(OH)C(O)-D-Gal-β-(1→4)-D-Glc-β-(1→4)-D-Glc-β-(1→4)-D-Glc-β-(1→6)]-2(or3)-O-Ac-D-Glc-α-(1→6)]_n = [D-GlcA-β-(1→4)-2-O-Ac-D-GlcA-β-(1→4)-D-Glc-β-(1→4)-[3-O-CH₃-CH₂CH(OH)C(O)-D-Gal-β-(1→3)-4,6-CH₃(COO^–)C-D-Glc-β-(1→4)-D-Glc-β-(1→4)-D-Glc-β-(1→6)]-2(or3)-O-Ac-D-Glc-α-(1→6)]_n + phosphate

Other name(s): PssM

Systematic name: phosphoenolpyruvate:[D-GlcA-β-(1→4)-2-O-Ac-D-GlcA-β-(1→4)-D-Glc-β-(1→4)-[3-O-CH₃-CH₂CH(OH)C(O)-D-Gal-β-(1→4)-D-Glc-β-(1→4)-D-Glc-β-(1→4)-D-Glc-β-(1→6)]-2(or3)-O-Ac-D-Glc-α-(1→6)]_n 4,6-O-(1-carboxyethan-1,1-diyl)transferase

Comments: The enzyme is responsible for pyruvylation of subterminal glucose in the acidic octasaccharide repeating unit of the exopolysaccharide of Rhizobium leguminosarum (bv. viciae strain VF39) which is necessary to establish nitrogen-fixing symbiosis with Pisum sativum, Vicia faba, and Vicia sativa.

1. Ivashina, T.V., Fedorova, E.E., Ashina, N.P., Kalinchuk, N.A., Druzhinina, T.N., Shashkov, A.S., Shibaev, V.N. and Ksenzenko, V.N. Mutation in the pssM gene encoding ketal pyruvate transferase leads to disruption of Rhizobium leguminosarum bv. viciae—Pisum sativum symbiosis. J. Appl. Microbiol. 109 (2010) 731-742. [PMID: 20233262]

[EC 2.5.1.98 created 2012]

EC 2.7.7.81

Accepted name: pseudaminic acid cytidylyltransferase

Reaction: CTP + 5,7-bis(acetylamino)-3,5,7,9-tetradeoxy-L-glycero-α-L-manno-2-nonulopyranosonic acid = diphosphate + CMP-5,7-bis(acetylamino)-3,5,7,9-tetradeoxy-L-glycero-α-L-manno-2-nonulopyranosonic acid

Glossary: pseudaminic acid = 5,7-bis(acetylamino)-3,5,7,9-tetradeoxy-L-glycero-α-L-manno-2-nonulopyranosonic acid

Other name(s): PseF

Systematic name: CTP:5,7-diacetamido-3,5,7,9-tetradeoxy-L-glycero-α-L-manno-nonulosonic acid cytidylyltransferase

Comments: Mg²⁺ is required for activity.

1. Schoenhofen, I.C., McNally, D.J., Brisson, J.R. and Logan, S.M. Elucidation of the CMP-pseudaminic acid pathway in Helicobacter pylori: synthesis from UDP-N-acetylglucosamine by a single enzymatic reaction. Glycobiology 16 (2006) 8C. [PMID: 16751642]

[EC 2.7.7.81 created 2012]

EC 3.1.7.10

Accepted name: (13E)-labda-7,13-dien-15-ol synthase

Reaction: geranylgeranyl diphosphate + H₂O = (13E)-labda-7,13-dien-15-ol + diphosphate

For diagram of reaction click here and mechanism click here.

Other name(s): labda-7,13E-dien-15-ol synthase

Systematic name: geranylgeranyl-diphosphate diphosphohydrolase [(13E)-labda-7,13-dien-15-ol-forming]

Comments: The enzyme from the lycophyte Selaginella moellendorffii is bifunctional, initially forming (13E)-labda-7,13-dien-15-yl diphosphate, which is hydrolysed to the alcohol.

References:

1. Mafu, S., Hillwig, M.L. and Peters, R.J. A novel labda-7,13E-dien-15-ol-producing bifunctional diterpene synthase from Selaginella moellendorffii. Chembiochem. 12 (2011) 1984-1987. [PMID: 21751328]

[EC 3.1.7.10 created 2012]

*EC 3.2.1.172

Accepted name: unsaturated rhamnogalacturonyl hydrolase

Reaction: 2-O-(4-deoxy-β-L-threo-hex-4-enopyranuronosyl)-α-L-rhamnopyranose + H₂O = 5-dehydro-4-deoxy-D-glucuronate + L-rhamnopyranose

Accepted name: leukotriene-C₄ hydrolase

Glossary: 6-deoxy-2-O-(4-deoxy-β-L-threo-hex-4-enopyranuronosyl)-α-L-mannopyranose = 2-O-(4-deoxy-β-L-threo-hex-4-enopyranuronosyl)-α-L-rhamnopyranose
5-dehydro-4-deoxy-D-glucuronate = (4S,5R)-4,5-dihydroxy-2,6-dioxohexanoate

Other name(s): YteR; YesR

Systematic name: 2-O-(4-deoxy-β-L-threo-hex-4-enopyranuronosyl)-α-L-rhamnopyranose hydrolase

Comments: The enzyme is part of the degradation system for rhamnogalacturonan I in Bacillus subtilis strain 168.

