ExplorEnz: EC 1*

References:

1.	Bertsova, Y.V., Serebryakova, M.V., Baykov, A.A. and Bogachev, A.V. A novel, NADH-dependent acrylate reductase in Vibrio harveyi. Appl. Environ. Microbiol. 88:e0051922 (2022). [DOI] [PMID: 35612301]

[EC 1.3.1.125 created 2022]

1.3.1.126

Accepted name:

2-epi-5-epi-valiolone dehydrogenase

Reaction:

2-epi-5-epi-valiolone + NAD⁺ = demethylgadusol + NADH + H⁺

Glossary:

2-epi-5-epi-valiolone = (2S,3S,4S,5R)-2,3,4,5-tetrahydroxy-5-(hydroxymethyl)cyclohexan-1-one
demethylgadusol = (4R,5R)-2,3,4,5-tetrahydroxy-5-(hydroxymethyl)cyclohex-2-en-1-one

Other name(s):

gadusol synthase

Systematic name:

2-epi-5-epi-valiolone:NAD⁺ 2,3-oxidoreductase

Comments:

The enzyme, present in egg-laying vertebrates, is involved in biosynthesis of the UV absorbing compound gadusol. It is a bifunctional enzyme that also catalyses EC 2.1.1.391, demethylgadusol O-methyltransferase.

Links to other databases:

References:

1.	Osborn, A.R., Almabruk, K.H., Holzwarth, G., Asamizu, S., LaDu, J., Kean, K.M., Karplus, P.A., Tanguay, R.L., Bakalinsky, A.T. and Mahmud, T. De novo synthesis of a sunscreen compound in vertebrates. Elife 4 (2015) . [DOI] [PMID: 25965179]

[EC 1.3.1.126 created 2023]

1.3.1.127

Deleted entry:

vomilenine 19,20-reductase. Now classified under EC 1.3.1.73, 1,2-dihydrovomilenine 19,20-reductase

[EC 1.3.1.127 created 2024, deleted 2024]

1.3.1.128

Accepted name:

precondylocarpine acetate reductase

Reaction:

dehydrosecondine + acetate + NADP⁺ = precondylocarpine acetate + NADPH + H⁺ (overall reaction)
(1a) dihydroprecondylocarpine acetate + NADP⁺ = precondylocarpine acetate + NADPH + H⁺
(1b) dihydroprecondylocarpine acetate (enamine form) = dihydroprecondylocarpine acetate (spontaneous)
(1c) dehydrosecondine + acetate = dihydroprecondylocarpine acetate (enamine form) (spontaneous)

For diagram of biosythesis of stemmadenine and related alkaloids, click here

Other name(s):

DPAS (gene name); dihydroprecondylocarpine acetate synthase

Systematic name:

precondylocarpine acetate:NADP⁺ oxidoreductase

Comments:

The enzyme, characterized from the plant Catharanthus roseus (Madagascar periwinkle), participates in a pathway that leads to the production of a number of monoterpene alkaloids, as well as the bisindole alkaloids vinblastine and vincristine, which are used as anticancer drugs. The enzyme forms the iminium ion form of dihydroprecondylocarpine acetate, which spontaneously rearranges and undergoes deacylation, producing dehydrosecodine.

Links to other databases:

References:

1.	Caputi, L., Franke, J., Farrow, S.C., Chung, K., Payne, R.ME., Nguyen, T.D., Dang, T.T., Soares Teto Carqueijeiro, I., Koudounas, K., Duge de Bernonville, T., Ameyaw, B., Jones, D.M., Vieira, I.JC., Courdavault, V. and O'Connor, S.E. Missing enzymes in the biosynthesis of the anticancer drug vinblastine in Madagascar periwinkle. Science 360 (2018) 1235–1239. [DOI] [PMID: 29724909]
2.	Caputi, L., Franke, J., Bussey, K., Farrow, S.C., Vieira, I.JC., Stevenson, C.EM., Lawson, D.M. and O'Connor, S.E. Structural basis of cycloaddition in biosynthesis of iboga and aspidosperma alkaloids. Nat. Chem. Biol. 16 (2020) 383–386. [DOI] [PMID: 32066966]
3.	DeMars, M.D., 2nd and O'Connor, S.E. Evolution and diversification of carboxylesterase-like [4+2] cyclases in aspidosperma and iboga alkaloid biosynthesis. Proc. Natl. Acad. Sci. USA 121:e2318586121 (2024). [DOI] [PMID: 38319969]

[EC 1.3.1.128 created 2024]

1.3.2.1

Transferred entry:

butyryl-CoA dehydrogenase. Now EC 1.3.99.2, butyryl-CoA dehydrogenase

[EC 1.3.2.1 created 1961, deleted 1964]

1.3.2.2

Transferred entry:

acyl-CoA dehydrogenase. Now EC 1.3.99.3, acyl-CoA dehydrogenase

[EC 1.3.2.2 created 1961, deleted 1964]

1.3.2.3

Accepted name:

L-galactonolactone dehydrogenase

Reaction:

L-galactono-1,4-lactone + 4 ferricytochrome c = L-dehydroascorbate + 4 ferrocytochrome c + 4 H⁺ (overall reaction)
(1a) L-galactono-1,4-lactone + 2 ferricytochrome c = L-ascorbate + 2 ferrocytochrome c + 2 H⁺
(1b) L-ascorbate + 2 ferricytochrome c = L-dehydroascorbate + 2 ferrocytochrome c + 2 H⁺ (spontaneous)

Other name(s):

galactonolactone dehydrogenase; L-galactono-γ-lactone dehydrogenase; L-galactono-γ-lactone:ferricytochrome-c oxidoreductase; GLDHase; GLDase

Systematic name:

L-galactono-1,4-lactone:ferricytochrome-c oxidoreductase

Comments:

This enzyme catalyses the final step in the biosynthesis of L-ascorbic acid in higher plants and in nearly all higher animals with the exception of primates and some birds [5]. The enzyme is very specific for its substrate L-galactono-1,4-lactone as D-galactono-γ-lactone, D-gulono-γ-lactone, L-gulono-γ-lactone, D-erythronic-γ-lactone, D-xylonic-γ-lactone, L-mannono-γ-lactone, D-galactonate, D-glucuronate and D-gluconate are not substrates [5]. FAD, NAD⁺, NADP⁺ and O₂ (cf. EC 1.3.3.12, L-galactonolactone oxidase) cannot act as electron acceptor [5].

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, MetaCyc, PDB, CAS registry number: 9029-02-1

References:

1.	Mapson, L.W. and Breslow, E. Properties of partially purified L-galactono-γ-lactone dehydrogenase. Biochem. J. 65 (1957) 29.
2.	Mapson, L.W., Isherwood, F.A. and Chen, Y.T. Biological synthesis of L-ascorbic acid: the conversion of L-galactono-γ-lactone into L-ascorbic acid by plant mitochondria. Biochem. J. 56 (1954) 21–28. [PMID: 13126087]
3.	Isherwood, F.A., Chen, Y.T. and Mapson, L.W. Synthesis of L-ascorbic acid in plants and animals. Biochem. J. 56 (1954) 1–15. [PMID: 13126085]
4.	Ôba, K., Ishikawa, S., Nishikawa, M., Mizuno, H. and Yamamoto, T. Purification and properties of L-galactono-γ-lactone dehydrogenase, a key enzyme for ascorbic acid biosynthesis, from sweet potato roots. J. Biochem. (Tokyo) 117 (1995) 120–124. [PMID: 7775377]
5.	Østergaard, J., Persiau, G., Davey, M.W., Bauw, G. and Van Montagu, M. Isolation of a cDNA coding for L-galactono-γ-lactone dehydrogenase, an enzyme involved in the biosynthesis of ascorbic acid in plants. Purification, characterization, cDNA cloning, and expression in yeast. J. Biol. Chem. 272 (1997) 30009–30016. [DOI] [PMID: 9374475]

[EC 1.3.2.3 created 1961, modified 2006]

1.3.2.4

Accepted name:

fumarate reductase (cytochrome)

Reaction:

succinate + 2 ferricytochrome c = fumarate + 2 ferrocytochrome c

Other name(s):

fccA (gene name); fcc3 (gene name); flavocytochrome c₃

Systematic name:

succinate:ferricytochrome-c oxidoreductase

Comments:

Contains a non-covalently bound FAD cofactor and four heme c groups. The enzyme, characterized from the bacterium Shewanella frigidimarina, is a soluble periplasmic protein that functions as a terminal electron acceptor during anaerobic growth. The direct electron donor is the membrane-bound tetraheme c-type cytochrome CymA (EC 7.1.1.8, quinol—cytochrome-c reductase), which receives the electrons from the membrane quinol pool.

Links to other databases:

References:

1.	Pealing, S.L., Black, A.C., Manson, F.D., Ward, F.B., Chapman, S.K. and Reid, G.A. Sequence of the gene encoding flavocytochrome c from Shewanella putrefaciens: a tetraheme flavoenzyme that is a soluble fumarate reductase related to the membrane-bound enzymes from other bacteria. Biochemistry 31 (1992) 12132–12140. [DOI] [PMID: 1333793]
2.	Pealing, S.L., Cheesman, M.R., Reid, G.A., Thomson, A.J., Ward, F.B. and Chapman, S.K. Spectroscopic and kinetic studies of the tetraheme flavocytochrome c from Shewanella putrefaciens NCIMB400. Biochemistry 34 (1995) 6153–6158. [DOI] [PMID: 7742319]
3.	Gordon, E.HJ., Pealing, S.L., Chapman, S.K., Ward, F.B. and Reid, G.A. Physiological function and regulation of flavocytochrome c₃, the soluble fumarate reductase from Shewanella putrefaciens NCIMB 400. Microbiology (Reading) 144 (1998) 937–945. [DOI] [PMID: 9579067]
4.	Doherty, M.K., Pealing, S.L., Miles, C.S., Moysey, R., Taylor, P., Walkinshaw, M.D., Reid, G.A. and Chapman, S.K. Identification of the active site acid/base catalyst in a bacterial fumarate reductase: a kinetic and crystallographic study. Biochemistry 39 (2000) 10695–10701. [DOI] [PMID: 10978153]
5.	Reid, G.A., Miles, C.S., Moysey, R.K., Pankhurst, K.L. and Chapman, S.K. Catalysis in fumarate reductase. Biochim. Biophys Acta 1459 (2000) 310–315. [DOI] [PMID: 11004445]
6.	Schwalb, C., Chapman, S.K. and Reid, G.A. The membrane-bound tetrahaem c-type cytochrome CymA interacts directly with the soluble fumarate reductase in Shewanella. Biochem Soc Trans. 30 (2002) 658–662. [DOI] [PMID: 12196158]