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

References:

1. Itoh, T., Ochiai, A., Mikami, B., Hashimoto, W. and Murata, K. A novel glycoside hydrolase family 105: the structure of family 105 unsaturated rhamnogalacturonyl hydrolase complexed with a disaccharide in comparison with family 88 enzyme complexed with the disaccharide. J. Mol. Biol. 360 (2006) 573-585. [PMID: 16781735]

2. Zhang, R., Minh, T., Lezondra, L., Korolev, S., Moy, S.F., Collart, F. and Joachimiak, A. 1.6 Å crystal structure of YteR protein from Bacillus subtilis, a predicted lyase. Proteins 60 (2005) 561-565. [PMID: 15906318]

3. Itoh, T., Ochiai, A., Mikami, B., Hashimoto, W. and Murata, K. Structure of unsaturated rhamnogalacturonyl hydrolase complexed with substrate. Biochem. Biophys. Res. Commun. 347 (2006) 1021-1029. [PMID: 16870154]

[EC 3.2.1.172 created 2011, modified 2012]

EC 3.4.19.14

Reaction: leukotriene C₄ + H₂O = leukotriene D₄ + L-glutamate

Other name(s): γ-glutamyl leukotrienase; GGT5

Comments: The mouse enzyme is specific for leukotriene C₄, while the human enzyme also has considerable activity towards glutathione and oxidized glutathione (cf. EC 3.4.19.13, glutathione hydrolase) [3-4].

References:

1. Carter, B.Z., Wiseman, A.L., Orkiszewski, R., Ballard, K.D., Ou, C.N. and Lieberman, M.W. Metabolism of leukotriene C₄ in γ-glutamyl transpeptidase-deficient mice. J. Biol. Chem. 272 (1997) 12305-12310. [PMID: 9139674]

2. Shi, Z.Z., Han, B., Habib, G.M., Matzuk, M.M. and Lieberman, M.W. Disruption of γ-glutamyl leukotrienase results in disruption of leukotriene D₄ synthesis in vivo and attenuation of the acute inflammatory response. Mol. Cell Biol. 21 (2001) 5389-5395. [PMID: 11463821]

3. Han, B., Luo, G., Shi, Z.Z., Barrios, R., Atwood, D., Liu, W., Habib, G.M., Sifers, R.N., Corry, D.B. and Lieberman, M.W. γ-glutamyl leukotrienase, a novel endothelial membrane protein, is specifically responsible for leukotriene D₄ formation in vivo. Am J Pathol 161 (2002) 481-490. [PMID: 12163373]

4. Wickham, S., West, M.B., Cook, P.F. and Hanigan, M.H. Gamma-glutamyl compounds: substrate specificity of γ-glutamyl transpeptidase enzymes. Anal. Biochem. 414 (2011) 208-214. [PMID: 21447318]

[EC 3.4.19.14 created 2012]

EC 3.5.4.32

Accepted name: 8-oxoguanine deaminase

Reaction: 8-oxoguanine + H₂O = urate + NH₃

Glossary: 8-oxoguanine = 2-amino-7,9-dihydro-1H-purine-6,8-dione

Other name(s): 8-OGD

Systematic name: 8-oxoguanine aminohydrolase

Comments: Zn²⁺ is bound in the active site. 8-Oxoguanine is formed via the oxidation of guanine within DNA by reactive oxygen species. If uncorrected, this modification leads to the incorporation of 8-oxoG:A mismatches and eventually to G:C to T:A transversions.

1. Hall, R.S., Fedorov, A.A., Marti-Arbona, R., Fedorov, E.V., Kolb, P., Sauder, J.M., Burley, S.K., Shoichet, B.K., Almo, S.C. and Raushel, F.M. The hunt for 8-oxoguanine deaminase. J. Am. Chem. Soc. 132 (2010) 1762-1763. [PMID: 20088583]

[EC 3.5.4.32 created 2012]

[EC 3.6.1.30 Deleted entry: m⁷G(5')pppN diphosphatase. Now covered by EC 3.6.1.59 [m⁷GpppX diphosphatase] and EC 3.6.1.62 [m⁷GpppN-mRNA hydrolase]. (EC 3.6.1.30 created 1978, deleted 2012)]

EC 3.6.1.58

Accepted name: 8-oxo-dGDP phosphatase

Reaction: 8-oxo-dGDP + H₂O = 8-oxo-dGMP + phosphate

Glossary: 8-oxo-dGDP = 8-oxo-7,8-dihydro-2'-deoxyguanosine 5'-diphosphate

Other name(s): NUDT5

Systematic name: 8-oxo-dGDP phosphohydrolase

Comments: The enzyme catalyses the hydrolysis of both 8-oxo-dGDP and 8-oxo-GDP thereby preventing translational errors caused by oxidative damage. The preferred in vivo substrate is not known. The enzyme does not degrade 8-oxo-dGTP and 8-oxo-GTP to the monophosphates (cf. EC 3.6.1.55, 8-oxo-dGTP diphosphatase) [1,2]. Ribonucleotide diphosphates and deoxyribonucleotide diphosphates are hydrolysed with broad specificity. The bifunctional enzyme NUDT5 also hydrolyses ADP-ribose to AMP and D-ribose 5-phosphate (cf. EC 3.6.1.13, ADP-ribose diphosphatase) [4].