[EC 1.3.2.4 created 2022]

1.3.3.1

Transferred entry:

dihydroorotate oxidase. Now EC 1.3.98.1 [dihydroorotate dehydrogenase (fumarate)]

[EC 1.3.3.1 created 1961, deleted 2011]

1.3.3.2

Transferred entry:

now EC 1.14.21.6, lathosterol oxidase. NAD(P)H had not been included previously, so enzyme had to be reclassified

[EC 1.3.3.2 created 1972, deleted 2005]

1.3.3.3

Accepted name:

coproporphyrinogen oxidase

Reaction:

coproporphyrinogen III + O₂ + 2 H⁺ = protoporphyrinogen-IX + 2 CO₂ + 2 H₂O

For diagram of the later stages of porphyrin biosynthesis, click here

Other name(s):

coproporphyrinogen III oxidase; coproporphyrinogenase

Systematic name:

coproporphyrinogen:oxygen oxidoreductase (decarboxylating)

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, MetaCyc, PDB, CAS registry number: 9076-84-0

References:

1.	Battle, A.M., Benson, A. and Rimington, C. Purification and properties of coproporphyrinogenase. Biochem. J. 97 (1965) 731–740. [PMID: 5881662]
2.	Medlock, A.E. and Dailey, H.A. Human coproporphyrinogen oxidase is not a metalloprotein. J. Biol. Chem. 271 (1996) 32507–32510. [DOI] [PMID: 8955072]
3.	Kohno, H., Furukawa, T., Yoshinaga, T., Tokunaga, R. and Taketani, S. Coproporphyrinogen oxidase. Purification, molecular cloning, and induction of mRNA during erythroid differentiation. J. Biol. Chem. 268 (1993) 21359–21363. [PMID: 8407975]

[EC 1.3.3.3 created 1972, modified 2003]

1.3.3.4

Accepted name:

protoporphyrinogen oxidase

Reaction:

protoporphyrinogen IX + 3 O₂ = protoporphyrin IX + 3 H₂O₂

For diagram of the later stages of porphyrin biosynthesis, click here

Other name(s):

protoporphyrinogen IX oxidase; protoporphyrinogenase; PPO; Protox; HemG; HemY

Systematic name:

protoporphyrinogen-IX:oxygen oxidoreductase

Comments:

This is the last common enzyme in the biosynthesis of chlorophylls and heme [8]. Two isoenzymes exist in plants: one in plastids and the other in mitochondria. This is the target enzyme of phthalimide-type and diphenylether-type herbicides [8]. The enzyme from oxygen-dependent species contains FAD [9]. Also slowly oxidizes mesoporphyrinogen IX.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, MetaCyc, PDB, CAS registry number: 53986-32-6

References:

1.	Poulson, R. The enzymic conversion of protoporphyrinogen IX to protoporphyrin IX in mammalian mitochondria. J. Biol. Chem. 251 (1976) 3730–3733. [PMID: 6461]
2.	Poulson, R. and Polglase, W.J. The enzymic conversion of protoporphyrinogen IX to protoporphyrin IX. Protoporphyrinogen oxidase activity in mitochondrial extracts of Saccharomyces cerevisiae. J. Biol. Chem. 250 (1975) 1269–1274. [PMID: 234450]
3.	Dailey, H.A. and Dailey, T.A. Protoporphyrinogen oxidase of Myxococcus xanthus. Expression, purification, and characterization of the cloned enzyme. J. Biol. Chem. 271 (1996) 8714–8718. [DOI] [PMID: 8621504]
4.	Wang, K.F., Dailey, T.A. and Dailey, H.A. Expression and characterization of the terminal heme synthetic enzymes from the hyperthermophile Aquifex aeolicus. FEMS Microbiol. Lett. 202 (2001) 115–119. [DOI] [PMID: 11506917]
5.	Corrigall, A.V., Siziba, K.B., Maneli, M.H., Shephard, E.G., Ziman, M., Dailey, T.A., Dailey, H.A., Kirsch, R.E. and Meissner, P.N. Purification of and kinetic studies on a cloned protoporphyrinogen oxidase from the aerobic bacterium Bacillus subtilis. Arch. Biochem. Biophys. 358 (1998) 251–256. [DOI] [PMID: 9784236]
6.	Ferreira, G.C. and Dailey, H.A. Mouse protoporphyrinogen oxidase. Kinetic parameters and demonstration of inhibition by bilirubin. Biochem. J. 250 (1988) 597–603. [PMID: 2451512]
7.	Dailey, T.A. and Dailey, H.A. Human protoporphyrinogen oxidase: expression, purification, and characterization of the cloned enzyme. Protein Sci. 5 (1996) 98–105. [DOI] [PMID: 8771201]
8.	Che, F.S., Watanabe, N., Iwano, M., Inokuchi, H., Takayama, S., Yoshida, S. and Isogai, A. Molecular characterization and subcellular localization of protoporphyrinogen oxidase in spinach chloroplasts. Plant Physiol. 124 (2000) 59–70. [PMID: 10982422]
9.	Dailey, T.A. and Dailey, H.A. Identification of an FAD superfamily containing protoporphyrinogen oxidases, monoamine oxidases, and phytoene desaturase. Expression and characterization of phytoene desaturase of Myxococcus xanthus. J. Biol. Chem. 273 (1998) 13658–13662. [DOI] [PMID: 9593705]

[EC 1.3.3.4 created 1978, modified 2003]

1.3.3.5

Accepted name:

bilirubin oxidase

Reaction:

2 bilirubin + O₂ = 2 biliverdin + 2 H₂O

For diagram of biliverdin metabolism, click here

Other name(s):

bilirubin oxidase M-1

Systematic name:

bilirubin:oxygen oxidoreductase

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, MetaCyc, PDB, CAS registry number: 80619-01-8

References:

1.	Murao, S. and Tanaka, N. A new enzyme bilirubin oxidase produced by Myrothecium verrucaria MT-1. Agric. Biol. Chem. 45 (1981) 2383–2384.
2.	Tanaka, N. and Murao, S. Reaction of bilirubin oxidase produced by Myrothecium verrucaria MT-1. Agr. Biol. Chem. 49 (1985) 843–844.

[EC 1.3.3.5 created 1984]

1.3.3.6

Accepted name:

acyl-CoA oxidase

Reaction:

acyl-CoA + O₂ = trans-2,3-dehydroacyl-CoA + H₂O₂

Other name(s):

fatty acyl-CoA oxidase; acyl coenzyme A oxidase; fatty acyl-coenzyme A oxidase

Systematic name:

acyl-CoA:oxygen 2-oxidoreductase

Comments:

A flavoprotein (FAD). Acts on CoA derivatives of fatty acids with chain lengths from 8 to 18.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, MetaCyc, PDB, CAS registry number: 61116-22-1

References:

1.	Kawaguchi, A., Tsubotani, S., Seyama, Y., Yamakawa, T., Osumi, T., Hashimoto, T., Kikuchi, T., Ando, M. and Okuda, S. Stereochemistry of dehydrogenation catalyzed by acyl-CoA oxidase. J. Biochem. (Tokyo) 88 (1980) 1481–1486. [PMID: 7462191]
2.	Osumi, T., Hashimoto, T. and Ui, N. Purification and properties of acyl-CoA oxidase from rat liver. J. Biochem. (Tokyo) 87 (1980) 1735–1746. [PMID: 7400120]

[EC 1.3.3.6 created 1986]

1.3.3.7

Accepted name:

dihydrouracil oxidase

Reaction:

5,6-dihydrouracil + O₂ = uracil + H₂O₂

Systematic name:

5,6-dihydrouracil:oxygen oxidoreductase

Comments:

Also oxidizes dihydrothymine to thymine. A flavoprotein (FMN).

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 104327-11-9

References:

1.	Owaki, J., Uzura, K., Minami, Z. and Kusai, K. Partial-purification and characterization of dihydrouracil oxidase, a flavoprotein from Rhodotorula glutinis. J. Ferment. Technol. 64 (1986) 205–210.

[EC 1.3.3.7 created 1989]

1.3.3.8

Accepted name:

tetrahydroberberine oxidase

Reaction:

(S)-tetrahydroberberine + 2 O₂ = berberine + 2 H₂O₂

For diagram of canadine biosynthesis, click here and for diagram of columbamine, palmatine and corydaline biosynthesis, click here

Other name(s):

(S)-THB oxidase

Systematic name:

(S)-tetrahydroberberine:oxygen oxidoreductase

Comments:

The enzyme from Berberis sp. is a flavoprotein; that from Coptis japonica is not. (R)-Tetrahydroberberines are not oxidized.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 114705-00-9

References:

1.	Amann, M., Nagakura, N. and Zenk, M.H. (S)-Tetrahydroprotoberberine oxidase the final enzyme in protoberberine biosynthesis. Tetrahedron Lett. 25 (1984) 953–954.
2.	Okada, N., Shinmyo, A., Okada, H. and Yamada, Y. Purification and characterization of (S)-tetrahydroberberine oxidase from cultured Coptis japonica cells. Phytochemistry 27 (1988) 979–982.

[EC 1.3.3.8 created 1990 (EC 1.5.3.8 created 1989, incorporated 1992)]

1.3.3.9

Transferred entry:

secologanin synthase. Now EC 1.14.19.62, secologanin synthase

[EC 1.3.3.9 created 2002, deleted 2018]

1.3.3.10

Accepted name:

tryptophan α,β-oxidase

Reaction:

L-tryptophan + O₂ = α,β-didehydrotryptophan + H₂O₂

Other name(s):

L-tryptophan 2′,3′-oxidase; L-tryptophan α,β-dehydrogenase

Systematic name:

L-tryptophan:oxygen α,β-oxidoreductase

Comments:

Requires heme. The enzyme from Chromobacterium violaceum is specific for tryptophan derivatives possessing its carboxyl group free or as an amide or ester, and an unsubstituted indole ring. Also catalyses the α,β dehydrogenation of L-tryptophan side chains in peptides. The product of the reaction can hydrolyse spontaneously to form (indol-3-yl)pyruvate.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 156859-19-7

References:

1.	Genet, R., Denoyelle, C. and Menez, A. Purification and partial characterization of an amino acid α,β-dehydrogenase, L-tryptophan 2′,3′-oxidase from Chromobacterium violaceum. J. Biol. Chem. 269 (1994) 18177–18184. [PMID: 8027079]
2.	Genet, R., Benetti, P.H., Hammadi, A. and Menez, A. L-Tryptophan 2′,3′-oxidase from Chromobacterium violaceum. Substrate specificity and mechanistic implications. J. Biol. Chem. 270 (1995) 23540–23545. [DOI] [PMID: 7559518]

[EC 1.3.3.10 created 2000 as EC 1.4.3.17, transferred 2003 to EC 1.3.3.10]

1.3.3.11

Accepted name:

pyrroloquinoline-quinone synthase

Reaction:

6-(2-amino-2-carboxyethyl)-7,8-dioxo-1,2,3,4,7,8-hexahydroquinoline-2,4-dicarboxylate + 3 O₂ = 4,5-dioxo-4,5-dihydro-1H-pyrrolo[2,3-f]quinoline-2,7,9-tricarboxylate + 2 H₂O₂ + 2 H₂O

For diagram of reaction, click here

Other name(s):

PqqC; 6-(2-amino-2-carboxyethyl)-7,8-dioxo-1,2,3,4,5,6,7,8-octahydroquinoline-2,4-dicarboxylate:oxygen oxidoreductase (cyclizing) [incorrect]

Systematic name:

6-(2-amino-2-carboxyethyl)-7,8-dioxo-1,2,3,4,7,8-hexahydroquinoline-2,4-dicarboxylate:oxygen oxidoreductase (cyclizing)

Comments:

So far only a single turnover of the enzyme has been observed, and the pyrroloquinoline quinone remains bound to it. It is not yet known what releases the product in the bacterium.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, MetaCyc, PDB, CAS registry number: 353484-42-1

References:

1.	Magnusson, O.T., Toyama, H., Saeki, M., Schwarzenbacher, R. and Klinman, J.P. The structure of a biosynthetic intermediate of pyrroloquinoline quinone (PQQ) and elucidation of the final step of PQQ biosynthesis. J. Am. Chem. Soc. 126 (2004) 5342–5343. [DOI] [PMID: 15113189]
2.	Magnusson, O.T., Toyama, H., Saeki, M., Rojas, A., Reed, J.C., Liddington, R.C., Klinman, J.P. and Schwarzenbacher, R. Quinone biogenesis: Structure and mechanism of PqqC, the final catalyst in the production of pyrroloquinoline quinone. Proc. Natl. Acad. Sci. USA 101 (2004) 7913–7918. [DOI] [PMID: 15148379]
3.	Toyama, H., Chistoserdova, L. and Lidstrom, M.E. Sequence analysis of pqq genes required for biosynthesis of pyrroloquinoline quinone in Methylobacterium extorquens AM1 and the purification of a biosynthetic intermediate. Microbiology 143 (1997) 595–602. [DOI] [PMID: 9043136]
4.	Toyama, H., Fukumoto, H., Saeki, M., Matsushita, K., Adachi, O. and Lidstrom, M.E. PqqC/D, which converts a biosynthetic intermediate to pyrroloquinoline quinone. Biochem. Biophys. Res. Commun. 299 (2002) 268–272. [PMID: 1243798]
5.	Schwarzenbacher, R., Stenner-Liewen, F., Liewen, H., Reed, J.C. and Liddington, R.C. Crystal structure of PqqC from Klebsiella pneumoniae at 2.1 A resolution. Proteins 56 (2004) 401–403. [DOI] [PMID: 15211525]

[EC 1.3.3.11 created 2005]

1.3.3.12

Accepted name:

L-galactonolactone oxidase

Reaction:

L-galactono-1,4-lactone + O₂ = L-ascorbate + H₂O₂

Other name(s):

L-galactono-1,4-lactone oxidase

Systematic name:

L-galactono-1,4-lactone:oxygen 3-oxidoreductase

Comments:

A flavoprotein. Acts on the 1,4-lactones of L-galactonic, D-altronic, L-fuconic, D-arabinic and D-threonic acids; not identical with EC 1.1.3.8 L-gulonolactone oxidase. (cf. EC 1.3.2.3 galactonolactone dehydrogenase).

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, MetaCyc, CAS registry number: 69403-13-0

References:

1.	Bleeg, H.S. and Christensen, F. Biosynthesis of ascorbate in yeast. Purification of L-galactono-1,4-lactone oxidase with properties different from mammalian L-gulonolactone oxidase. Eur. J. Biochem. 127 (1982) 391–396. [DOI] [PMID: 6754380]

[EC 1.3.3.12 created 1984 as EC 1.1.3.24, transferred 2006 to EC 1.3.3.12]

1.3.3.13

Accepted name:

albonoursin synthase

Reaction:

cyclo(L-leucyl-L-phenylalanyl) + 2 O₂ = albonoursin + 2 H₂O₂ (overall reaction)
(1a) cyclo(L-leucyl-L-phenylalanyl) + O₂ = cyclo[(Z)-α,β-didehydrophenylalanyl-L-leucyl] + H₂O₂
(1b) cyclo[(Z)-α,β-didehydrophenylalanyl-L-leucyl] + O₂ = albonoursin + H₂O₂

For diagram of cyclic dipeptide biosynthesis, click here

Glossary:

cyclo(L-leucyl-L-phenylalanyl) = (3S,6S)-3-benzyl-6-(2-methylpropyl)piperazine-2,5-dione
cyclo[(Z)-α,β-didehydrophenylalanyl-L-leucyl] = (3Z,6S)-3-benzylidene-6-(2-methylpropyl)piperazine-2,5-dione
albonoursin = (3Z,6Z)-3-benzylidene-6-(2-methylpropylidene)piperazine-2,5-dione

Other name(s):

cyclo(dipeptide):oxygen oxidoreductase; cyclic dipeptide oxidase; AlbA

Systematic name:

cyclo(L-leucyl-L-phenylalanyl):oxygen oxidoreductase

Comments:

A flavoprotein from the bacterium Streptomyces noursei. The enzyme can also oxidize several other cyclo dipeptides, the best being cyclo(L-tryptophyl-L-tryptophyl) and cyclo(L-phenylalanyl-L-phenylalanyl) [1,2].

Links to other databases:

References:

1.	Gondry, M., Lautru, S., Fusai, G., Meunier, G., Menez, A. and Genet, R. Cyclic dipeptide oxidase from Streptomyces noursei. Isolation, purification and partial characterization of a novel, amino acyl α,β-dehydrogenase. Eur. J. Biochem. 268 (2001) 1712–1721. [DOI] [PMID: 11248691]
2.	Lautru, S., Gondry, M., Genet, R. and Pernodet, J.L. The albonoursin gene cluster of S. noursei. Biosynthesis of diketopiperazine metabolites independent of nonribosomal peptide synthetases. Chem. Biol. 9 (2002) 1355–1364. [DOI] [PMID: 12498889]

[EC 1.3.3.13 created 2013]

1.3.3.14

Accepted name:

aclacinomycin-A oxidase

Reaction:

aclacinomycin A + O₂ = aclacinomycin Y + H₂O₂

For diagram of aclacinomycin A and Y biosynthesis, click here

Glossary:

aclacinomycin A = 2-ethyl-1,2,3,4,6,11-hexahydro-2,5,7-trihydroxy-6,11-dioxo-4-[[2,3,6-trideoxy-4-O-[2,6-dideoxy-4-O-[(2R,6S)-tetrahydro-6-methyl-5-oxo-2H-pyran-2-yl]-α-L-lyxo-hexopyranosyl]-3-(dimethylamino)-α-L-lyxo-hexopyranosyl]oxy]naphthacene-1-carboxylic acid methyl ester
aclacinomycin Y = 2-ethyl-1,2,3,4,6,11-hexahydro-2,5,7-trihydroxy-6,11-dioxo-4-[[2,3,6-trideoxy-4-O-[2,6-dideoxy-4-O-[(2R,6S)-5,6-dihydro-6-methyl-5-oxo-2H-pyran-2-yl]-α-L-lyxo-hexopyranosyl]-3-(dimethylamino)-α-L-lyxo-hexopyranosyl]oxy]naphthacene-1-carboxylic acid methyl ester

Other name(s):

AknOx (ambiguous); aclacinomycin oxidoreductase (ambiguous)

Systematic name:

aclacinomycin-A:oxygen oxidoreductase

Comments:

A flavoprotein (FAD). This bifunctional enzyme is a secreted flavin-dependent enzyme that is involved in the modification of the terminal sugar residues in the biosynthesis of aclacinomycins. The enzyme utilizes the same active site to catalyse the oxidation of the rhodinose moiety of aclacinomycin N to the cinerulose A moiety of aclacinomycin A (cf. EC 1.1.3.45) and the oxidation of the latter to the L-aculose moiety of aclacinomycin Y.

Links to other databases:

References:

1.	Yoshimoto, A., Ogasawara, T., Kitamura, I., Oki, T., Inui, T., Takeuchi, T. and Umezawa, H. Enzymatic conversion of aclacinomycin A to Y by a specific oxidoreductase in Streptomyces. J. Antibiot. (Tokyo) 32 (1979) 472–481. [PMID: 528393]
2.	Alexeev, I., Sultana, A., Mantsala, P., Niemi, J. and Schneider, G. Aclacinomycin oxidoreductase (AknOx) from the biosynthetic pathway of the antibiotic aclacinomycin is an unusual flavoenzyme with a dual active site. Proc. Natl. Acad. Sci. USA 104 (2007) 6170–6175. [DOI] [PMID: 17395717]
3.	Sultana, A., Alexeev, I., Kursula, I., Mantsala, P., Niemi, J. and Schneider, G. Structure determination by multiwavelength anomalous diffraction of aclacinomycin oxidoreductase: indications of multidomain pseudomerohedral twinning. Acta Crystallogr. D Biol. Crystallogr. 63 (2007) 149–159. [DOI] [PMID: 17242508]

[EC 1.3.3.14 created 2013]

1.3.3.15

Accepted name:

coproporphyrinogen III oxidase (coproporphyrin-forming)

Reaction:

coproporphyrinogen III + 3 O₂ = coproporphyrin III + 3 H₂O₂

Other name(s):

hemY (gene name)

Systematic name:

coproporphyrinogen-III:oxygen oxidoreductase (coproporphyrin-forming)

Comments:

Contains FAD. The enzyme, present in Gram-positive bacteria, participates in heme biosynthesis. It can also catalyse the reaction of EC 1.3.3.4, protoporphyrinogen oxidase, at a lower level.