References:

1. Ishibashi, T., Hayakawa, H., Ito, R., Miyazawa, M., Yamagata, Y. and Sekiguchi, M. Mammalian enzymes for preventing transcriptional errors caused by oxidative damage. Nucleic Acids Res. 33 (2005) 3779-3784. [PMID: 16002790]

2. Ishibashi, T., Hayakawa, H. and Sekiguchi, M. A novel mechanism for preventing mutations caused by oxidation of guanine nucleotides. EMBO Rep. 4 (2003) 479-483. [PMID: 12717453]

3. Kamiya, H., Hori, M., Arimori, T., Sekiguchi, M., Yamagata, Y. and Harashima, H. NUDT5 hydrolyzes oxidized deoxyribonucleoside diphosphates with broad substrate specificity. DNA Repair (Amst) 8 (2009) 1250-1254. [PMID: 19699693]

4. Ito, R., Sekiguchi, M., Setoyama, D., Nakatsu, Y., Yamagata, Y. and Hayakawa, H. Cleavage of oxidized guanine nucleotide and ADP sugar by human NUDT5 protein. J. Biochem. 149 (2011) 731-738. [PMID: 21389046]

5. Zha, M., Zhong, C., Peng, Y., Hu, H. and Ding, J. Crystal structures of human NUDT5 reveal insights into the structural basis of the substrate specificity. J. Mol. Biol. 364 (2006) 1021-1033. [PMID: 17052728]

[EC 3.6.1.58 created 2012]

EC 3.6.1.59

Accepted name: m⁷GpppX diphosphatase

Reaction: (1) m⁷G5'ppp5’N(3'ppp5’N)_n + H₂O = 7-methylguanosine 5'-phosphate + pp5’N(3'ppp5’N)_n
(2) 7-methylguanosine 5'-diphosphate + H₂O = 7-methylguanosine 5'-phosphate + phosphate

Other name(s): DcpS; m⁷GpppX pyrophosphatase; m⁷GpppN m⁷GMP phosphohydrolase

Systematic name: m⁷G⁵'ppp5’N m⁷GMP phosphohydrolase

Comments: Decapping is an important process in the control of eukaryotic mRNA degradation. m⁷GpppX diphosphatase functions to clear the cell of cap structure following decay of the RNA body [2]. m⁷GpppX diphosphatase is capable of acting on an mRNA once it is degraded down to 10 nucleotides, designated in reaction (1) as m⁷G⁵'ppp5’N(3'ppp5’N)n (n = 1-8) [3].

1. Malys, N. and McCarthy, J.E. Dcs2, a novel stress-induced modulator of m⁷GpppX pyrophosphatase activity that locates to P bodies. J. Mol. Biol. 363 (2006) 370-382. [PMID: 16963086]

2. Liu, S.W., Rajagopal, V., Patel, S.S. and Kiledjian, M. Mechanistic and kinetic analysis of the DcpS scavenger decapping enzyme. J. Biol. Chem. 283 (2008) 16427-16436. [PMID: 18441014]

3. Liu, H., Rodgers, N.D., Jiao, X. and Kiledjian, M. The scavenger mRNA decapping enzyme DcpS is a member of the HIT family of pyrophosphatases. EMBO J. 21 (2002) 4699-4708. [PMID: 12198172]

4. van Dijk, E., Le Hir, H. and Seraphin, B. DcpS can act in the 5'-3' mRNA decay pathway in addition to the 3'-5' pathway. Proc. Natl. Acad. Sci. USA 100 (2003) 12081-12086. [PMID: 14523240]

5. Liu, H., Rodgers, N.D., Jiao, X. and Kiledjian, M. The scavenger mRNA decapping enzyme DcpS is a member of the HIT family of pyrophosphatases. EMBO J. 21 (2002) 4699-4708. [PMID: 12198172]

6. Chen, N., Walsh, M.A., Liu, Y., Parker, R. and Song, H. Crystal structures of human DcpS in ligand-free and m⁷GDP-bound forms suggest a dynamic mechanism for scavenger mRNA decapping. J. Mol. Biol. 347 (2005) 707-718. [PMID: 15769464]

[EC 3.6.1.59 created 2012]

EC 3.6.1.60

Accepted name: diadenosine hexaphosphate hydrolase (AMP-forming)

Reaction: (1) P¹,P⁶-bis(5'-adenosyl)hexaphosphate + H₂O = adenosine 5'-pentaphosphate + AMP
(2) P¹,P⁵-bis(5'-adenosyl)pentaphosphate + H₂O = adenosine 5'-tetraphosphate + AMP

Other name(s): hAps1; NUDT11 (gene name); hAps2; NUDT10 (gene name)

Systematic name: P¹,P⁶-bis(5'-adenosyl)hexaphosphate nucleotidohydrolase (AMP-forming)

Comments: A divalent cation is essential for activity. Mn²⁺ (2-6 mM) is most effective. The enzyme controls intracellular levels of P¹,P⁵-bis(5'-adenosyl)pentaphosphate and P1,P6-bis(5'-adenosyl)hexaphosphate. Weak activity with P1,P4-bis(5'-adenosyl)tetraphosphate. Marked preference for adenine over guanine nucleotides.