Links to other databases:

References:

1.	Hansson, M. and Hederstedt, L. Bacillus subtilis HemY is a peripheral membrane protein essential for protoheme IX synthesis which can oxidize coproporphyrinogen III and protoporphyrinogen IX. J. Bacteriol. 176 (1994) 5962–5970. [DOI] [PMID: 7928957]
2.	Corrigall, A.V., Siziba, K.B., Maneli, M.H., Shephard, E.G., Ziman, M., Dailey, T.A., Dailey, H.A., Kirsch, R.E. and Meissner, P.N. Purification of and kinetic studies on a cloned protoporphyrinogen oxidase from the aerobic bacterium Bacillus subtilis. Arch. Biochem. Biophys. 358 (1998) 251–256. [DOI] [PMID: 9784236]
3.	Qin, X., Sun, L., Wen, X., Yang, X., Tan, Y., Jin, H., Cao, Q., Zhou, W., Xi, Z. and Shen, Y. Structural insight into unique properties of protoporphyrinogen oxidase from Bacillus subtilis. J. Struct. Biol. 170 (2010) 76–82. [DOI] [PMID: 19944166]
4.	Dailey, H.A., Gerdes, S., Dailey, T.A., Burch, J.S. and Phillips, J.D. Noncanonical coproporphyrin-dependent bacterial heme biosynthesis pathway that does not use protoporphyrin. Proc. Natl. Acad. Sci. USA 112 (2015) 2210–2215. [DOI] [PMID: 25646457]

[EC 1.3.3.15 created 2016]

1.3.3.16

Accepted name:

oxazoline dehydrogenase

Reaction:

(1) a [protein]-(1S,4R)-2-(C-substituted-aminomethyl)-4-acyl-2-thiazoline + O₂ = a [protein]-(S)-2-(C-substituted-aminomethyl)-4-acyl-1,3-thiazole + H₂O₂
(2) a [protein]-(S,S)-2-(C-substituted-aminomethyl)-4-acyl-2-oxazoline + O₂ = a [protein]-(S)-2-(C-substituted-aminomethyl)-4-acyl-1,3-oxazole + H₂O₂
(3) a [protein]-(S,S)-2-(C-substituted-aminomethyl)-4-acyl-5-methyl-2-oxazoline + O₂ = a [protein]-(S)-2-(C-substituted-aminomethyl)-4-acyl-5-methyl-1,3-oxazole + H₂O₂

Other name(s):

azoline oxidase; thiazoline oxidase; cyanobactin oxidase; patG (gene name); mcaG (gene name); artG (gene name); lynG (gene name); tenG (gene name)

Systematic name:

a [protein]-2-oxazoline:oxygen oxidoreductase (2-oxazole-forming)

Comments:

Contains FMN. This enzyme oxidizes 2-oxazoline, 5-methyl-2-oxazoline, and 2-thiazoline within peptides, which were formed by EC 6.2.2.2, oxazoline synthase, and EC 6.2.2.3, thiazoline synthase, to the respective pyrrole-type rings. The enzyme is found as either a stand-alone protein or as a domain within a multifunctional protein (the G protein) that also functions as a peptidase.

Links to other databases:

References:

1.	Li, Y.M., Milne, J.C., Madison, L.L., Kolter, R. and Walsh, C.T. From peptide precursors to oxazole and thiazole-containing peptide antibiotics: microcin B17 synthase. Science 274 (1996) 1188–1193. [PMID: 8895467]
2.	Schmidt, E.W., Nelson, J.T., Rasko, D.A., Sudek, S., Eisen, J.A., Haygood, M.G. and Ravel, J. Patellamide A and C biosynthesis by a microcin-like pathway in Prochloron didemni, the cyanobacterial symbiont of Lissoclinum patella. Proc. Natl. Acad. Sci. USA 102 (2005) 7315–7320. [PMID: 15883371]
3.	Bent, A.F., Mann, G., Houssen, W.E., Mykhaylyk, V., Duman, R., Thomas, L., Jaspars, M., Wagner, A. and Naismith, J.H. Structure of the cyanobactin oxidase ThcOx from Cyanothece sp. PCC 7425, the first structure to be solved at Diamond Light Source beamline I23 by means of S-SAD. Acta Crystallogr D Struct Biol 72 (2016) 1174–1180. [PMID: 27841750]
4.	Ghilarov, D., Stevenson, C.EM., Travin, D.Y., Piskunova, J., Serebryakova, M., Maxwell, A., Lawson, D.M. and Severinov, K. Architecture of microcin B17 synthetase: an octameric protein complex converting a ribosomally synthesized peptide into a DNA gyrase poison. Mol. Cell 73 (2019) 749–762.e5. [PMID: 30661981]

[EC 1.3.3.16 created 2020]

1.3.3.17

Accepted name:

benzylmalonyl-CoA dehydrogenase

Reaction:

benzylmalonyl-CoA + O₂ = (E)-cinnamoyl-CoA + CO₂ + H₂O₂

Other name(s):

iaaF (gene name)

Systematic name:

benzylmalonyl-CoA:oxygen oxidoreductase (decarboxylating)

Comments:

The enzyme, characterized from the bacterium Aromatoleum aromaticum, is involved in degradation of (indol-3-yl)acetate, where it is believed to function on (2-aminobenzyl)malonyl-CoA.

Links to other databases:

References:

1.	Schuhle, K., Saft, M., Vogeli, B., Erb, T.J. and Heider, J. Benzylmalonyl-CoA dehydrogenase, an enzyme involved in bacterial auxin degradation. Arch. Microbiol. 203 (2021) 4149–4159. [DOI] [PMID: 34059946]

[EC 1.3.3.17 created 2022]

1.3.4.1

Accepted name:

fumarate reductase (CoM/CoB)

Reaction:

fumarate + CoM + CoB = succinate + CoM-S-S-CoB

Glossary:

CoB = coenzyme B = N-(7-sulfanylheptanoyl)threonine = N-(7-mercaptoheptanoyl)threonine (deprecated)
CoM = coenzyme M = 2-sulfanylethane-1-sulfonate = 2-mercaptoethanesulfonate (deprecated)

Other name(s):

thiol:fumarate reductase; Tfr

Systematic name:

fumarate CoM:CoB oxidoreductase (succinate-forming)

Comments:

The enzyme, isolated from the archaeon Methanobacterium thermoautotrophicum, is very oxygen sensitive. It cannot use reduced flavins, reduced coenzyme F₄₂₀, or NAD(P)H as an electron donor. Distinct from EC 1.3.1.6 [fumarate reductase (NADH)] and EC 1.3.5.1 [succinate dehydrogenase (ubiquinone)].

Links to other databases:

References:

1.	Khandekar, S.S. and Eirich, L.D. Purification and characterization of an anabolic fumarate reductase from Methanobacterium thermoautotrophicum. Appl. Environ. Microbiol. 55 (1989) 856–861. [PMID: 2499256]
2.	Heim, S., Kunkel, A., Thauer, R.K. and Hedderich, R. Thiol:fumarate reductase (Tfr) from Methanobacterium thermoautotrophicum. Identification of the catalytic sites for fumarate reduction and thiol oxidation. Eur. J. Biochem. 253 (1998) 292–299. [DOI] [PMID: 9578488]

[EC 1.3.4.1 created 2014 as EC 1.3.98.2, transferred 2014 to EC 1.3.4.1]

1.3.5.1

Accepted name:

succinate dehydrogenase

Reaction:

succinate + a quinone = fumarate + a quinol

For diagram of the citric acid cycle, click here

Other name(s):

succinate dehydrogenase (quinone); succinate dehydrogenase (ubiquinone); succinic dehydrogenase; complex II (ambiguous); succinate dehydrogenase complex; SDH (ambiguous); succinate:ubiquinone oxidoreductase; fumarate reductase (quinol); FRD; menaquinol-fumarate oxidoreductase; succinate dehydrogenase (menaquinone); succinate:menaquinone oxidoreductase; fumarate reductase (menaquinone)

Systematic name:

succinate:quinone oxidoreductase

Comments:

A complex generally comprising an FAD-containing component that also binds the carboxylate substrate (A subunit), a component that contains three different iron-sulfur centers [2Fe-2S], [4Fe-4S], and [3Fe-4S] (B subunit), and a hydrophobic membrane-anchor component (C, or C and D subunits) that is also the site of the interaction with quinones. The enzyme is found in the inner mitochondrial membrane in eukaryotes and the plasma membrane of bacteria and archaea, with the hydrophilic domain extending into the mitochondrial matrix and the cytoplasm, respectively. Under aerobic conditions the enzyme catalyses succinate oxidation, a key step in the citric acid (TCA) cycle, transferring the electrons to quinones in the membrane, thus linking the TCA cycle with the aerobic respiratory chain (where it is known as complex II). Under anaerobic conditions the enzyme functions as a fumarate reductase, transferring electrons from the quinol pool to fumarate, and participating in anaerobic respiration with fumarate as the terminal electron acceptor. The enzyme interacts with the quinone produced by the organism, such as ubiquinone, menaquinone, caldariellaquinone, thermoplasmaquinone, rhodoquinone etc. Some of the enzymes contain two heme subunits in their membrane anchor subunit. These enzymes catalyse an electrogenic reaction and are thus classified as EC 7.1.1.12, succinate dehydrogenase (electrogenic, proton-motive force generating).

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, MetaCyc, PDB, CAS registry number: 9028-11-9

References:

1.	Kita, K., Vibat, C.R., Meinhardt, S., Guest, J.R. and Gennis, R.B. One-step purification from Escherichia coli of complex II (succinate: ubiquinone oxidoreductase) associated with succinate-reducible cytochrome b₅₅₆. J. Biol. Chem. 264 (1989) 2672–2677. [PMID: 2644269]
2.	Van Hellemond, J.J. and Tielens, A.G. Expression and functional properties of fumarate reductase. Biochem. J. 304 (1994) 321–331. [PMID: 7998964]
3.	Iverson, T.M., Luna-Chavez, C., Cecchini, G. and Rees, D.C. Structure of the Escherichia coli fumarate reductase respiratory complex. Science 284 (1999) 1961–1966. [DOI] [PMID: 10373108]
4.	Cecchini, G., Schroder, I., Gunsalus, R.P. and Maklashina, E. Succinate dehydrogenase and fumarate reductase from Escherichia coli. Biochim. Biophys. Acta 1553 (2002) 140–157. [DOI] [PMID: 11803023]
5.	Figueroa, P., Leon, G., Elorza, A., Holuigue, L., Araya, A. and Jordana, X. The four subunits of mitochondrial respiratory complex II are encoded by multiple nuclear genes and targeted to mitochondria in Arabidopsis thaliana. Plant Mol. Biol. 50 (2002) 725–734. [PMID: 12374303]
6.	Cecchini, G. Function and structure of complex II of the respiratory chain. Annu. Rev. Biochem. 72 (2003) 77–109. [DOI] [PMID: 14527321]
7.	Oyedotun, K.S. and Lemire, B.D. The quaternary structure of the Saccharomyces cerevisiae succinate dehydrogenase. Homology modeling, cofactor docking, and molecular dynamics simulation studies. J. Biol. Chem. 279 (2004) 9424–9431. [DOI] [PMID: 14672929]
8.	Kurokawa, T. and Sakamoto, J. Purification and characterization of succinate:menaquinone oxidoreductase from Corynebacterium glutamicum. Arch. Microbiol. 183 (2005) 317–324. [DOI] [PMID: 15883782]
9.	Iwata, F., Shinjyo, N., Amino, H., Sakamoto, K., Islam, M.K., Tsuji, N. and Kita, K. Change of subunit composition of mitochondrial complex II (succinate-ubiquinone reductase/quinol-fumarate reductase) in Ascaris suum during the migration in the experimental host. Parasitol Int 57 (2008) 54–61. [DOI] [PMID: 17933581]

[EC 1.3.5.1 created 1983 (EC 1.3.99.1 created 1961, incorporated 2014, EC 1.3.5.4 created 2010, incorporated 2022), modified 2022]

1.3.5.2

Accepted name:

dihydroorotate dehydrogenase (quinone)

Reaction:

(S)-dihydroorotate + a quinone = orotate + a quinol

Other name(s):

dihydroorotate:ubiquinone oxidoreductase; (S)-dihydroorotate:(acceptor) oxidoreductase; (S)-dihydroorotate:acceptor oxidoreductase; DHOdehase (ambiguous); DHOD (ambiguous); DHODase (ambiguous); DHODH

Systematic name:

(S)-dihydroorotate:quinone oxidoreductase

Comments:

This Class 2 dihydroorotate dehydrogenase enzyme contains FMN [4]. The enzyme is found in eukaryotes in the mitochondrial membrane, in cyanobacteria, and in some Gram-negative and Gram-positive bacteria associated with the cytoplasmic membrane [2,5,6]. The reaction is the only redox reaction in the de-novo biosynthesis of pyrimidine nucleotides [2,4]. The best quinone electron acceptors for the enzyme from bovine liver are ubiquinone-6 and ubiquinone-7, although simple quinones, such as benzoquinone, can also act as acceptor at lower rates [2]. Methyl-, ethyl-, tert-butyl and benzyl (S)-dihydroorotates are also substrates, but methyl esters of (S)-1-methyl and (S)-3-methyl and (S)-1,3-dimethyldihydroorotates are not [2]. Class 1 dihydroorotate dehydrogenases use either fumarate (EC 1.3.98.1), NAD⁺ (EC 1.3.1.14) or NADP⁺ (EC 1.3.1.15) as electron acceptor.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, MetaCyc, PDB, CAS registry number: 59088-23-2

References:

1.	Forman, H.J. and Kennedy, J. Mammalian dihydroorotate dehydrogenase: physical and catalytic properties of the primary enzyme. Arch. Biochem. Biophys. 191 (1978) 23–31. [DOI] [PMID: 216313]
2.	Hines, V., Keys, L.D., III and Johnston, M. Purification and properties of the bovine liver mitochondrial dihydroorotate dehydrogenase. J. Biol. Chem. 261 (1986) 11386–11392. [PMID: 3733756]
3.	Bader, B., Knecht, W., Fries, M. and Löffler, M. Expression, purification, and characterization of histidine-tagged rat and human flavoenzyme dihydroorotate dehydrogenase. Protein Expr. Purif. 13 (1998) 414–422. [DOI] [PMID: 9693067]
4.	Fagan, R.L., Nelson, M.N., Pagano, P.M. and Palfey, B.A. Mechanism of flavin reduction in Class 2 dihydroorotate dehydrogenases. Biochemistry 45 (2006) 14926–14932. [DOI] [PMID: 17154530]
5.	Björnberg, O., Grüner, A.C., Roepstorff, P. and Jensen, K.F. The activity of Escherichia coli dihydroorotate dehydrogenase is dependent on a conserved loop identified by sequence homology, mutagenesis, and limited proteolysis. Biochemistry 38 (1999) 2899–2908. [DOI] [PMID: 10074342]
6.	Nara, T., Hshimoto, T. and Aoki, T. Evolutionary implications of the mosaic pyrimidine-biosynthetic pathway in eukaryotes. Gene 257 (2000) 209–222. [DOI] [PMID: 11080587]

[EC 1.3.5.2 created 1983 as EC 1.3.99.11, transferred 2009 to EC 1.3.5.2, modified 2011]

1.3.5.3

Accepted name:

protoporphyrinogen IX dehydrogenase (quinone)

Reaction:

protoporphyrinogen IX + 3 quinone = protoporphyrin IX + 3 quinol

Other name(s):

HemG; protoporphyrinogen IX dehydrogenase (menaquinone)

Systematic name:

protoporphyrinogen IX:quinone oxidoreductase

Comments:

Contains FMN. The enzyme participates in heme b biosynthesis. In the bacterium Escherichia coli it interacts with either ubiquinone or menaquinone, depending on whether the organism grows aerobically or anaerobically.

Links to other databases:

References:

1.	Boynton, T.O., Daugherty, L.E., Dailey, T.A. and Dailey, H.A. Identification of Escherichia coli HemG as a novel, menadione-dependent flavodoxin with protoporphyrinogen oxidase activity. Biochemistry 48 (2009) 6705–6711. [DOI] [PMID: 19583219]
2.	Möbius, K., Arias-Cartin, R., Breckau, D., Hännig, A.L., Riedmann, K., Biedendieck, R., Schroder, S., Becher, D., Magalon, A., Moser, J., Jahn, M. and Jahn, D. Heme biosynthesis is coupled to electron transport chains for energy generation. Proc. Natl. Acad. Sci. USA 107 (2010) 10436–10441. [PMID: 20484676]

[EC 1.3.5.3 created 2010, modified 2020]

1.3.5.4

Transferred entry:

fumarate reductase (quinol), now included in EC 1.3.5.1, succinate dehydrogenase.

[EC 1.3.5.4 created 2010, modified 2013, deleted 2022]

1.3.5.5

Accepted name:

15-cis-phytoene desaturase

Reaction:

15-cis-phytoene + 2 plastoquinone = 9,15,9′-tricis-ζ-carotene + 2 plastoquinol (overall reaction)
(1a) 15-cis-phytoene + plastoquinone = 15,9′-dicis-phytofluene + plastoquinol
(1b) 15,9′-dicis-phytofluene + plastoquinone = 9,15,9′-tricis-ζ-carotene + plastoquinol

For diagram of plant and cyanobacteria carotenoid biosynthesis, click here

Other name(s):

phytoene desaturase (ambiguous); PDS; plant-type phytoene desaturase

Systematic name:

15-cis-phytoene:plastoquinone oxidoreductase

Comments:

This enzyme is involved in carotenoid biosynthesis in plants and cyanobacteria. The enzyme from Synechococcus can also use NAD⁺ and NADP⁺ as electron acceptor under anaerobic conditions. The enzyme from Gentiana lutea shows no activity with NAD⁺ or NADP⁺ [1].

Links to other databases:

References:

1.	Breitenbach, J., Zhu, C. and Sandmann, G. Bleaching herbicide norflurazon inhibits phytoene desaturase by competition with the cofactors. J. Agric. Food Chem. 49 (2001) 5270–5272. [DOI] [PMID: 11714315]
2.	Schneider, C., Boger, P. and Sandmann, G. Phytoene desaturase: heterologous expression in an active state, purification, and biochemical properties. Protein Expr. Purif. 10 (1997) 175–179. [DOI] [PMID: 9226712]
3.	Fraser, P.D., Linden, H. and Sandmann, G. Purification and reactivation of recombinant Synechococcus phytoene desaturase from an overexpressing strain of Escherichia coli. Biochem. J. 291 (1993) 687–692. [PMID: 8489496]
4.	Breitenbach, J. and Sandmann, G. ζ-Carotene cis isomers as products and substrates in the plant poly-cis carotenoid biosynthetic pathway to lycopene. Planta 220 (2005) 785–793. [DOI] [PMID: 15503129]

[EC 1.3.5.5 created 2011]

1.3.5.6

Accepted name:

9,9′-dicis-ζ-carotene desaturase

Reaction:

9,9′-dicis-ζ-carotene + 2 quinone = 7,9,7′,9′-tetracis-lycopene + 2 quinol (overall reaction)
(1a) 9,9′-dicis-ζ-carotene + a quinone = 7,9,9′-tricis-neurosporene + a quinol
(1b) 7,9,9′-tricis-neurosporene + a quinone = 7,9,7′,9′-tetracis-lycopene + a quinol

For diagram of plant and cyanobacteria carotenoid biosynthesis, click here

Glossary:

prolycopene = 7,9,7′,9′-tetracis-lycopene

Other name(s):

ζ-carotene desaturase; ZDS

Systematic name:

9,9′-dicis-ζ-corotene:quinone oxidoreductase

Comments:

This enzyme is involved in carotenoid biosynthesis in plants and cyanobacteria.