1. Leslie, N.R., McLennan, A.G. and Safrany, S.T. Cloning and characterisation of hAps1 and hAps2, human diadenosine polyphosphate-metabolising Nudix hydrolases. BMC Biochem 3 (2002) 20. [PMID: 12121577]

2. Safrany, S.T., Ingram, S.W., Cartwright, J.L., Falck, J.R., McLennan, A.G., Barnes, L.D. and Shears, S.B. The diadenosine hexaphosphate hydrolases from Schizosaccharomyces pombe and Saccharomyces cerevisiae are homologues of the human diphosphoinositol polyphosphate phosphohydrolase. Overlapping substrate specificities in a MutT-type protein. J. Biol. Chem. 274 (1999) 21735-21740. [PMID: 10419486]

[EC 3.6.1.60 created 2012]

EC 3.6.1.61

Accepted name: diadenosine hexaphosphate hydrolase (ATP-forming)

Reaction: (1) P¹,P⁶-bis(5'-adenosyl)hexaphosphate + H₂O = 2 ATP
(2) P¹,P⁵-bis(5'-adenosyl)pentaphosphate + H₂O = ATP + ADP
(3) P¹,P⁴-bis(5'-adenosyl)tetraphosphate + H₂O = ATP + AMP

Other name(s): Ndx1

Systematic name: P¹,P⁶-bis(5'-adenosyl)hexaphosphate nucleotidohydrolase (ATP-forming)

Comments: The enzyme requires the presence of the divalent cations (Mn²⁺, Mg²⁺, Zn²⁺, and Co²⁺). It hydrolyses P¹,P⁴-bis(5-guanosyl) tetraphosphate very slowly [cf. EC 3.6.1.17, bis(5-nucleosyl)-tetraphosphatase (asymmetrical)].

References:

1. Iwai, T., Kuramitsu, S. and Masui, R. The Nudix hydrolase Ndx1 from Thermus thermophilus HB8 is a diadenosine hexaphosphate hydrolase with a novel activity. J. Biol. Chem. 279 (2004) 21732-21739. [PMID: 15024014]

[EC 3.6.1.61 created 2012]

EC 3.6.1.62

Accepted name: m⁷GpppN-mRNA hydrolase

Reaction: m⁷G5'ppp5'-mRNA + H₂O = m⁷GDP + 5'-phospho-mRNA

Glossary: N⁷-methylguanosine 5'-diphosphate = m⁷GDP

Other name(s): Dcp2; NUDT16; D10 protein; D9 protein; D10 decapping enzyme; decapping enzyme

Systematic name: m⁷GpppN-mRNA m⁷GDP phosphohydrolase

Comments: Decapping of mRNA is a critical step in eukaryotic mRNA turnover. The enzyme is unable to cleave a free cap structure (m⁷GpppG) [3]. The enzyme from Vaccinia virus is synergistically activated in the presence of Mg²⁺ and Mn²⁺ [5].

1. Xu, J., Yang, J.Y., Niu, Q.W. and Chua, N.H. Arabidopsis DCP2, DCP1, and VARICOSE form a decapping complex required for postembryonic development. Plant Cell 18 (2006) 3386-3398. [PMID: 17158604]

2. Lu, G., Zhang, J., Li, Y., Li, Z., Zhang, N., Xu, X., Wang, T., Guan, Z., Gao, G.F. and Yan, J. hNUDT16: a universal decapping enzyme for small nucleolar RNA and cytoplasmic mRNA. Protein Cell 2 (2011) 64-73. [PMID: 21337011]

3. van Dijk, E., Cougot, N., Meyer, S., Babajko, S., Wahle, E. and Seraphin, B. Human Dcp2: a catalytically active mRNA decapping enzyme located in specific cytoplasmic structures. EMBO J. 21 (2002) 6915-6924. [PMID: 12486012]

4. Parrish, S., Resch, W. and Moss, B. Vaccinia virus D10 protein has mRNA decapping activity, providing a mechanism for control of host and viral gene expression. Proc. Natl. Acad. Sci. USA 104 (2007) 2139-2144. [PMID: 17283339]

5. Souliere, M.F., Perreault, J.P. and Bisaillon, M. Characterization of the vaccinia virus D10 decapping enzyme provides evidence for a two-metal-ion mechanism. Biochem. J. 420 (2009) 27-35. [PMID: 19210265]

6. Parrish, S. and Moss, B. Characterization of a second vaccinia virus mRNA-decapping enzyme conserved in poxviruses. J. Virol. 81 (2007) 12973-12978. [PMID: 17881455]

7. Song, M.G., Li, Y. and Kiledjian, M. Multiple mRNA decapping enzymes in mammalian cells. Mol. Cell 40 (2010) 423-432. [PMID: 21070968]

[EC 3.6.1.62 created 2012]

EC 3.7.1.17

Accepted name: 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase

Reaction: (1E,2Z)-3-hydroxy-5,9,17-trioxo-4,5:9,10-disecoandrosta-1(10),2-dien-4-oate + H₂O = 3-[(3aS,4S,7aS)-7a-methyl-1,5-dioxo-octahydro-1H-inden-4-yl]propanoate + (2Z,4Z)-2-hydroxyhexa-2,4-dienoate

Other name(s): tesD (gene name); hsaD (gene name)

Systematic name: 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase ( (2Z,4Z)-2-hydroxyhexa-2,4-dienoate-forming)

Comments: The enzyme is involved in the bacterial degradation of the steroid ring structure, and is involved in degradation of multiple steroids, such as testosterone [1], cholesterol [2], and sitosterol.

1. Horinouchi, M., Hayashi, T., Koshino, H., Kurita, T. and Kudo, T. Identification of 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid, 4-hydroxy-2-oxohexanoic acid, and 2-hydroxyhexa-2,4-dienoic acid and related enzymes involved in testosterone degradation in Comamonas testosteroni TA441. Appl. Environ. Microbiol. 71 (2005) 5275-5281. [PMID: 16151114]

2. Van der Geize, R., Yam, K., Heuser, T., Wilbrink, M.H., Hara, H., Anderton, M.C., Sim, E., Dijkhuizen, L., Davies, J.E., Mohn, W.W. and Eltis, L.D. A gene cluster encoding cholesterol catabolism in a soil actinomycete provides insight into Mycobacterium tuberculosis survival in macrophages. Proc. Natl. Acad. Sci. USA 104 (2007) 1947-1952. [PMID: 17264217]

3. Lack, N., Lowe, E.D., Liu, J., Eltis, L.D., Noble, M.E., Sim, E. and Westwood, I.M. Structure of HsaD, a steroid-degrading hydrolase, from Mycobacterium tuberculosis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64 (2008) 2-7. [PMID: 18097091]

4. Lack, N.A., Yam, K.C., Lowe, E.D., Horsman, G.P., Owen, R.L., Sim, E. and Eltis, L.D. Characterization of a carbon-carbon hydrolase from Mycobacterium tuberculosis involved in cholesterol metabolism. J. Biol. Chem. 285 (2010) 434-443. [PMID: 19875455]

[EC 3.7.1.17 created 2012]

*EC 4.2.1.88

Accepted name: synephrine dehydratase

Reaction: (R)-synephrine = (4-hydroxyphenyl)acetaldehyde + methylamine

Glossary: (R)-synephrine = D-(–)-synephrine = 4-[(1R)-1-hydroxy-2-(methylamino)ethyl]phenol

Other name(s): syringinase

Systematic name: (R)-synephrine hydro-lyase (methylamine-forming)

Comments: Removal of H₂O from (R)-synephrine produces a 2,3-enamine, which hydrolyses to the products shown in the reaction above. The enzyme from Arthrobacter synephrinum is highly specific [1].

Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 104118-54-9

References:

1. Veeraswamy, M., Devi, N.A., Krishnan Kutty, R. and Subba Rao, P.V. Conversion of (±) synephrine into p-hydroxyphenylacetaldehyde by Arthrobacter synephrinum. A novel enzymic reaction. Biochem. J. 159 (1976) 807-809. [PMID: 1008837]

2. Manne, V., Kutty, K.R. and Pillarisetti, S.R. Purification and properties of synephrinase from Arthrobacter synephrinum. Arch. Biochem. Biophys. 248 (1986) 324-334. [PMID: 3729420]

[EC 4.2.1.88 created 1989, modified 2012]

*EC 4.2.3.18

Accepted name: abieta-7,13-diene synthase

Reaction: (+)-copalyl diphosphate = abieta-7,13-diene + diphosphate

For diagram of reaction click here and for the mechanism click here

Glossary: (+)-copalyl diphosphate = (2E)-3-methyl-5-[(1S,4aS,8aS)-5,5,8a-trimethyl-2-methylidenedecahydronaphthalen-1-yl]pent-2-en-1-yl trihydrogen diphosphate
abieta-7,13-diene = (4aS,4bR,10aS)-7-isopropyl-1,1,4a-trimethyl-1,2,3,4,4a,4b,5,6,10,10a-decahydrophenanthrene

Other name(s): copalyl-diphosphate diphosphate-lyase (cyclizing) (ambiguous); abietadiene synthase (ambiguous)

Systematic name: (+)-copalyl-diphosphate diphosphate-lyase [cyclizing, abieta-7,13-diene-forming]

Comments: Part of a bifunctional enzyme involved in the biosynthesis of abietadiene. See also EC 5.5.1.12, copalyl diphosphate synthase. Requires Mg²⁺.

Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 157972-08-2

References:

1. Peters, R.J., Flory, J.E., Jetter, R., Ravn, M.M., Lee, H.J., Coates, R.M. and Croteau, R.B. Abietadiene synthase from grand fir (Abies grandis): characterization and mechanism of action of the "pseudomature" recombinant enzyme. Biochemistry 39 (2000) 15592-15602. [PMID: 11112547]

2. Peters, R.J., Ravn, M.M., Coates, R.M. and Croteau, R.B. Bifunctional abietadiene synthase: free diffusive transfer of the (+)-copalyl diphosphate intermediate between two distinct active sites. J. Am. Chem. Soc. 123 (2001) 8974-8978. [PMID: 11552804]

3. Peters, R.J. and Croteau, R.B. Abietadiene synthase catalysis: mutational analysis of a prenyl diphosphate ionization-initiated cyclization and rearrangement. Proc. Natl. Acad. Sci. USA 99 (2002) 580-584. [PMID: 11805316]