Links to other databases:

References:

1.	Albrecht, M., Linden, H. and Sandmann, G. Biochemical characterization of purified ζ-carotene desaturase from Anabaena PCC 7120 after expression in E. coli. Eur. J. Biochem. 236 (1996) 115–120. [DOI] [PMID: 8617254]
2.	Josse, E.M., Simkin, A.J., Gaffe, J., Laboure, A.M., Kuntz, M. and Carol, P. A plastid terminal oxidase associated with carotenoid desaturation during chromoplast differentiation. Plant Physiol. 123 (2000) 1427–1436. [PMID: 10938359]
3.	Breitenbach, J., Kuntz, M., Takaichi, S. and Sandmann, G. Catalytic properties of an expressed and purified higher plant type ζ-carotene desaturase from Capsicum annuum. Eur. J. Biochem. 265 (1999) 376–383. [DOI] [PMID: 10491195]
4.	Breitenbach, J. and Sandmann, G. ζ-Carotene cis isomers as products and substrates in the plant poly-cis carotenoid biosynthetic pathway to lycopene. Planta 220 (2005) 785–793. [DOI] [PMID: 15503129]

[EC 1.3.5.6 created 1999 as EC 1.14.99.30, transferred 2011 to EC 1.3.5.6]

1.3.7.1

Accepted name:

6-hydroxynicotinate reductase

Reaction:

6-oxo-1,4,5,6-tetrahydronicotinate + oxidized ferredoxin = 6-hydroxynicotinate + reduced ferredoxin

For diagram of nicotinate catabolism, click here

Other name(s):

6-oxotetrahydronicotinate dehydrogenase; 6-hydroxynicotinic reductase; HNA reductase; 1,4,5,6-tetrahydro-6-oxonicotinate:ferredoxin oxidoreductase

Systematic name:

6-oxo-1,4,5,6-tetrahydronicotinate:ferredoxin oxidoreductase

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, MetaCyc, CAS registry number: 9030-84-6

References:

1.	Holcenberg, J.S. and Tsai, L. Nicotinic acid metabolism. IV. Ferredoxin-dependent reduction of 6-hydroxynicotinic acid to 6-oxo-1,4,5,6-tetrahydronicotinic acid. J. Biol. Chem. 244 (1969) 1204–1211. [PMID: 5767303]

[EC 1.3.7.1 created 1972]

1.3.7.2

Accepted name:

15,16-dihydrobiliverdin:ferredoxin oxidoreductase

Reaction:

15,16-dihydrobiliverdin + oxidized ferredoxin = biliverdin IXα + reduced ferredoxin

For diagram of biliverdin metabolism, click here

Other name(s):

PebA

Systematic name:

15,16-dihydrobiliverdin:ferredoxin oxidoreductase

Comments:

Catalyses the two-electron reduction of biliverdin IXα at the C15 methine bridge. It has been proposed that this enzyme and EC 1.3.7.3, phycoerythrobilin:ferredoxin oxidoreductase, function as a dual enzyme complex in the conversion of biliverdin IXα into phycoerythrobilin.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, MetaCyc, PDB, CAS registry number: 347401-20-1

References:

1.	Frankenberg, N., Mukougawa, K., Kohchi, T. and Lagarias, J.C. Functional genomic analysis of the HY2 family of ferredoxin-dependent bilin reductases from oxygenic photosynthetic organisms. Plant Cell 13 (2001) 965–978. [PMID: 11283349]

[EC 1.3.7.2 created 2002]

1.3.7.3

Accepted name:

phycoerythrobilin:ferredoxin oxidoreductase

Reaction:

(3Z)-phycoerythrobilin + oxidized ferredoxin = 15,16-dihydrobiliverdin + reduced ferredoxin

For diagram of biliverdin metabolism, click here

Other name(s):

PebB

Systematic name:

(3Z)-phycoerythrobilin:ferredoxin oxidoreductase

Comments:

Catalyses the two-electron reduction of the C2 and C3¹ diene system of 15,16-dihydrobiliverdin. Specific for 15,16-dihydrobiliverdin. It has been proposed that this enzyme and EC 1.3.7.2, 15,16-dihydrobiliverdin:ferredoxin oxidoreductase, function as a dual enzyme complex in the conversion of biliverdin IXα to phycoerythrobilin.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, MetaCyc, CAS registry number: 347401-21-2

References:

1.	Frankenberg, N., Mukougawa, K., Kohchi, T. and Lagarias, J.C. Functional genomic analysis of the HY2 family of ferredoxin-dependent bilin reductases from oxygenic photosynthetic organisms. Plant Cell 13 (2001) 965–978. [PMID: 11283349]

[EC 1.3.7.3 created 2002]

1.3.7.4

Accepted name:

phytochromobilin:ferredoxin oxidoreductase

Reaction:

(3Z)-phytochromobilin + 2 oxidized ferredoxin = biliverdin IXα + 2 reduced ferredoxin

For diagram of biliverdin metabolism, click here

Other name(s):

HY2; PPhi B synthase; phytochromobilin synthase

Systematic name:

(3Z)-phytochromobilin:ferredoxin oxidoreductase

Comments:

Catalyses the two-electron reduction of biliverdin IXα. Can use [2Fe-2S] ferredoxins from a number of sources as acceptor but not the [4Fe-4S] ferredoxin from Clostridium pasteurianum. The isomerization of (3Z)-phytochromobilin to (3E)-phytochromobilin is thought to occur prior to covalent attachment to apophytochrome in the plant cell cytoplasm. Flavodoxins can be used instead of ferredoxin.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, MetaCyc, PDB, CAS registry number: 138263-99-7

References:

1.	Frankenberg, N., Mukougawa, K., Kohchi, T. and Lagarias, J.C. Functional genomic analysis of the HY2 family of ferredoxin-dependent bilin reductases from oxygenic photosynthetic organisms. Plant Cell 13 (2001) 965–978. [PMID: 11283349]
2.	McDowell, M.T. and Lagarias, J.C. Purification and biochemical properties of phytochromobilin synthase from etiolated oat seedlings. Plant Physiol. 126 (2001) 1546–1554. [PMID: 11500553]
3.	Terry, M.J., Wahleithner, J.A. and Lagarias, J.C. Biosynthesis of the plant photoreceptor phytochrome. Arch. Biochem. Biophys. 306 (1993) 1–15. [DOI] [PMID: 8215388]

[EC 1.3.7.4 created 2002]

1.3.7.5

Accepted name:

phycocyanobilin:ferredoxin oxidoreductase

Reaction:

(3Z)-phycocyanobilin + 4 oxidized ferredoxin = biliverdin IXα + 4 reduced ferredoxin

For diagram of biliverdin metabolism, click here

Systematic name:

(3Z)-phycocyanobilin:ferredoxin oxidoreductase

Comments:

Catalyses the four-electron reduction of biliverdin IXα (2-electron reduction at both the A and D rings). Reaction proceeds via an isolatable 2-electron intermediate, 18¹,18²-dihydrobiliverdin. Flavodoxins can be used instead of ferredoxin. The direct conversion of biliverdin IXα (BV) to (3Z)-phycocyanolbilin (PCB) in the cyanobacteria Synechocystis sp. PCC 6803, Anabaena sp. PCC7120 and Nostoc punctiforme is in contrast to the proposed pathways of PCB biosynthesis in the red alga Cyanidium caldarium, which involves (3Z)-phycoerythrobilin (PEB) as an intermediate [2] and in the green alga Mesotaenium caldariorum, in which PCB is an isolable intermediate.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, MetaCyc, PDB, CAS registry number: 347401-12-1

References:

1.	Frankenberg, N., Mukougawa, K., Kohchi, T. and Lagarias, J.C. Functional genomic analysis of the HY2 family of ferredoxin-dependent bilin reductases from oxygenic photosynthetic organisms. Plant Cell 13 (2001) 965–978. [PMID: 11283349]
2.	Beale, S.I. Biosynthesis of phycobilins. Chem. Rev. 93 (1993) 785–802.
3.	Wu, S.-H., McDowell, M.T. and Lagarias, J.C. Phycocyanobilin is the natural chromophore precursor of phytochrome from the green alga Mesotaenium caldariorum. J. Biol. Chem. 272 (1997) 25700–25705. [DOI] [PMID: 9325294]

[EC 1.3.7.5 created 2002, modified 2014]

1.3.7.6

Accepted name:

phycoerythrobilin synthase

Reaction:

(3Z)-phycoerythrobilin + 2 oxidized ferredoxin = biliverdin IXα + 2 reduced ferredoxin

Other name(s):

PebS

Systematic name:

(3Z)-phycoerythrobilin:ferredoxin oxidoreductase (from biliverdin IXα)

Comments:

This enzyme, from a cyanophage infecting oceanic cyanobacteria of the Prochlorococcus genus, uses a four-electron reduction to carry out the reactions catalysed by EC 1.3.7.2 (15,16-dihydrobiliverdin:ferredoxin oxidoreductase) and EC 1.3.7.3 (phycoerythrobilin:ferredoxin oxidoreductase). 15,16-Dihydrobiliverdin is formed as a bound intermediate. Free 15,16-dihydrobiliverdin can also act as a substrate to form phycoerythrobilin.

Links to other databases:

References:

1.	Dammeyer, T., Bagby, S.C., Sullivan, M.B., Chisholm, S.W. and Frankenberg-Dinkel, N. Efficient phage-mediated pigment biosynthesis in oceanic cyanobacteria. Curr. Biol. 18 (2008) 442–448. [DOI] [PMID: 18356052]

[EC 1.3.7.6 created 2008]

1.3.7.7

Accepted name:

ferredoxin:protochlorophyllide reductase (ATP-dependent)

Reaction:

chlorophyllide a + oxidized ferredoxin + 2 ADP + 2 phosphate = protochlorophyllide a + reduced ferredoxin + 2 ATP + 2 H₂O

For diagram of chlorophyll biosynthesis (later stages), click here

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.

Links to other databases:

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. [DOI] [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. [DOI] [PMID: 20400946]

[EC 1.3.7.7 created 2011, modified 2013]

1.3.7.8

Accepted name:

benzoyl-CoA reductase

Reaction:

cyclohexa-1,5-diene-1-carbonyl-CoA + oxidized ferredoxin + 2 ADP + 2 phosphate = benzoyl-CoA + reduced ferredoxin + 2 ATP + 2 H₂O

For diagram of Benzoyl-CoA catabolism, click here

Other name(s):

benzoyl-CoA reductase (dearomatizing)

Systematic name:

cyclohexa-1,5-diene-1-carbonyl-CoA:ferredoxin oxidoreductase (aromatizing, ATP-forming)

Comments:

An iron-sulfur protein. Requires Mg²⁺ or Mn²⁺. Inactive towards aromatic acids that are not CoA esters but will also catalyse the reaction: ammonia + acceptor + 2 ADP + 2 phosphate = hydroxylamine + reduced acceptor + 2 ATP + H₂O. In the presence of reduced acceptor, but in the absence of oxidizable substrate, the enzyme catalyses the hydrolysis of ATP to ADP plus phosphate.