4. Peters, R.J. and Croteau, R.B. Abietadiene synthase catalysis: conserved residues involved in protonation-initiated cyclization of geranylgeranyl diphosphate to (+)-copalyl diphosphate. Biochemistry 41 (2002) 1836-1842. [PMID: 11827528]

5. Ravn, M.M., Peters, R.J., Coates, R.M. and Croteau, R. Mechanism of abietadiene synthase catalysis: stereochemistry and stabilization of the cryptic pimarenyl carbocation intermediates. J. Am. Chem. Soc. 124 (2002) 6998-7006. [PMID: 12059223]

[EC 4.2.3.18 created 2002, modified 2012]

*EC 4.2.3.68

Accepted name: β-eudesmol synthase

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

For diagram of rection click here and for mechanism click here

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

Comments: The recombinant enzyme from ginger (Zingiber zerumbet) gives 62.6% β-eudesmol, 16.8% 10-epi-γ-eudesmol (cf. EC 4.2.3.84, 10-epi-γ-eudesmol synthase), 10% α-eudesmol (cf. EC 4.2.3.85, α-eudesmol synthase), and 5.6% aristolene.

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

References:

1. Yu, F., Harada, H., Yamasaki, K., Okamoto, S., Hirase, S., Tanaka, Y., Misawa, N. and Utsumi, R. Isolation and functional characterization of a β-eudesmol synthase, a new sesquiterpene synthase from Zingiber zerumbet Smith. FEBS Lett. 582 (2008) 565-572. [PMID: 18242187]

[EC 4.2.3.68 created 2011, modified 2011, modified 2012]

*EC 4.2.3.69

Accepted name: (+)-α-barbatene synthase

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

For diagram of reaction click here and for mechanism click here

Other name(s): AtBS

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(+)-α-barbatene-forming]

Comments: The recombinant enzyme from the plant Arabidopsis thaliana produces 27.3% α-barbatene, 17.8% thujopsene (cf. EC 4.2.3.79, thujopsene synthase) and 9.9% β-chamigrene (cf. EC 4.2.3.78, β-chamigrene synthase) [1] plus traces of other sesquiterpenoids [2].

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

References:

1. Wu, S., Schoenbeck, M.A., Greenhagen, B.T., Takahashi, S., Lee, S., Coates, R.M. and Chappell, J. Surrogate splicing for functional analysis of sesquiterpene synthase genes. Plant Physiol. 138 (2005) 1322-1333. [PMID: 15965019]

2. Tholl, D., Chen, F., Petri, J., Gershenzon, J. and Pichersky, E. Two sesquiterpene synthases are responsible for the complex mixture of sesquiterpenes emitted from Arabidopsis flowers. Plant J. 42 (2005) 757-771. [PMID: 15918888]

[EC 4.2.3.69 created 2011, modified 2012]

EC 4.2.3.94

Accepted name: γ-curcumene synthase

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

Accepted name: (–)-α-cuprenene synthase

Other name(s): PatTpsA (gene name)

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

Comments: One of five sesquiterpenoid synthases in Pogostemon cablin (patchouli).

References:

1. Deguerry, F., Pastore, L., Wu, S., Clark, A., Chappell, J. and Schalk, M. The diverse sesquiterpene profile of patchouli, Pogostemon cablin, is correlated with a limited number of sesquiterpene synthases. Arch. Biochem. Biophys. 454 (2006) 123-136. [PMID: 16970904]

[EC 4.2.3.94 created 2012]

EC 4.2.3.95

Reaction: (2E,6E)-farnesyl diphosphate = (–)-α-cuprenene + diphosphate

Accepted name: avermitilol synthase

Other name(s): Cop6

Systematic name: (–)-α-cuprenene hydrolase [cyclizing, (–)-α-cuprenene-forming]

Comments: The enzyme from the fungus Coprinopsis cinerea produces (–)-α-cuprenene with high selectivity.

References:

1. Lopez-Gallego, F., Agger, S.A., Abate-Pella, D., Distefano, M.D. and Schmidt-Dannert, C. Sesquiterpene synthases Cop4 and Cop6 from Coprinus cinereus: catalytic promiscuity and cyclization of farnesyl pyrophosphate geometric isomers. Chembiochem. 11 (2010) 1093-1106. [PMID: 20419721]

[EC 4.2.3.95 created 2012]

EC 4.2.3.96

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

Accepted name: (–)-δ-cadinene synthase

Systematic name: avermitilol hydrolase (cyclizing, avermitilol-forming)

Comments: Requires Mg²⁺. The recombinent enzyme gives avermitilol (85%) plus traces of germacrene A, germacrene B and viridiflorol. The (1S)-hydrogen of farnesyl diphosphate is retained.

References:

1. Chou, W.K., Fanizza, I., Uchiyama, T., Komatsu, M., Ikeda, H. and Cane, D.E. Genome mining in Streptomyces avermitilis: cloning and characterization of SAV_76, the synthase for a new sesquiterpene, avermitilol. J. Am. Chem. Soc. 132 (2010) 8850-8851. [PMID: 20536237]

[EC 4.2.3.96 created 2012]

EC 4.2.3.97

Reaction: (2E,6E)-farnesyl diphosphate = (–)-δ-cadinene + diphosphate

Accepted name: (+)-T-muurolol synthase

Glossary: (–)-δ-cadinene = (1R,8aS)-4,7-dimethyl-1-(propan-2-yl)-1,2,3,5,6,8a-hexahydronaphthalene

Systematic name: (2E,6E)-farnesyl diphosphate diphosphate-lyase (cyclizing, (–)-δ-cadinene-forming)

Comments: The cyclization mechanism involves an intermediate nerolidyl diphosphate leading to a helminthogermacradienyl cation. Following a 1,3-hydride shift of the original 1-pro-S hydrogen of (2E,6E)-farnesyl diphosphate, cyclization and deprotonation gives (–)-δ-cadinene.

References:

1. Hu, Y., Chou, W.K., Hopson, R. and Cane, D.E. Genome mining in Streptomyces clavuligerus: expression and biochemical characterization of two new cryptic sesquiterpene synthases. Chem. Biol. 18 (2011) 32-37. [PMID: 21276937]

[EC 4.2.3.97 created 2012]

EC 4.2.3.98

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

Accepted name: labdatriene synthase

Glossary: (+)-T-muurolol = (1R,4R,4aS,8aR)-1,6-dimethyl-4-(propan-2-yl)-1,2,3,4,4a,7,8,8a-octahydronaphthalen-1-ol

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, (+)-T-muurolol-forming)

Comments: The cyclization mechanism involves an intermediate nerolidyl diphosphate leading to a helminthogermacradienyl cation. After a 1,3-hydride shift of the original 1-pro-S hydrogen of farnesyl diphosphate, cyclization and deprotonation result in (+)-T-muurolol.

References:

[EC 4.2.3.98 created 2012]

EC 4.2.3.99

Reaction: 9α-copalyl diphosphate = (12E)-9α-labda-8(17),12,14-triene + diphosphate

Accepted name: bicyclogermacrene synthase

Glossary: 9α-copalyl diphosphate = syn-copalyl diphosphate = (2E)-3-methyl-5-[(1R,4aS,8aS)-5,5,8a-trimethyl-2-methylidenedecahydronaphthalen-1-yl]pent-2-en-1-yl trihydrogen diphosphate
(12E)-9α-labda-8(17),12,14-triene = (4aS,5R,8aS)-1,1,4a-trimethyl-6-methylidene-5-[(2E)-3-methylpenta-2,4-dien-1-yl]decahydronaphthalene

Other name(s): OsKSL10 (gene name)

Systematic name: 9α-copalyl-diphosphate diphosphate-lyase [(12E)-9α-labda-8(17),12,14-triene-forming]

Comments: The enzyme from rice (Oryza sativa), expressed in Escherichia coli, also produces ent-sandaracopimara-8(14),15-diene from ent-copalyl diphosphate, another naturally occuring copalyl isomer in rice (cf. ent-sandaracopimaradiene synthase, EC 4.2.3.29).

References:

1. Morrone, D., Hillwig, M.L., Mead, M.E., Lowry, L., Fulton, D.B. and Peters, R.J. Evident and latent plasticity across the rice diterpene synthase family with potential implications for the evolution of diterpenoid metabolism in the cereals. Biochem. J. 435 (2011) 589-595. [PMID: 21323642]

[EC 4.2.3.99 created 2012]

EC 4.2.3.100

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

Accepted name: 7-epi-sesquithujene synthase

Other name(s): Ov-TPS4

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

Comments: The enzyme from oregano (Origanum vulgare) gives mainly bicyclogermacrene with Mn²⁺ as a cofactor. With Mg²⁺ a more complex mixture is produced.

References:

1. Crocoll, C., Asbach, J., Novak, J., Gershenzon, J. and Degenhardt, J. Terpene synthases of oregano (Origanum vulgare L.) and their roles in the pathway and regulation of terpene biosynthesis. Plant Mol. Biol. 73 (2010) 587-603. [PMID: 20419468]

[EC 4.2.3.100 created 2012]

EC 4.2.3.101

Reaction: (2E,6E)-farnesyl diphosphate = 7-epi-sesquithujene + diphosphate

For diagram of reaction click here and mechanism click here.

Other name(s): TPS4-B73

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (7-epi-sesquithujene-forming)

Comments: The enzyme from Zea mays, variety B73, gives mainly 7-epi-sesquithujene with (S)-β-bisabolene and traces of other sesquiterpenoids, cf. EC 4.2.3.55 (S)-β-bisabolene synthase. It requires Mg²⁺ or Mn²⁺. The product ratio is dependent on which metal ion is present. 7-epi-Sesquithujene is an attractant for the emerald ash borer beetle.

References:

1. Köllner, T.G., Schnee, C., Gershenzon, J. and Degenhardt, J. The variability of sesquiterpenes emitted from two Zea mays cultivars is controlled by allelic variation of two terpene synthase genes encoding stereoselective multiple product enzymes. Plant Cell 16 (2004) 1115-1131. [PMID: 15075399]

[EC 4.2.3.101 created 2012]

EC 4.2.3.102

Accepted name: sesquithujene synthase

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

For diagram of reaction click here and mechanism click here.