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, Gene, KEGG, MetaCyc, CAS registry number: 176591-18-7

References:

1.	Boll, M. and Fuchs, G. Benzoyl-coenzyme A reductase (dearomatizing), a key enzyme of anaerobic aromatic metabolism. ATP dependence of the reaction, purification and some properties of the enzyme from Thauera aromatica strain K172. Eur. J. Biochem. 234 (1995) 921–933. [DOI] [PMID: 8575453]
2.	Kung, J.W., Baumann, S., von Bergen, M., Muller, M., Hagedoorn, P.L., Hagen, W.R. and Boll, M. Reversible biological Birch reduction at an extremely low redox potential. J. Am. Chem. Soc. 132 (2010) 9850–9856. [DOI] [PMID: 20578740]

[EC 1.3.7.8 created 1999 as EC 1.3.99.15, transferred 2011 to EC 1.3.7.8, modified 2011]

1.3.7.9

Transferred entry:

4-hydroxybenzoyl-CoA reductase. Now classified as EC 1.1.7.1, 4-hydroxybenzoyl-CoA reductase.

[EC 1.3.7.9 created 2000 as EC 1.3.99.20, transferred 2011 to EC 1.3.7.9, deleted 2020]

1.3.7.10

Transferred entry:

pentalenolactone synthase. Now EC 1.14.19.8, pentalenolactone synthase

[EC 1.3.7.10 created 2012, deleted 2013]

1.3.7.11

Accepted name:

2,3-bis-O-geranylgeranyl-sn-glycero-phospholipid reductase

Reaction:

a 2,3-bis-(O-phytanyl)-sn-glycero-phospholipid + 16 oxidized ferredoxin [iron-sulfur] cluster = a 2,3-bis-(O-geranylgeranyl)-sn-glycero-phospholipid + 16 reduced ferredoxin [iron-sulfur] cluster + 16 H⁺

For diagram of archaetidylserine biosynthesis, click here

Glossary:

phytanol = 3,7,11,15-tetramethylhexadecan-1-ol

Other name(s):

AF0464 (gene name); 2,3-bis-O-geranylgeranyl-sn-glycerol 1-phosphate reductase (donor)

Systematic name:

2,3-bis-(O-phytanyl)-sn-glycero-phospholipid:ferredoxin oxidoreductase

Comments:

A flavoprotein (FAD). The enzyme is involved in the biosynthesis of archaeal membrane lipids. It catalyses the reduction of all 8 double bonds in 2,3-bis-O-geranylgeranyl-sn-glycero-phospholipids and all 4 double bonds in 3-O-geranylgeranyl-sn-glycerol phospholipids with comparable activity. Unlike EC 1.3.1.101, 2,3-bis-O-geranylgeranyl-sn-glycerol 1-phosphate reductase [NAD(P)H], this enzyme shows no activity with NADPH, and requires a dedicated ferredoxin [4].

Links to other databases:

References:

1.	Murakami, M., Shibuya, K., Nakayama, T., Nishino, T., Yoshimura, T. and Hemmi, H. Geranylgeranyl reductase involved in the biosynthesis of archaeal membrane lipids in the hyperthermophilic archaeon Archaeoglobus fulgidus. FEBS J. 274 (2007) 805–814. [DOI] [PMID: 17288560]
2.	Sato, S., Murakami, M., Yoshimura, T. and Hemmi, H. Specific partial reduction of geranylgeranyl diphosphate by an enzyme from the thermoacidophilic archaeon Sulfolobus acidocaldarius yields a reactive prenyl donor, not a dead-end product. J. Bacteriol. 190 (2008) 3923–3929. [DOI] [PMID: 18375567]
3.	Sasaki, D., Fujihashi, M., Iwata, Y., Murakami, M., Yoshimura, T., Hemmi, H. and Miki, K. Structure and mutation analysis of archaeal geranylgeranyl reductase. J. Mol. Biol. 409 (2011) 543–557. [DOI] [PMID: 21515284]
4.	Isobe, K., Ogawa, T., Hirose, K., Yokoi, T., Yoshimura, T. and Hemmi, H. Geranylgeranyl reductase and ferredoxin from Methanosarcina acetivorans are required for the synthesis of fully reduced archaeal membrane lipid in Escherichia coli cells. J. Bacteriol. 196 (2014) 417–423. [DOI] [PMID: 24214941]

[EC 1.3.7.11 created 2013 as EC 1.3.99.34, transferred 2015 to EC 1.3.7.11 ]

1.3.7.12

Accepted name:

red chlorophyll catabolite reductase

Reaction:

primary fluorescent chlorophyll catabolite + 2 oxidized ferredoxin [iron-sulfur] cluster = red chlorophyll catabolite + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H⁺

For diagram of chlorophyll catabolism, click here

Glossary:

red chlorophyll catabolite = RCC = (7S,8S,10¹R)-8-(2-carboxyethyl)-17-ethyl-19-formyl-10¹-(methoxycarbonyl)-3,7,13,18-tetramethyl-2-vinyl-8,23-dihydro-7H-10,12-ethanobiladiene-ab-1,10²(21H)-dione
primary fluorescent chlorophyll catabolite = pFCC = (8²R,12S,13S)-12-(2-carboxyethyl)-3-ethyl-1-formyl-8²-(methoxycarbonyl)-2,7,13,17-tetramethyl-18-vinyl-12,13-dihydro-8,10-ethanobilene-b-8¹,19(16H)-dione

Other name(s):

RCCR; RCC reductase; red Chl catabolite reductase

Systematic name:

primary fluorescent chlorophyll catabolite:ferredoxin oxidoreductase

Comments:

The enzyme participates in chlorophyll degradation, which occurs during leaf senescence and fruit ripening in higher plants. The reaction requires reduced ferredoxin, which is generated from NADPH produced either through the pentose-phosphate pathway or by the action of photosystem I [1,2]. This reaction takes place while red chlorophyll catabolite is still bound to EC 1.14.15.17, pheophorbide a oxygenase [3]. Depending on the plant species used as the source of enzyme, one of two possible C-1 epimers of primary fluorescent chlorophyll catabolite (pFCC), pFCC-1 or pFCC-2, is normally formed, with all genera or species within a family producing the same isomer [3,4]. After modification and export, pFCCs are eventually imported into the vacuole, where the acidic environment causes their non-enzymic conversion into colourless breakdown products called non-fluorescent chlorophyll catabolites (NCCs) [2].

Links to other databases:

References:

1.	Rodoni, S., Mühlecker, W., Anderl, M., Kräutler, B., Moser, D., Thomas, H., Matile, P. and Hörtensteiner, S. Chlorophyll breakdown in senescent chloroplasts. Cleavage of pheophorbide a in two enzymic steps. Plant Physiol. 115 (1997) 669–676. [PMID: 12223835]
2.	Wüthrich, K.L., Bovet, L., Hunziker, P.E., Donnison, I.S. and Hörtensteiner, S. Molecular cloning, functional expression and characterisation of RCC reductase involved in chlorophyll catabolism. Plant J. 21 (2000) 189–198. [DOI] [PMID: 10743659]
3.	Pružinská, A., Anders, I., Aubry, S., Schenk, N., Tapernoux-Lüthi, E., Müller, T., Kräutler, B. and Hörtensteiner, S. In vivo participation of red chlorophyll catabolite reductase in chlorophyll breakdown. Plant Cell 19 (2007) 369–387. [DOI] [PMID: 17237353]
4.	Hörtensteiner, S. Chlorophyll degradation during senescence. Annu. Rev. Plant Biol. 57 (2006) 55–77. [DOI] [PMID: 16669755]
5.	Rodoni, S., Vicentini, F., Schellenberg, M., Matile, P. and Hörtensteiner, S. Partial purification and characterization of red chlorophyll catabolite reductase, a stroma protein involved in chlorophyll breakdown. Plant Physiol. 115 (1997) 677–682. [PMID: 12223836]

[EC 1.3.7.12 created 2007 as EC 1.3.1.80, transferred 2016 to EC 1.3.7.12]

1.3.7.13

Accepted name:

3,8-divinyl protochlorophyllide a 8-vinyl-reductase (ferredoxin)

Reaction:

protochlorophyllide a + 2 oxidized ferredoxin [iron-sulfur] cluster = 3,8-divinyl protochlorophyllide a + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H⁺

For diagram of chlorophyll biosynthesis (later stages), click here

Other name(s):

bciB (gene name); cyano-type divinyl chlorophyllide a 8-vinyl-reductase

Systematic name:

protochlorophyllide-a:ferredoxin C-8¹-oxidoreductase

Comments:

The enzyme, found in many phototrophic bacteria, land plants, and some green and red algae, is involved in the production of monovinyl versions of (bacterio)chlorophyll pigments from their divinyl precursors. Binds two [4Fe-4S] clusters and an FAD cofactor. It can also act on 3,8-divinyl chlorophyllide a, 3,8-divinyl chlorophyll a, and chlorophyll c₂. cf. EC 1.3.1.75, 3,8-divinyl protochlorophyllide a 8-vinyl-reductase (NADPH).

Links to other databases:

References:

1.	Chew, A.G. and Bryant, D.A. Characterization of a plant-like protochlorophyllide a divinyl reductase in green sulfur bacteria. J. Biol. Chem. 282 (2007) 2967–2975. [DOI] [PMID: 17148453]
2.	Saunders, A.H., Golbeck, J.H. and Bryant, D.A. Characterization of BciB: a ferredoxin-dependent 8-vinyl-protochlorophyllide reductase from the green sulfur bacterium Chloroherpeton thalassium. Biochemistry 52 (2013) 8442–8451. [DOI] [PMID: 24151992]
3.	Ito, H. and Tanaka, A. Evolution of a new chlorophyll metabolic pathway driven by the dynamic changes in enzyme promiscuous activity. Plant Cell Physiol. 55 (2014) 593–603. [DOI] [PMID: 24399236]

[EC 1.3.7.13 created 2016]

1.3.7.14

Accepted name:

3,8-divinyl chlorophyllide a reductase

Reaction:

bacteriochlorophyllide g + 2 oxidized ferredoxin [iron-sulfur] cluster + ADP + phosphate = 3,8-divinyl chlorophyllide a + 2 reduced ferredoxin [iron-sulfur] cluster + ATP + H₂O + 2 H⁺

For diagram of bacteriochlorophllide g biosynthesis, click here

Systematic name:

bacteriochlorophyllide-g:ferredoxin C-8¹-oxidoreductase

Comments:

The enzyme, found only in bacteriochlorophyll b-producing bacteria, catalyses the introduction of a C-8 ethylidene group. The enzyme contains a [4Fe-4S] cluster, and structurally resembles the Fe protein/MoFe protein complex of nitrogenase. It is very similar to EC 1.3.7.15, chlorophyllide a reductase, and is composed of three subunits. Two of them form the catalytic component, while the third one functions as an ATP-dependent reductase component that catalyses the electron transfer from ferredoxin to the catalytic component.