Other name(s): TPS5-Del1

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

Comments: The enzyme from Zea mays, variety Delprim, gives mainly sesquithujene with (S)-β-bisabolene and (E)-β-farnesene plus traces of other sesquiterpenoids, cf. EC 4.2.3.55 [(S)-β-bisabolene synthase] and EC 4.2.3.47 (β-farnesene synthase). It requires Mg²⁺ or Mn²⁺. The exact product ratio is dependent on which metal ion is present.

References:

[EC 4.2.3.102 created 2012]

EC 4.2.3.103

Accepted name: ent-isokaurene synthase

Reaction: ent-copalyl diphosphate = ent-isokaurene + diphosphate

For diagram of reaction click here and mechanism click here.

Other name(s): OsKSL5i; OsKSL6

Systematic name: ent-copalyl-diphosphate diphosphate-lyase (cyclizing, ent-isokaurene-forming)

Comments: Two enzymes of the rice sub-species Oryza sativa ssp. indica, OsKSL5 and OsKSL6, produce ent-isokaurene. A variant of OsKSL5 from the sub-species Oryza sativa ssp. japonica produces ent-pimara-8(14),15-diene instead [cf. EC 4.2.3.30, ent-pimara-8(14),15-diene synthase].

References:

1. Xu, M., Wilderman, P.R., Morrone, D., Xu, J., Roy, A., Margis-Pinheiro, M., Upadhyaya, N.M., Coates, R.M. and Peters, R.J. Functional characterization of the rice kaurene synthase-like gene family. Phytochemistry 68 (2007) 312-326. [PMID: 17141283]

2. Xu, M., Wilderman, P.R. and Peters, R.J. Following evolution’s lead to a single residue switch for diterpene synthase product outcome. Proc. Natl. Acad. Sci. USA 104 (2007) 7397-7401. [PMID: 17456599]

[EC 4.2.3.103 created 2012]

EC 4.2.3.104

Accepted name: α-humulene synthase

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

Accepted name: 5-dehydro-4-deoxy-D-glucuronate isomerase

Other name(s): ZSS1

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

Comments: The enzyme from Zingiber zerumbet, shampoo ginger, also gives traces of β-caryophyllene.

References:

1. Yu, F., Okamto, S., Nakasone, K., Adachi, K., Matsuda, S., Harada, H., Misawa, N. and Utsumi, R. Molecular cloning and functional characterization of α-humulene synthase, a possible key enzyme of zerumbone biosynthesis in shampoo ginger (Zingiber zerumbet Smith). Planta 227 (2008) 1291-1299. [PMID: 18273640]

[EC 4.2.3.104 created 2012]

*EC 5.3.1.17

Reaction: 5-dehydro-4-deoxy-D-glucuronate = 3-deoxy-D-glycero-2,5-hexodiulosonate

Glossary: 5-dehydro-4-deoxy-D-glucuronate = (4S,5R)-4,5-dihydroxy-2,6-dioxohexanoate
3-deoxy-D-glycero-2,5-hexodiulosonate = (4S)-4,6-dihydroxy-2,5-dioxohexanoate

Other name(s): 4-deoxy-L-threo-5-hexulose uronate isomerase; 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase; kduI (gene name)

Systematic name: 5-dehydro-4-deoxy-D-glucuronate aldose-ketose-isomerase

Comments: The enzyme is involved in the degradation of polygalacturonate, a later stage in the degradation of pectin by many microorganisms.

Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 37318-44-8

References:

1. Preiss, J. 4-Deoxy-L-threo-5-hexosulose uronic acid isomerase. Methods Enzymol. 9 (1966) 602-604.

2. Condemine, G. and Robert-Baudouy, J. Analysis of an Erwinia chrysanthemi gene cluster involved in pectin degradation. Mol. Microbiol. 5 (1991) 2191-2202. [PMID: 1766386]

3. Dunten, P., Jaffe, H. and Aksamit, R.R. Crystallization of 5-keto-4-deoxyuronate isomerase from Escherichia coli. Acta Crystallogr. D Biol. Crystallogr. 54 (1998) 678-680. [PMID: 9761873]

4. Crowther, R.L. and Georgiadis, M.M. The crystal structure of 5-keto-4-deoxyuronate isomerase from Escherichia coli. Proteins 61 (2005) 680-684. [PMID: 16152643]

[EC 5.3.1.17 created 1972, modified 2012]

*EC 5.4.4.4

Accepted name: geraniol isomerase

Reaction: geraniol = (3S)-linalool

Systematic name: geraniol hydroxymutase

Comments: In absence of oxygen the bifunctional linalool dehydratase-isomerase can catalyse in vitro two reactions, the isomerization of (3S)-linalool to geraniol and the hydration of myrcene to (3S)-linalool, the latter activity being classified as EC 4.2.1.127, linalool dehydratase.

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

References:

1. Brodkorb, D., Gottschall, M., Marmulla, R., Lüddeke, F. and Harder, J. Linalool dehydratase-isomerase, a bifunctional enzyme in the anaerobic degradation of monoterpenes. J. Biol. Chem. 285 (2010) 30436-30442. [PMID: 20663876]

2. L�ddeke, F. and Harder, J. Enantiospecific (S)-(+)-linalool formation from β-myrcene by linalool dehydratase-isomerase. Z. Naturforsch. C 66 (2011) 409-412. [PMID: 21950166]

[EC 5.4.4.4 created 2011, modified 2012]

EC 5.4.99.57

Accepted name: baruol synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = baruol