Links to other databases:

References:

1.	Tsukatani, Y., Yamamoto, H., Harada, J., Yoshitomi, T., Nomata, J., Kasahara, M., Mizoguchi, T., Fujita, Y. and Tamiaki, H. An unexpectedly branched biosynthetic pathway for bacteriochlorophyll b capable of absorbing near-infrared light. Sci. Rep. 3:1217 (2013). [DOI] [PMID: 23386973]
2.	Tsukatani, Y., Harada, J., Nomata, J., Yamamoto, H., Fujita, Y., Mizoguchi, T. and Tamiaki, H. Rhodobacter sphaeroides mutants overexpressing chlorophyllide a oxidoreductase of Blastochloris viridis elucidate functions of enzymes in late bacteriochlorophyll biosynthetic pathways. Sci. Rep. 5:9741 (2015). [DOI] [PMID: 25978726]

[EC 1.3.7.14 created 2016]

1.3.7.15

Accepted name:

chlorophyllide a reductase

Reaction:

(1) 3-deacetyl-3-vinylbacteriochlorophyllide a + 2 oxidized ferredoxin [iron-sulfur] cluster + ADP + phosphate = chlorophyllide a + 2 reduced ferredoxin [iron-sulfur] cluster + ATP + H₂O + 2 H⁺
(2) bacteriochlorophyllide a + 2 oxidized ferredoxin [iron-sulfur] cluster + ADP + phosphate = 3-acetyl-3-devinylchlorophyllide a + 2 reduced ferredoxin [iron-sulfur] cluster + ATP + H₂O + 2 H⁺
(3) 3-deacetyl-3-(1-hydroxyethyl)bacteriochlorophyllide a + 2 oxidized ferredoxin [iron-sulfur] cluster + ADP + phosphate = 3-devinyl-3-(1-hydroxyethyl)chlorophyllide a + 2 reduced ferredoxin [iron-sulfur] cluster + ATP + H₂O + 2 H⁺

For diagram of chlorophyll catabolism, click here

Other name(s):

bchX (gene name); bchY (gene name); bchZ (gene name); COR

Systematic name:

bacteriochlorophyllide-a:ferredoxin 7,8-oxidoreductase

Comments:

The enzyme, together with EC 1.1.1.396, bacteriochlorophyllide-a dehydrogenase, and EC 4.2.1.165, chlorophyllide-a 3¹-hydratase, is involved in the conversion of chlorophyllide a to bacteriochlorophyllide a. These enzymes can act in multiple orders, resulting in the formation of different intermediates, but the final product of the cumulative action of the three enzymes is always bacteriochlorophyllide a. This enzyme catalyses a trans-reduction of the B-ring; the product has the (7R,8R)-configuration. In addition, the enzyme has a latent activity of EC 1.3.7.13, 3,8-divinyl protochlorophyllide a 8-vinyl-reductase (ferredoxin) [4]. 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.

Links to other databases:

References:

1.	Nomata, J., Mizoguchi, T., Tamiaki, H. and Fujita, Y. A second nitrogenase-like enzyme for bacteriochlorophyll biosynthesis: reconstitution of chlorophyllide a reductase with purified X-protein (BchX) and YZ-protein (BchY-BchZ) from Rhodobacter capsulatus. J. Biol. Chem. 281 (2006) 15021–15028. [DOI] [PMID: 16571720]
2.	Tsukatani, Y., Yamamoto, H., Harada, J., Yoshitomi, T., Nomata, J., Kasahara, M., Mizoguchi, T., Fujita, Y. and Tamiaki, H. An unexpectedly branched biosynthetic pathway for bacteriochlorophyll b capable of absorbing near-infrared light. Sci. Rep. 3:1217 (2013). [DOI] [PMID: 23386973]
3.	Lange, C., Kiesel, S., Peters, S., Virus, S., Scheer, H., Jahn, D. and Moser, J. Broadened substrate specificity of 3-hydroxyethyl bacteriochlorophyllide a dehydrogenase (BchC) indicates a new route for the biosynthesis of bacteriochlorophyll a. J. Biol. Chem. 290 (2015) 19697–19709. [DOI] [PMID: 26088139]
4.	Harada, J., Mizoguchi, T., Tsukatani, Y., Yokono, M., Tanaka, A. and Tamiaki, H. Chlorophyllide a oxidoreductase works as one of the divinyl reductases specifically involved in bacteriochlorophyll a biosynthesis. J. Biol. Chem. 289 (2014) 12716–12726. [DOI] [PMID: 24637023]

[EC 1.3.7.15 created 1965 as EC 1.3.99.35, modified 2012, transferred 2016 to EC 1.3.7.15]

1.3.8.1

Accepted name:

short-chain acyl-CoA dehydrogenase

Reaction:

a short-chain acyl-CoA + electron-transfer flavoprotein = a short-chain trans-2,3-dehydroacyl-CoA + reduced electron-transfer flavoprotein

Glossary:

a short-chain acyl-CoA = an acyl-CoA thioester where the acyl chain contains less than 6 carbon atoms.

Other name(s):

butyryl-CoA dehydrogenase; butanoyl-CoA dehydrogenase; butyryl dehydrogenase; unsaturated acyl-CoA reductase; ethylene reductase; enoyl-coenzyme A reductase; unsaturated acyl coenzyme A reductase; butyryl coenzyme A dehydrogenase; short-chain acyl CoA dehydrogenase; short-chain acyl-coenzyme A dehydrogenase; 3-hydroxyacyl CoA reductase; butanoyl-CoA:(acceptor) 2,3-oxidoreductase; ACADS (gene name).

Systematic name:

short-chain acyl-CoA:electron-transfer flavoprotein 2,3-oxidoreductase

Comments:

Contains a tightly-bound FAD cofactor. One of several enzymes that catalyse the first step in fatty acids β-oxidation. The enzyme catalyses the oxidation of saturated short-chain acyl-CoA thioesters to give a trans 2,3-unsaturated product by removal of the two pro-R-hydrogen atoms. The enzyme from beef liver accepts substrates with acyl chain lengths of 3 to 8 carbon atoms. The highest activity was reported with either butanoyl-CoA [2] or pentanoyl-CoA [4]. The enzyme from rat has only 10% activity with hexanoyl-CoA (compared to butanoyl-CoA) and no activity with octanoyl-CoA [6]. cf. EC 1.3.8.7, medium-chain acyl-CoA dehydrogenase, EC 1.3.8.8, long-chain acyl-CoA dehydrogenase, and EC 1.3.8.9, very-long-chain acyl-CoA dehydrogenase.

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, Gene, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9027-88-7

References:

1.	Mahler, H.R. Studies on the fatty acid oxidizing system of animal tissue. IV. The prosthetic group of butyryl coenzyme A dehydrogenase. J. Biol. Chem. 206 (1954) 13–26. [PMID: 13130522]
2.	Green, D.E., Mii, S., Mahler, H.R. and Bock, R.M. Studies on the fatty acid oxidizing system of animal tissue. III. Butyryl coenzyme A dehydrogenase. J. Biol. Chem. 206 (1954) 1–12. [PMID: 13130521]
3.	Beinert, H. Acyl coenzyme A dehydrogenase. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Ed.), The Enzymes, 2nd edn, vol. 7, Academic Press, New York, 1963, pp. 447–466.
4.	Shaw, L. and Engel, P.C. The purification and properties of ox liver short-chain acyl-CoA dehydrogenase. Biochem. J. 218 (1984) 511–520. [PMID: 6712627]
5.	Thorpe, C. and Kim, J.J. Structure and mechanism of action of the acyl-CoA dehydrogenases. FASEB J. 9 (1995) 718–725. [PMID: 7601336]
6.	Ikeda, Y., Ikeda, K.O. and Tanaka, K. Purification and characterization of short-chain, medium-chain, and long-chain acyl-CoA dehydrogenases from rat liver mitochondria. Isolation of the holo- and apoenzymes and conversion of the apoenzyme to the holoenzyme. J. Biol. Chem. 260 (1985) 1311–1325. [PMID: 3968063]
7.	McMahon, B., Gallagher, M.E. and Mayhew, S.G. The protein coded by the PP2216 gene of Pseudomonas putida KT2440 is an acyl-CoA dehydrogenase that oxidises only short-chain aliphatic substrates. FEMS Microbiol. Lett. 250 (2005) 121–127. [DOI] [PMID: 16024185]

[EC 1.3.8.1 created 1961 as EC 1.3.2.1, transferred 1964 to EC 1.3.99.2, transferred 2011 to EC 1.3.8.1, modified 2012]

1.3.8.2

Accepted name:

4,4′-diapophytoene desaturase (4,4′-diapolycopene-forming)

Reaction:

15-cis-4,4′-diapophytoene + 4 FAD = all-trans-4,4′-diapolycopene + 4 FADH₂ (overall reaction)
(1a) 15-cis-4,4′-diapophytoene + FAD = all-trans-4,4′-diapophytofluene + FADH₂
(1b) all-trans-4,4′-diapophytofluene + FAD = all-trans-4,4′-diapo-ζ-carotene + FADH₂
(1c) all-trans-4,4′-diapo-ζ-carotene + FAD = all-trans-4,4′-diaponeurosporene + FADH₂
(1d) all-trans-4,4′-diaponeurosporene + FAD = all-trans-4,4′-diapolycopene + FADH₂

For diagram of C₃₀ carotenoid biosynthesis, click here

Other name(s):

dehydrosqualene desaturase (ambiguous); CrtN (ambiguous); 4,4′-diapophytoene:FAD oxidoreductase (ambiguous); 15-cis-4,4′-diapophytoene:FAD oxidoreductase; 4,4′-diapophytoene desaturase (ambiguous)

Systematic name:

15-cis-4,4′-diapophytoene:FAD oxidoreductase (4,4′-diapolycopene-forming)

Comments:

The enzyme catalyses four successive dehydrogenations, resulting in production of 4,4′-diapolycopene. While the enzyme from Staphylococcus aureus was only shown to produce 4,4′-diaponeurosporene in vivo [4], it is able to catalyse the last reaction in vitro [5].

Links to other databases: