Proposed Changes to the Enzyme List

References:

1.	Tao, L., Schenzle, A., Odom, J.M. and Cheng, Q. Novel carotenoid oxidase involved in biosynthesis of 4,4′-diapolycopene dialdehyde. Appl. Environ. Microbiol. 71 (2005) 3294–3301. [DOI] [PMID: 15933032]
2.	Steiger, S., Perez-Fons, L., Cutting, S.M., Fraser, P.D. and Sandmann, G. Annotation and functional assignment of the genes for the C₃₀ carotenoid pathways from the genomes of two bacteria: Bacillus indicus and Bacillus firmus. Microbiology 161 (2015) 194–202. [DOI] [PMID: 25326460]

[EC 1.2.99.10 created 2017]

1.3.1.113

Accepted name:

(4-alkanoyl-5-oxo-2,5-dihydrofuran-3-yl)methyl phosphate reductase

Reaction:

a [(3S,4R)-4-alkanoyl-5-oxooxolan-3-yl]methyl phosphate + NADP⁺ = a (4-alkanoyl-5-oxo-2,5-dihydrofuran-3-yl)methyl phosphate + NADPH + H⁺

Other name(s):

bprA (gene name); scbC (gene name)

Systematic name:

[(3S,4R)-4-alkanoyl-5-oxooxolan-3-yl]methyl-phosphate:NADP⁺ oxidoreductase

Comments:

The enzyme, characterized from the bacteria Streptomyces griseus and Streptomyces coelicolor, is involved in the biosynthesis of γ-butyrolactone autoregulators that control secondary metabolism and morphological development in Streptomyces bacteria.

Links to other databases:

References:

1.	Kato, J.Y., Funa, N., Watanabe, H., Ohnishi, Y. and Horinouchi, S. Biosynthesis of γ-butyrolactone autoregulators that switch on secondary metabolism and morphological development in Streptomyces. Proc. Natl. Acad. Sci. USA 104 (2007) 2378–2383. [DOI] [PMID: 17277085]
2.	Biarnes-Carrera, M., Lee, C.K., Nihira, T., Breitling, R. and Takano, E. Orthogonal regulatory circuits for Escherichia coli based on the γ-butyrolactone system of Streptomyces coelicolor. ACS Synth. Biol. 7 (2018) 1043–1055. [PMID: 29510026]

[EC 1.3.1.113 created 2017]

1.3.8.14

Accepted name:

L-prolyl-[peptidyl-carrier protein] dehydrogenase

Reaction:

L-prolyl-[peptidyl-carrier protein] + 2 electron-transfer flavoprotein = 1H-pyrrole-2-carbonyl-[peptidyl-carrier protein] + 2 reduced electron-transfer flavoprotein

Other name(s):

pigA (gene name); bmp3 (gene name); pltE (gene name); redW (gene name); (L-prolyl)-[peptidyl-carrier protein]:electron-transfer flavoprotein oxidoreductase

Systematic name:

L-prolyl-[peptidyl-carrier protein]:electron-transfer flavoprotein oxidoreductase

Comments:

Contains FAD. The enzyme participates in the biosynthesis of several pyrrole-containing compounds, such as undecylprodigiosin, prodigiosin, pyoluteorin, and coumermycin A1. It is believed to catalyse the formation of a Δ²-pyrrolin-2-carbonyl-[peptidyl-carrier protein] intermediate, followed by a two-electron oxidation to 1H-pyrrol-2-carbonyl-[peptidyl-carrier protein].

Links to other databases:

References:

1.	Thomas, M.G., Burkart, M.D. and Walsh, C.T. Conversion of L-proline to pyrrolyl-2-carboxyl-S-PCP during undecylprodigiosin and pyoluteorin biosynthesis. Chem. Biol. 9 (2002) 171–184. [DOI] [PMID: 11880032]
2.	Harris, A.K., Williamson, N.R., Slater, H., Cox, A., Abbasi, S., Foulds, I., Simonsen, H.T., Leeper, F.J. and Salmond, G.P. The Serratia gene cluster encoding biosynthesis of the red antibiotic, prodigiosin, shows species- and strain-dependent genome context variation. Microbiology 150 (2004) 3547–3560. [DOI] [PMID: 15528645]

[EC 1.3.8.14 created 2017]

1.8.2.6

Accepted name:

S-disulfanyl-L-cysteine oxidoreductase

Reaction:

[SoxY protein]-S-disulfanyl-L-cysteine + 6 ferricytochrome c + 3 H₂O = [SoxY protein]-S-sulfosulfanyl-L-cysteine + 6 ferrocytochrome c + 6 H⁺

Other name(s):

SoxCD; sulfur dehydrogenase

Systematic name:

[SoxY protein]-S-disulfanyl-L-cysteine:cytochrome-c oxidoreductase

Comments:

The enzyme is part of the Sox enzyme system, which participates in a bacterial thiosulfate oxidation pathway that produces sulfate. The enzyme from the bacterium Paracoccus pantotrophus contains a molybdoprotein component and a diheme c-type cytochrome component. The enzyme successively oxidizes the outer sulfur atom in [SoxY protein]-S-disulfanyl-L-cysteine, using three water molecules and forming [SoxY protein]-S-sulfosulfanyl-L-cysteine. During the process, six electrons are transferred to the electron chain via cytochrome c.

Links to other databases:

References:

1.	Friedrich, C.G., Rother, D., Bardischewsky, F., Quentmeier, A. and Fischer, J. Oxidation of reduced inorganic sulfur compounds by bacteria: emergence of a common mechanism. Appl. Environ. Microbiol. 67 (2001) 2873–2882. [DOI] [PMID: 11425697]
2.	Bardischewsky, F., Quentmeier, A., Rother, D., Hellwig, P., Kostka, S. and Friedrich, C.G. Sulfur dehydrogenase of Paracoccus pantotrophus: the heme-2 domain of the molybdoprotein cytochrome c complex is dispensable for catalytic activity. Biochemistry 44 (2005) 7024–7034. [DOI] [PMID: 15865447]
3.	Grabarczyk, D.B. and Berks, B.C. Intermediates in the Sox sulfur oxidation pathway are bound to a sulfane conjugate of the carrier protein SoxYZ. PLoS One 12:e0173395 (2017). [DOI] [PMID: 28257465]

[EC 1.8.2.6 created 2018]

*EC

1.8.5.4

Accepted name:

bacterial sulfide:quinone reductase

Reaction:

n HS^- + n quinone = polysulfide + n quinol

Other name(s):

sqr (gene name); sulfide:quinone reductase (ambiguous); sulfide:quinone oxidoreductase

Systematic name:

sulfide:quinone oxidoreductase (polysulfide-producing)

Comments:

Contains FAD. Ubiquinone, plastoquinone or menaquinone can act as acceptor in different species. In some organisms the enzyme catalyses the formation of sulfur globules. It repeats the catalytic cycle without releasing the product, producing a polysulfide of up to 10 sulfur atoms. The reaction stops when the maximum length of the polysulfide that can be accommodated in the sulfide oxidation pocket is achieved. The enzyme also plays an important role in anoxygenic bacterial photosynthesis. cf. EC 1.8.5.8, sulfide quinone oxidoreductase.

Links to other databases:

References:

1.	Arieli, B., Shahak, Y., Taglicht, D., Hauska, G. and Padan, E. Purification and characterization of sulfide-quinone reductase, a novel enzyme driving anoxygenic photosynthesis in Oscillatoria limnetica. J. Biol. Chem. 269 (1994) 5705–5711. [PMID: 8119908]
2.	Reinartz, M., Tschape, J., Bruser, T., Truper, H.G. and Dahl, C. Sulfide oxidation in the phototrophic sulfur bacterium Chromatium vinosum. Arch. Microbiol. 170 (1998) 59–68. [PMID: 9639604]
3.	Nubel, T., Klughammer, C., Huber, R., Hauska, G. and Schutz, M. Sulfide:quinone oxidoreductase in membranes of the hyperthermophilic bacterium Aquifex aeolicus (VF5). Arch. Microbiol. 173 (2000) 233–244. [PMID: 10816041]
4.	Brito, J.A., Sousa, F.L., Stelter, M., Bandeiras, T.M., Vonrhein, C., Teixeira, M., Pereira, M.M. and Archer, M. Structural and functional insights into sulfide:quinone oxidoreductase. Biochemistry 48 (2009) 5613–5622. [DOI] [PMID: 19438211]
5.	Cherney, M.M., Zhang, Y., Solomonson, M., Weiner, J.H. and James, M.N. Crystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans: insights into sulfidotrophic respiration and detoxification. J. Mol. Biol. 398 (2010) 292–305. [DOI] [PMID: 20303979]
6.	Marcia, M., Langer, J.D., Parcej, D., Vogel, V., Peng, G. and Michel, H. Characterizing a monotopic membrane enzyme. Biochemical, enzymatic and crystallization studies on Aquifex aeolicus sulfide:quinone oxidoreductase. Biochim. Biophys. Acta 1798 (2010) 2114–2123. [DOI] [PMID: 20691146]
7.	Xin, Y., Liu, H., Cui, F., Liu, H. and Xun, L. Recombinant Escherichia coli with sulfide:quinone oxidoreductase and persulfide dioxygenase rapidly oxidises sulfide to sulfite and thiosulfate via a new pathway. Environ. Microbiol. 18 (2016) 5123–5136. [PMID: 27573649]

[EC 1.8.5.4 created 2011, modified 2017, modified 2019]

*EC

1.8.5.5

Accepted name:

thiosulfate reductase (quinone)

Reaction:

sulfite + hydrogen sulfide + a quinone = thiosulfate + a quinol

Other name(s):

phsABC (gene names)

Systematic name:

sulfite,hydrogen sulfide:quinone oxidoreductase

Comments:

The enzyme, characterized from the bacterium Salmonella enterica, is similar to EC 1.17.5.3, formate dehydrogenase-N. It contains a molybdopterin-guanine dinucleotide, five [4Fe-4S] clusters and two heme b groups. The reaction occurs in vivo in the direction of thiosulfate disproportionation, which is highly endergonic. It is driven by the proton motive force that occurs across the cytoplasmic membrane.

Links to other databases:

References:

1.	Kwan, H.S. and Barrett, E.L. Map locations and functions of Salmonella typhimurium men genes. J. Bacteriol. 159 (1984) 1090–1092. [PMID: 6384182]
2.	Clark, M.A. and Barrett, E.L. The phs gene and hydrogen sulfide production by Salmonella typhimurium. J. Bacteriol. 169 (1987) 2391–2397. [DOI] [PMID: 3108233]
3.	Alami, N. and Hallenbeck, P.C. Cloning and characterization of a gene cluster, phsBCDEF, necessary for the production of hydrogen sulfide from thiosulfate by Salmonella typhimurium. Gene 156 (1995) 53–57. [DOI] [PMID: 7737516]
4.	Heinzinger, N.K., Fujimoto, S.Y., Clark, M.A., Moreno, M.S. and Barrett, E.L. Sequence analysis of the phs operon in Salmonella typhimurium and the contribution of thiosulfate reduction to anaerobic energy metabolism. J. Bacteriol. 177 (1995) 2813–2820. [DOI] [PMID: 7751291]
5.	Stoffels, L., Krehenbrink, M., Berks, B.C. and Unden, G. Thiosulfate reduction in Salmonella enterica is driven by the proton motive force. J. Bacteriol. 194 (2012) 475–485. [DOI] [PMID: 22081391]

[EC 1.8.5.5 created 2016, modified 2017]

1.8.5.8

Accepted name:

eukaryotic sulfide quinone oxidoreductase

Reaction:

hydrogen sulfide + glutathione + a quinone = S-sulfanylglutathione + a quinol

Other name(s):

SQR; SQOR; SQRDL (gene name)

Systematic name:

sulfide:glutathione,quinone oxidoreductase

Comments:

Contains FAD. This eukaryotic enzyme, located at the inner mitochondrial membrane, catalyses the first step in the metabolism of sulfide. While both sulfite and glutathione have been shown to act as sulfane sulfur acceptors in vitro, it is thought that the latter acts as the main acceptor in vivo. The electrons are transferred via FAD and quinones to the electron transfer chain. Unlike the bacterial homolog (EC 1.8.5.4, bacterial sulfide:quinone reductase), which repeats the catalytic cycle without releasing the product, producing a polysulfide, the eukaryotic enzyme transfers the persulfide to an acceptor at the end of each catalytic cycle.

Links to other databases:

References:

1.	Vande Weghe, J.G. and Ow, D.W. A fission yeast gene for mitochondrial sulfide oxidation. J. Biol. Chem. 274 (1999) 13250–13257. [DOI] [PMID: 10224084]
2.	Hildebrandt, T.M. and Grieshaber, M.K. Three enzymatic activities catalyze the oxidation of sulfide to thiosulfate in mammalian and invertebrate mitochondria. FEBS J. 275 (2008) 3352–3361. [DOI] [PMID: 18494801]
3.	Jackson, M.R., Melideo, S.L. and Jorns, M.S. Human sulfide:quinone oxidoreductase catalyzes the first step in hydrogen sulfide metabolism and produces a sulfane sulfur metabolite. Biochemistry 51 (2012) 6804–6815. [DOI] [PMID: 22852582]
4.	Libiad, M., Yadav, P.K., Vitvitsky, V., Martinov, M. and Banerjee, R. Organization of the human mitochondrial hydrogen sulfide oxidation pathway. J. Biol. Chem. 289 (2014) 30901–30910. [DOI] [PMID: 25225291]

[EC 1.8.5.8 created 2017]

1.8.7.3

Accepted name:

ferredoxin:CoB-CoM heterodisulfide reductase

Reaction:

2 oxidized ferredoxin [iron-sulfur] cluster + CoB + CoM = 2 reduced ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB + 2 H⁺

Glossary:

CoB = coenzyme B = N-(7-sulfanylheptanoyl)threonine = N-(7-mercaptoheptanoyl)threonine 3-O-phosphate (deprecated)
CoM = coenzyme M = 2-sulfanylethane-1-sulfonate = 2-mercaptoethanesulfonate (deprecated)
CoM-S-S-CoB = CoB-CoM heterodisulfide = N-{7-[(2-sulfoethyl)dithio]heptanoyl}-O³-phospho-L-threonine =
O³-phospho-N-{7-[2-(2-sulfoethyl)disulfan-1-yl]heptanoyl}-L-threonine

Other name(s):

hdrABC (gene names); hdrA1B1C1 (gene names); hdrA2B2C2 (gene names)

Systematic name:

CoB,CoM:ferredoxin oxidoreductase

Comments:

HdrABC is an enzyme complex that is found in most methanogens and catalyses the reduction of the CoB-CoM heterodisulfide back to CoB and CoM. HdrA contains a FAD cofactor that acts as the entry point for electrons, which are transferred via HdrC to the HdrB catalytic subunit. One form of the enzyme from Methanosarcina acetivorans (HdrA2B2C2) can also catalyse EC 1.8.98.4, coenzyme F₄₂₀:CoB-CoM heterodisulfide,ferredoxin reductase. cf. EC 1.8.98.5, H₂:CoB-CoM heterodisulfide,ferredoxin reductase, EC 1.8.98.6, formate:CoB-CoM heterodisulfide,ferredoxin reductase, and EC 1.8.98.1, dihydromethanophenazine:CoB-CoM heterodisulfide reductase.

Links to other databases:

References:

1.	Buan, N.R. and Metcalf, W.W. Methanogenesis by Methanosarcina acetivorans involves two structurally and functionally distinct classes of heterodisulfide reductase. Mol. Microbiol. 75 (2010) 843–853. [DOI] [PMID: 19968794]
2.	Yan, Z., Wang, M. and Ferry, J.G. A ferredoxin- and F₄₂₀H₂-dependent, electron-bifurcating, heterodisulfide reductase with homologs in the domains Bacteria and Archaea. mBio 8 (2017) e02285-16. [DOI] [PMID: 28174314]

[EC 1.8.7.3 created 2017]

*EC

1.8.98.1

Accepted name:

dihydromethanophenazine:CoB-CoM heterodisulfide reductase

Reaction:

CoB + CoM + methanophenazine = CoM-S-S-CoB + dihydromethanophenazine

For diagram of methane biosynthesis, click here

Glossary:

CoB = coenzyme B = N-(7-sulfanylheptanoyl)threonine = N-(7-mercaptoheptanoyl)threonine 3-O-phosphate (deprecated)
CoM = coenzyme M = 2-sulfanylethane-1-sulfonate = 2-mercaptoethanesulfonate (deprecated)
methanophenazine = 2-{[(6E,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl]oxy}phenazine
CoM-S-S-CoB = CoB-CoM heterodisulfide = N-{7-[(2-sulfoethyl)dithio]heptanoyl}-O³-phospho-L-threonine = O³-phospho-N-{7-[2-(2-sulfoethyl)disulfan-1-yl]heptanoyl}-L-threonine

Other name(s):

hdrDE (gene names); CoB—CoM heterodisulfide reductase (ambiguous); heterodisulfide reductase (ambiguous); coenzyme B:coenzyme M:methanophenazine oxidoreductase

Systematic name:

CoB:CoM:methanophenazine oxidoreductase

Comments:

This enzyme, found in methanogenic archaea that belong to the Methanosarcinales order, regenerates CoM and CoB after the action of EC 2.8.4.1, coenzyme-B sulfoethylthiotransferase. It is a membrane-bound enzyme that contains (per heterodimeric unit) two distinct b-type hemes and two [4Fe-4S] clusters. cf. EC 1.8.7.3, ferredoxin:CoB-CoM heterodisulfide reductase, EC 1.8.98.5, H₂:CoB-CoM heterodisulfide,ferredoxin reductase, EC 1.8.98.6, formate:CoB-CoM heterodisulfide,ferredoxin reductase and EC 1.8.98.4, coenzyme F₄₂₀:CoB-CoM heterodisulfide,ferredoxin reductase.

Links to other databases:

References:

1.	Hedderich, R., Berkessel, A. and Thauer, R.K. Purification and properties of heterodisulfide reductase from Methanobacterium thermoautotrophicum (strain Marburg). Eur. J. Biochem. 193 (1990) 255–261. [DOI] [PMID: 2121478]
2.	Abken, H.J., Tietze, M., Brodersen, J., Bäumer, S., Beifuss, U. and Deppenmeier, U. Isolation and characterization of methanophenazine and function of phenazines in membrane-bound electron transport of Methanosarcina mazei gol. J. Bacteriol. 180 (1998) 2027–2032. [PMID: 9555882]
3.	Simianu, M., Murakami, E., Brewer, J.M. and Ragsdale, S.W. Purification and properties of the heme- and iron-sulfur-containing heterodisulfide reductase from Methanosarcina thermophila. Biochemistry 37 (1998) 10027–10039. [DOI] [PMID: 9665708]
4.	Murakami, E., Deppenmeier, U. and Ragsdale, S.W. Characterization of the intramolecular electron transfer pathway from 2-hydroxyphenazine to the heterodisulfide reductase from Methanosarcina thermophila. J. Biol. Chem. 276 (2001) 2432–2439. [DOI] [PMID: 11034998]

[EC 1.8.98.1 created 2003, modified 2017]

1.8.98.4

Accepted name:

coenzyme F₄₂₀:CoB-CoM heterodisulfide,ferredoxin reductase

Reaction:

2 oxidized coenzyme F₄₂₀ + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H⁺ = 2 reduced coenzyme F₄₂₀ + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB

Glossary:

Other name(s):

hdrA2B2C2 (gene names)

Systematic name:

CoB,CoM,ferredoxin:coenzyme F₄₂₀ oxidoreductase

Comments:

The enzyme, characterized from the archaeon Methanosarcina acetivorans, catalyses the reduction of CoB-CoM heterodisulfide back to CoB and CoM. The enzyme consists of three components, HdrA, HdrB and HdrC, all of which contain [4Fe-4S] clusters. Electrons enter at HdrA, which also contains FAD, and are transferred via HdrC to the catalytic component, HdrB. During methanogenesis from acetate the enzyme catalyses the activity of EC 1.8.7.3, ferredoxin:CoB-CoM heterodisulfide reductase. However, it can also use electron bifurcation to direct electron pairs from reduced coenzyme F₄₂₀ towards the reduction of both ferredoxin and CoB-CoM heterodisulfide. This activity is proposed to take place during Fe(III)-dependent anaerobic methane oxidation. cf. EC 1.8.98.5, H₂:CoB-CoM heterodisulfide,ferredoxin reductase, EC 1.8.98.6, formate:CoB-CoM heterodisulfide,ferredoxin reductase, and EC 1.8.98.1, dihydromethanophenazine:CoB-CoM heterodisulfide reductase.

Links to other databases:

References:

1.	Yan, Z., Wang, M. and Ferry, J.G. A ferredoxin- and F₄₂₀H₂-dependent, electron-bifurcating, heterodisulfide reductase with homologs in the domains Bacteria and Archaea. mBio 8 (2017) e02285-16. [DOI] [PMID: 28174314]

[EC 1.8.98.4 created 2017]

1.8.98.5

Accepted name:

H₂:CoB-CoM heterodisulfide,ferredoxin reductase

Reaction:

2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H⁺ = 2 H₂ + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB

Glossary:

Systematic name:

CoB,CoM,ferredoxin:H₂ oxidoreductase

Comments:

This enzyme complex is found in H₂-oxidizing CO₂-reducing methanogenic archaea such as Methanothermobacter thermautotrophicus. It consists of a cytoplasmic complex of HdrABC reductase and MvhAGD hydrogenase. Electron pairs donated by the hydrogenase are transferred via its δ subunit to the HdrA subunit of the reductase, where they are bifurcated, reducing both ferredoxin and CoB-CoM heterodisulfide. The reductase can also form a similar complex with formate dehydrogenase, see EC 1.8.98.6, formate:CoB-CoM heterodisulfide,ferredoxin reductase. cf. EC 1.8.7.3, ferredoxin:CoB-CoM heterodisulfide reductase, EC 1.8.98.4, coenzyme F₄₂₀:CoB-CoM heterodisulfide,ferredoxin reductase, and EC 1.8.98.1, dihydromethanophenazine:CoB-CoM heterodisulfide reductase.

Links to other databases:

References:

1.	Reeve, J.N., Beckler, G.S., Cram, D.S., Hamilton, P.T., Brown, J.W., Krzycki, J.A., Kolodziej, A.F., Alex, L., Orme-Johnson, W.H. and Walsh, C.T. A hydrogenase-linked gene in Methanobacterium thermoautotrophicum strain δ H encodes a polyferredoxin. Proc. Natl. Acad. Sci. USA 86 (1989) 3031–3035. [DOI] [PMID: 2654933]
2.	Hedderich, R., Koch, J., Linder, D. and Thauer, R.K. The heterodisulfide reductase from Methanobacterium thermoautotrophicum contains sequence motifs characteristic of pyridine-nucleotide-dependent thioredoxin reductases. Eur. J. Biochem. 225 (1994) 253–261. [DOI] [PMID: 7925445]
3.	Setzke, E., Hedderich, R., Heiden, S. and Thauer, R.K. H₂: heterodisulfide oxidoreductase complex from Methanobacterium thermoautotrophicum. Composition and properties. Eur. J. Biochem. 220 (1994) 139–148. [DOI] [PMID: 8119281]
4.	Stojanowic, A., Mander, G.J., Duin, E.C. and Hedderich, R. Physiological role of the F₄₂₀-non-reducing hydrogenase (Mvh) from Methanothermobacter marburgensis. Arch. Microbiol. 180 (2003) 194–203. [DOI] [PMID: 12856108]
5.	Kaster, A.K., Moll, J., Parey, K. and Thauer, R.K. Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic archaea. Proc. Natl. Acad. Sci. USA 108 (2011) 2981–2986. [DOI] [PMID: 21262829]
6.	Costa, K.C., Lie, T.J., Xia, Q. and Leigh, J.A. VhuD facilitates electron flow from H₂ or formate to heterodisulfide reductase in Methanococcus maripaludis. J. Bacteriol. 195 (2013) 5160–5165. [DOI] [PMID: 24039260]

[EC 1.8.98.5 created 2017]

1.8.98.6

Accepted name:

formate:CoB-CoM heterodisulfide,ferredoxin reductase

Reaction:

2 CO₂ + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H⁺ = 2 formate + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB

Glossary:

Systematic name:

coenzyme B,coenzyme M,ferredoxin:formate oxidoreductase

Comments:

The enzyme is found in formate-oxidizing CO₂-reducing methanogenic archaea such as Methanococcus maripaludis. It consists of a cytoplasmic complex of HdrABC reductase and formate dehydrogenase. Electron pairs donated by formate dehydrogenase are transferred to the HdrA subunit of the reductase, where they are bifurcated, reducing both ferredoxin and CoB-CoM heterodisulfide. cf. EC 1.8.7.3, ferredoxin:CoB-CoM heterodisulfide reductase, EC 1.8.98.4, coenzyme F₄₂₀:CoB-CoM heterodisulfide,ferredoxin reductase, EC 1.8.98.5, H₂:CoB-CoM heterodisulfide,ferredoxin reductase, and EC 1.8.98.1, dihydromethanophenazine:CoB-CoM heterodisulfide reductase.

Links to other databases:

References:

1.	Costa, K.C., Wong, P.M., Wang, T., Lie, T.J., Dodsworth, J.A., Swanson, I., Burn, J.A., Hackett, M. and Leigh, J.A. Protein complexing in a methanogen suggests electron bifurcation and electron delivery from formate to heterodisulfide reductase. Proc. Natl. Acad. Sci. USA 107 (2010) 11050–11055. [DOI] [PMID: 20534465]
2.	Costa, K.C., Lie, T.J., Xia, Q. and Leigh, J.A. VhuD facilitates electron flow from H₂ or formate to heterodisulfide reductase in Methanococcus maripaludis. J. Bacteriol. 195 (2013) 5160–5165. [DOI] [PMID: 24039260]

[EC 1.8.98.6 created 2017]

1.13.11.84

Accepted name:

crocetin dialdehyde synthase

Reaction:

zeaxanthin + 2 O₂ = crocetin dialdehyde + 2 3β-hydroxy-β-cyclocitral (overall reaction)
(1a) zeaxanthin + O₂ = 3β-hydroxy-8′-apo-β-carotenal + 3β-hydroxy-β-cyclocitral
(1b) 3β-hydroxy-8′-apo-β-carotenal + O₂ = crocetin dialdehyde + 3β-hydroxy-β-cyclocitral

Glossary:

crocetin dialdehyde = 8,8′-diapocarotene-8,8′-dial
zeaxanthin = (3R,3′R)-β,β-carotene-3,3′-diol
3β-hydroxy-β-cyclocitral = (4R)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-carboxaldehyde

Other name(s):

CCD2; zeaxanthin 7,8-dioxygenase

Systematic name:

zeaxanthin:oxygen 7′,8′-oxidoreductase (bond-cleaving)

Comments:

The enzyme, characterized from the plant Crocus sativus (saffron), acts twice, cleaving 3β-hydroxy-β-cyclocitral off each 3-hydroxy end group. It is part of the zeaxanthin degradation pathway in that plant, leading to the different compounds that impart the color, flavor and aroma of the saffron spice. The enzyme can similarly cleave the 7-8 double bond of other carotenoids with a 3-hydroxy-β-carotenoid end group.

Links to other databases:

References:

1.	Frusciante, S., Diretto, G., Bruno, M., Ferrante, P., Pietrella, M., Prado-Cabrero, A., Rubio-Moraga, A., Beyer, P., Gomez-Gomez, L., Al-Babili, S. and Giuliano, G. Novel carotenoid cleavage dioxygenase catalyzes the first dedicated step in saffron crocin biosynthesis. Proc. Natl. Acad. Sci. USA 111 (2014) 12246–12251. [DOI] [PMID: 25097262]
2.	Ahrazem, O., Rubio-Moraga, A., Berman, J., Capell, T., Christou, P., Zhu, C. and Gomez-Gomez, L. The carotenoid cleavage dioxygenase CCD2 catalysing the synthesis of crocetin in spring crocuses and saffron is a plastidial enzyme. New Phytol. 209 (2016) 650–663. [DOI] [PMID: 26377696]
3.	Ahrazem, O., Diretto, G., Argandona, J., Rubio-Moraga, A., Julve, J.M., Orzaez, D., Granell, A. and Gomez-Gomez, L. Evolutionarily distinct carotenoid cleavage dioxygenases are responsible for crocetin production in Buddleja davidii. J. Exp. Bot. 68 (2017) 4663–4677. [DOI] [PMID: 28981773]

[EC 1.13.11.84 created 2011 as EC 1.14.99.42, modified 2014, transferred 2017 to EC 1.13.11.84]

*EC

1.13.12.7

Accepted name:

firefly luciferase

Reaction:

D-firefly luciferin + O₂ + ATP = firefly oxyluciferin + CO₂ + AMP + diphosphate + hν

For diagram of reaction, click here

Glossary:

D-firefly luciferin = Photinus-luciferin = (S)-4,5-dihydro-2-(6-hydroxy-1,3-benzothiazol-2-yl)thiazole-4-carboxylate
firefly oxyluciferin = 4,5-dihydro-2-(6-hydroxy-1,3-benzothiazol-2-yl)thiazol-4-one

Other name(s):

Photinus-luciferin 4-monooxygenase (ATP-hydrolysing); luciferase (firefly luciferin); Photinus luciferin 4-monooxygenase (adenosine triphosphate-hydrolyzing); firefly luciferin luciferase; Photinus pyralis luciferase; Photinus-luciferin:oxygen 4-oxidoreductase (decarboxylating, ATP-hydrolysing)

Systematic name:

D-firefly luciferin:oxygen 4-oxidoreductase (decarboxylating, ATP-hydrolysing)

Comments:

The enzyme, which is found in fireflies (Lampyridae), is responsible for their biolouminescence. The reaction begins with the formation of an acid anhydride between the carboxylic group of D-firefly luciferin and AMP, with the release of diphosphate. An oxygenation follows, with release of the AMP group and formation of a very short-lived peroxide that cyclizes into a dioxetanone structure, which collapses, releasing a CO₂ molecule. The spontaneous breakdown of the dioxetanone (rather than the hydrolysis of the adenylate) releases the energy (about 50 kcal/mole) that is necessary to generate the excited state of oxyluciferin. The excited luciferin then emits a photon, returning to its ground state. The enzyme has a secondary acyl-CoA ligase activity when acting on L-firefly luciferin (see EC 6.2.1.52).

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 61970-00-1

References:

1.	Green, A. A. and McElroy, W. D. Crystalline firefly luciferase. Biochim. Biophys. Acta 20 (1956) 170–176. [DOI] [PMID: 13315363]
2.	White, E.H., McCapra, F., Field, G.F. and McElroy, W.D. The structure and synthesis of firefly luciferin. J. Am. Chem. Soc. 83 (1961) 2402–2403.
3.	Hopkins, T.A., Seliger, H.H., White, E.H. and Cass, M.W. The chemiluminescence of firefly luciferin. A model for the bioluminescent reaction and identification of the product excited state. J. Am. Chem. Soc. 89 (1967) 7148–7150. [PMID: 6064360]
4.	White, E.H., Rapaport, E., Hopkins, T.A. and Seliger, H.H. Chemi- and bioluminescence of firefly luciferin. J. Am. Chem. Soc. 91 (1969) 2178–2180. [PMID: 5784183]
5.	Koo, J.A., Schmidt, S.P. and Schuster, G.B. Bioluminescence of the firefly: key steps in the formation of the electronically excited state for model systems. Proc. Natl. Acad. Sci. USA 75 (1978) 30–33. [DOI] [PMID: 272645]
6.	de Wet, J.R., Wood, K.V., Helinski, D.R. and DeLuca, M. Cloning of firefly luciferase cDNA and the expression of active luciferase in Escherichia coli. Proc. Natl. Acad. Sci. USA 82 (1985) 7870–7873. [DOI] [PMID: 3906652]
7.	Nakamura, M., Maki, S., Amano, Y., Ohkita, Y., Niwa, K., Hirano, T., Ohmiya, Y. and Niwa, H. Firefly luciferase exhibits bimodal action depending on the luciferin chirality. Biochem. Biophys. Res. Commun. 331 (2005) 471–475. [DOI] [PMID: 15850783]
8.	Sundlov, J.A., Fontaine, D.M., Southworth, T.L., Branchini, B.R. and Gulick, A.M. Crystal structure of firefly luciferase in a second catalytic conformation supports a domain alternation mechanism. Biochemistry 51 (2012) 6493–6495. [DOI] [PMID: 22852753]

[EC 1.13.12.7 created 1976, modified 1981, modified 1982, modified 2017]

1.13.12.24

Accepted name:

calcium-regulated photoprotein

Reaction:

[apoaequorin] + coelenterazine + O₂ + 3 Ca²⁺ = [excited state blue fluorescent protein] + CO₂ (overall reaction)
(1a) [apoaequorin] + coelenterazine = [apoaequorin containing coelenterazine]
(1b) [apoaequorin containing coelenterazine] + O₂ = [aequorin]
(1c) [aequorin] + 3 Ca²⁺ = [aequorin] 1,2-dioxetan-3-one
(1d) [aequorin] 1,2-dioxetan-3-one = [excited state blue fluorescent protein] + CO₂

Glossary:

coelenterazine = 8-benzyl-2-(4-hydroxybenzyl)-6-(4-hydroxyphenyl)imidazo[1,2-a]pyrazin-3(7H)-one
coelenteramide = N-[3-benzyl-5-(4-hydroxyphenyl)pyrazin-2-yl]-2-(4-hydroxyphenyl)acetamide
aequorin = the non-covalent complex formed by apoaequorin polypeptide and coelenterazine-2-hydroperoxide.
blue fluorescent protein = the non-covalent complex formed by Ca²⁺-bound apoaequorin polypeptide and coelenteramide

Other name(s):

Ca²⁺-regulated photoprotein; calcium-activated photoprotein; aequorin; obelin; halistaurin; mitrocomin; phialidin; clytin; mnemiopsin; berovin

Systematic name:

coelenterazine:oxygen 2-oxidoreductase (decarboxylating, calcium-dependent)

Comments:

Ca²⁺-regulated photoproteins are found in a variety of bioluminescent marine organisms, mostly coelenterates, and are responsible for their light emission. The best studied enzyme is from the jellyfish Aequorea victoria. The enzyme tightly binds the imidazolopyrazinone derivative coelenterazine, which is then peroxidized by oxygen. The hydroperoxide is stably bound until three Ca²⁺ ions bind to the protein, inducing a structural change that results in the formation of a 1,2-dioxetan-3-one ring, followed by decarboxylation and generation of a protein-bound coelenteramide in an excited state. The calcium-bound protein-product complex is known as a blue fluorescent protein. In vivo the energy is transferred to a green fluorescent protein (GFP) by Förster resonance energy transfer. In vitro, in the absence of GFP, coelenteramide emits a photon of blue light while returning to its ground state.

Links to other databases:

References:

1.	Shimomura, O., Johnson, F. H., and Saiga, Y. Purification and properties of aequorin, a bio-(chemi-) luminescent protein from the jellyfish, Aequorea aequorea. Fed. Proc. 21 (1962) 401.
2.	Morise, H., Shimomura, O., Johnson, F.H. and Winant, J. Intermolecular energy transfer in the bioluminescent system of Aequorea. Biochemistry 13 (1974) 2656–2662. [PMID: 4151620]
3.	Inouye, S., Noguchi, M., Sakaki, Y., Takagi, Y., Miyata, T., Iwanaga, S., Miyata, T. and Tsuji, F.I. Cloning and sequence analysis of cDNA for the luminescent protein aequorin. Proc. Natl. Acad. Sci. USA 82 (1985) 3154–3158. [DOI] [PMID: 3858813]
4.	Head, J.F., Inouye, S., Teranishi, K. and Shimomura, O. The crystal structure of the photoprotein aequorin at 2.3 Å resolution. Nature 405 (2000) 372–376. [DOI] [PMID: 10830969]
5.	Deng, L., Vysotski, E.S., Markova, S.V., Liu, Z.J., Lee, J., Rose, J. and Wang, B.C. All three Ca²⁺-binding loops of photoproteins bind calcium ions: the crystal structures of calcium-loaded apo-aequorin and apo-obelin. Protein Sci. 14 (2005) 663–675. [DOI] [PMID: 15689515]

[EC 1.13.12.24 created 2018]

*EC

1.14.11.7

Accepted name:

procollagen-proline 3-dioxygenase

Reaction:

[procollagen]-L-proline + 2-oxoglutarate + O₂ = [procollagen]-trans-3-hydroxy-L-proline + succinate + CO₂

For diagram of reaction, click here

Other name(s):

proline,2-oxoglutarate 3-dioxygenase; prolyl 3-hydroxylase; protocollagen proline 3-hydroxylase; prolyl-4-hydroxyprolyl-glycyl-peptide,2-oxoglutarate:oxygen oxidoreductase, 3-hydroxylating

Systematic name:

[procollagen]-L-proline,2-oxoglutarate:oxygen oxidoreductase (3-hydroxylating)

Comments:

Requires Fe²⁺ and ascorbate. The enzyme forms a complex with protein disulfide isomerase, and is located in the endoplasmic reticulum. It modifies proline residues within the procollagen peptide of certain collagen types. The modification is essential for proper collagen triple helix formation.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 63551-75-7

References:

1.	Risteli, J., Tryggvason, K. and Kivirikko, K.I. Prolyl 3-hydroxylase: partial characterization of the enzyme from rat kidney cortex. Eur. J. Biochem. 73 (1977) 485–492. [DOI] [PMID: 191255]
2.	Risteli, J., Tryggvason, K. and Kivirikko, K.I. A rapid assay for prolyl 3-hydroxylase activity. Anal. Biochem. 84 (1978) 423–431. [DOI] [PMID: 204218]
3.	Vranka, J.A., Sakai, L.Y. and Bachinger, H.P. Prolyl 3-hydroxylase 1, enzyme characterization and identification of a novel family of enzymes. J. Biol. Chem. 279 (2004) 23615–23621. [DOI] [PMID: 15044469]
4.	Tiainen, P., Pasanen, A., Sormunen, R. and Myllyharju, J. Characterization of recombinant human prolyl 3-hydroxylase isoenzyme 2, an enzyme modifying the basement membrane collagen IV. J. Biol. Chem. 283 (2008) 19432–19439. [DOI] [PMID: 18487197]

[EC 1.14.11.7 created 1981, modified 1983, modified 2017]

1.14.11.58

Accepted name:

ornithine lipid ester-linked acyl 2-hydroxylase

Reaction:

an ornithine lipid + 2-oxoglutarate + O₂ = a 2-hydroxyornithine lipid + succinate + CO₂

Glossary:

an ornithine lipid = an N^α-[(3R)-3-(acyloxy)acyl]-L-ornithine
a 2-hydroxyornithine lipid = an N^α-[(3R)-3-(2-hydroxyacyloxy)acyl]-L-ornithine

Other name(s):

olsC (gene name)

Systematic name:

ornithine lipid,2-oxoglutarate:oxygen oxidoreductase (ester-linked acyl 2-hydroxylase)

Comments:

The enzyme, characterized from the bacterium Rhizobium tropici, catalyses the hydroxylation of C-2 of the fatty acyl group that is ester-linked to the 3-hydroxy position of the amide-linked fatty acid.

Links to other databases:

References:

1.	Rojas-Jimenez, K., Sohlenkamp, C., Geiger, O., Martinez-Romero, E., Werner, D. and Vinuesa, P. A ClC chloride channel homolog and ornithine-containing membrane lipids of Rhizobium tropici CIAT899 are involved in symbiotic efficiency and acid tolerance. Mol. Plant Microbe Interact. 18 (2005) 1175–1185. [DOI] [PMID: 16353552]
2.	Vences-Guzman, M.A., Guan, Z., Ormeno-Orrillo, E., Gonzalez-Silva, N., Lopez-Lara, I.M., Martinez-Romero, E., Geiger, O. and Sohlenkamp, C. Hydroxylated ornithine lipids increase stress tolerance in Rhizobium tropici CIAT899. Mol. Microbiol. 79 (2011) 1496–1514. [DOI] [PMID: 21205018]

[EC 1.14.11.58 created 2018]

1.14.11.59

Accepted name:

2,4-dihydroxy-1,4-benzoxazin-3-one-glucoside dioxygenase

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

For diagram of benzoxazinone biosynthesis, click here

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).

Links to other databases:

References:

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. [DOI] [PMID: 18192444]

[EC 1.14.11.59 created 2012 as EC 1.14.20.2, transferred 2018 to EC 1.14.11.59]

1.14.13.67

Transferred entry:

quinine 3-monooxygenase. Now EC 1.14.14.55, quinine 3-monooxygenase

[EC 1.14.13.67 created 2000, deleted 2017]

1.14.13.97

Transferred entry:

taurochenodeoxycholate 6α-hydroxylase. Now EC 1.14.14.57, taurochenodeoxycholate 6α-hydroxylase

[EC 1.14.13.97 created 2005, deleted 2018]

1.14.13.129

Transferred entry:

β-carotene 3-hydroxylase. Now EC 1.14.15.24, β-carotene 3-hydroxylase.

[EC 1.14.13.129 created 2011, deleted 2017]

1.14.13.157

Transferred entry:

1,8-cineole 2-exo-monooxygenase. Now EC 1.14.14.56, 1,8-cineole 2-exo-monooxygenase

[EC 1.14.13.157 created 2012, deleted 2017]

1.14.13.239

Accepted name:

carnitine monooxygenase

Reaction:

L-carnitine + NAD(P)H + H⁺ + O₂ = (3R)-3-hydroxy-4-oxobutanoate + trimethylamine + NAD(P)⁺ + H₂O

Glossary:

(3R)-3-hydroxy-4-oxobutanoate = L-malic semialdehyde

Other name(s):

cntAB (gene names); yeaWX (gene names)

Systematic name:

L-carnitine,NAD(P)H:oxygen oxidoreductase (trimethylamine-forming)

Comments:

The bacterial enzyme is a complex consisting of a reductase and an oxygenase components. The reductase subunit contains a flavin and a plant-type ferredoxin [2Fe-2S] cluster, while the oxygenase subunit is a Rieske-type protein in which a [2Fe-2S] cluster is coordinated by two histidine and two cysteine residues.

Links to other databases:

References:

1.	Ditullio, D., Anderson, D., Chen, C.S. and Sih, C.J. L-Carnitine via enzyme-catalyzed oxidative kinetic resolution. Bioorg. Med. Chem. 2 (1994) 415–420. [DOI] [PMID: 8000862]
2.	Zhu, Y., Jameson, E., Crosatti, M., Schafer, H., Rajakumar, K., Bugg, T.D. and Chen, Y. Carnitine metabolism to trimethylamine by an unusual Rieske-type oxygenase from human microbiota. Proc. Natl. Acad. Sci. USA 111 (2014) 4268–4273. [DOI] [PMID: 24591617]
3.	Koeth, R.A., Levison, B.S., Culley, M.K., Buffa, J.A., Wang, Z., Gregory, J.C., Org, E., Wu, Y., Li, L., Smith, J.D., Tang, W.H., DiDonato, J.A., Lusis, A.J. and Hazen, S.L. γ-Butyrobetaine is a proatherogenic intermediate in gut microbial metabolism of L-carnitine to TMAO. Cell Metab 20 (2014) 799–812. [DOI] [PMID: 25440057]

[EC 1.14.13.239 created 2017]

1.14.14.55

Accepted name:

quinine 3-monooxygenase

Reaction:

quinine + [reduced NADPH—hemoprotein reductase] + O₂ = 3-hydroxyquinine + [oxidized NADPH—hemoprotein reductase] + H₂O

Glossary:

quinine = a quinoline alkaloid

Other name(s):

CYP3A4 (gene name)

Systematic name:

quinine,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase

Comments:

A cytochrome P-450 (heme-thiolate) protein.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 50812-30-1, 213327-78-7

References:

1.	Relling, M.V., Evans, R., Dass, C., Desiderio, D.M. and Nemec, J. Human cytochrome P₄₅₀ metabolism of teniposide and etoposide. J. Pharmacol. Exp. Ther. 261 (1992) 491–496. [PMID: 1578365]
2.	Zhang, H., Coville, P.F., Walker, R.J., Miners, J.O., Birkett, D.J. and Wanwimolruk, S. Evidence for involvement of human CYP3A in the 3-hydroxylation of quinine. Br. J. Clin. Pharmacol. 43 (1997) 245–252. [DOI] [PMID: 9088578]
3.	Zhao, X.-J., Kawashiro, T. and Ishizaki, T. Mutual inhibition between quinine and etoposide by human liver microsomes. Evidence for cytochrome P4503A4 involvement in their major metabolic pathways. Drug Metab. Dispos. 26 (1998) 188–191. [PMID: 9456308]
4.	Zhao, X.-J., Yokoyama, H., Chiba, K., Wanwimolruk, S. and Ishizaki, T. Identification of human cytochrome P₄₅₀ isoforms involved in the 3-hydroxylation of quinine by human liver microsomes and nine recombinant human cytochromes P₄₅₀. J. Pharmacol. Exp. Ther. 279 (1996) 1327–1334. [PMID: 8968357]

[EC 1.14.14.55 created 2000 as EC 1.14.13.67, transferred 2017 to EC 1.14.14.55]

1.14.14.56

Accepted name:

1,8-cineole 2-exo-monooxygenase

Reaction:

1,8-cineole + [reduced NADPH—hemoprotein reductase] + O₂ = 2-exo-hydroxy-1,8-cineole + [oxidized NADPH—hemoprotein reductase] + H₂O

For diagram of 1,8-cineole catabolism, click here

Glossary:

1,8-cineole = 1,3,3-trimethyl-2-oxabicyclo[2.2.2]octane
2-exo-hydroxy-1,8-cineole = (1R,4S,6S)-1,3,3-trimethyl-2-oxabicyclo[2.2.2]octan-6-ol

Other name(s):

CYP3A4

Systematic name:

1,8-cineole,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (2-exo-hydroxylating)

Comments:

A cytochrome P-450 (heme-thiolate) protein. The mammalian enzyme, expressed in liver microsomes, performs a variety of oxidation reactions of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. cf. EC 1.14.14.55, quinine 3-monooxygenase, EC 1.14.14.57, taurochenodeoxycholate 6-hydroxylase and EC 1.14.14.73, albendazole monooxygenase (sulfoxide-forming).

Links to other databases:

References:

1.	Miyazawa, M., Shindo, M. and Shimada, T. Oxidation of 1,8-cineole, the monoterpene cyclic ether originated from Eucalyptus polybractea, by cytochrome P450 3A enzymes in rat and human liver microsomes. Drug Metab. Dispos. 29 (2001) 200–205. [PMID: 11159812]
2.	Miyazawa, M. and Shindo, M. Biotransformation of 1,8-cineole by human liver microsomes. Nat. Prod. Lett. 15 (2001) 49–53. [DOI] [PMID: 11547423]
3.	Miyazawa, M., Shindo, M. and Shimada, T. Roles of cytochrome P₄₅₀ 3A enzymes in the 2-hydroxylation of 1,4-cineole, a monoterpene cyclic ether, by rat and human liver microsomes. Xenobiotica 31 (2001) 713–723. [DOI] [PMID: 11695850]

[EC 1.14.14.56 created 2012 as EC 1.14.13.157, transferred 2017 to EC 1.14.14.56, modified 2018]

1.14.14.57

Accepted name:

taurochenodeoxycholate 6α-hydroxylase

Reaction:

(1) taurochenodeoxycholate + [reduced NADPH—hemoprotein reductase] + O₂ = taurohyocholate + [oxidized NADPH—hemoprotein reductase] + H₂O
(2) lithocholate + [reduced NADPH—hemoprotein reductase] + O₂ = hyodeoxycholate + [oxidized NADPH—hemoprotein reductase] + H₂O

For diagram of the biosynthesis of cholic-acid conjugates, click here

Glossary:

taurochenodeoxycholic acid = N-(3α,7α-dihydroxy-5β-cholan-24-oyl)taurine
taurohyocholic acid = N-(3α,6α,7α-trihydroxy-5β-cholan-24-oyl)taurine
hyodeoxycholate = 3α,6α-dihydroxy-5β-cholan-24-oate
lithocholate = 3α-hydroxy-5β-cholan-24-oate

Other name(s):

CYP3A4; CYP4A21; taurochenodeoxycholate 6α-monooxygenase

Systematic name:

taurochenodeoxycholate,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (6α-hydroxylating)

Comments:

A cytochrome P-450 (heme-thiolate) protein. Requires cytochrome b₅ for maximal activity. Acts on taurochenodeoxycholate, taurodeoxycholate and less readily on lithocholate and chenodeoxycholate. In adult pig (Sus scrofa), hyocholic acid replaces cholic acid as a primary bile acid [5].

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 105669-85-0

References:

1.	Araya, Z. and Wikvall, K. 6α-Hydroxylation of taurochenodeoxycholic acid and lithocholic acid by CYP3A4 in human liver microsomes. Biochim. Biophys. Acta 1438 (1999) 47–54. [DOI] [PMID: 10216279]
2.	Araya, Z., Hellman, U. and Hansson, R. Characterisation of taurochenodeoxycholic acid 6α-hydroxylase from pig liver microsomes. Eur. J. Biochem. 231 (1995) 855–861. [DOI] [PMID: 7649186]
3.	Kramer, W., Sauber, K., Baringhaus, K.H., Kurz, M., Stengelin, S., Lange, G., Corsiero, D., Girbig, F., Konig, W. and Weyland, C. Identification of the bile acid-binding site of the ileal lipid-binding protein by photoaffinity labeling, matrix-assisted laser desorption ionization-mass spectrometry, and NMR structure. J. Biol. Chem. 276 (2001) 7291–7301. [DOI] [PMID: 11069906]
4.	Lundell, K., Hansson, R. and Wikvall, K. Cloning and expression of a pig liver taurochenodeoxycholic acid 6α-hydroxylase (CYP4A21): a novel member of the CYP4A subfamily. J. Biol. Chem. 276 (2001) 9606–9612. [DOI] [PMID: 11113117]
5.	Lundell, K. and Wikvall, K. Gene structure of pig sterol 12α-hydroxylase (CYP8B1) and expression in fetal liver: comparison with expression of taurochenodeoxycholic acid 6α-hydroxylase (CYP4A21). Biochim. Biophys. Acta 1634 (2003) 86–96. [DOI] [PMID: 14643796]
6.	Russell, D.W. The enzymes, regulation, and genetics of bile acid synthesis. Annu. Rev. Biochem. 72 (2003) 137–174. [DOI] [PMID: 12543708]

[EC 1.14.14.57 created 2005 asEC 1.14.13.97, transferred 2018 to EC 1.14.14.57]

1.14.14.58

Accepted name:

trimethyltridecatetraene synthase

Reaction:

(6E,10E)-geranyllinalool + [reduced NADPH—hemoprotein reductase] + O₂ = (3E,7E)-4,8,12-trimethyltrideca-1,3,7,11-tetraene + [oxidized NADPH—hemoprotein reductase] + but-3-en-2-one + 2 H₂O

For diagram of acyclic diterpenoid biosynthesis, click here

Glossary:

(6E,10E)-geranyllinalool = (6E,10E)-3,7,11,15-tetramethylhexadeca-1,6,10,14-tetraen-3-ol

Other name(s):

CYP82G1; CYP92C5; CYP92C6; DMNT/TMTT homoterpene synthase

Systematic name:

(6E,10E)-geranyllinalool,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase

Comments:

A cytochrome P-450 (heme-thiolate) protein isolated from the plants Arabidopsis thaliana (thale cress) and Zea mays (maize). It forms this C₁₆ homoterpene in response to herbivore attack. In vitro some variants of the enzyme also convert (3S,6E)-nerolidol to (3E)-4,8-dimethylnona-1,3,7-triene (see EC 1.14.14.59, dimethylnonatriene synthase).

Links to other databases:

References:

1.	Lee, S., Badieyan, S., Bevan, D.R., Herde, M., Gatz, C. and Tholl, D. Herbivore-induced and floral homoterpene volatiles are biosynthesized by a single P450 enzyme (CYP82G1) in Arabidopsis. Proc. Natl. Acad. Sci. USA 107 (2010) 21205–21210. [DOI] [PMID: 21088219]
2.	Richter, A., Schaff, C., Zhang, Z., Lipka, A.E., Tian, F., Kollner, T.G., Schnee, C., Preiss, S., Irmisch, S., Jander, G., Boland, W., Gershenzon, J., Buckler, E.S. and Degenhardt, J. Characterization of biosynthetic pathways for the production of the volatile homoterpenes DMNT and TMTT in Zea mays. Plant Cell 28 (2016) 2651–2665. [DOI] [PMID: 27662898]

[EC 1.14.14.58 created 2018]

1.14.14.59

Accepted name:

dimethylnonatriene synthase

Reaction:

(3S,6E)-nerolidol + [reduced NADPH—hemoprotein reductase] + O₂ = (3E)-4,8-dimethylnona-1,3,7-triene + [oxidized NADPH—hemoprotein reductase] + but-3-en-2-one + 2 H₂O

For diagram of acyclic sesquiterpenoid biosynthesis, click here

Other name(s):

CYP82G1; CYP92C5; DMNT/TMTT homoterpene synthase

Systematic name:

(3S,6E)-nerolidol,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase

Comments:

A cytochrome P-450 (heme-thiolate) protein isolated from the plants Arabidopsis thaliana (thale cress) and Zea mays (maize). It forms this C₁₁ homoterpene in response to herbivore attack. In vitro the enzyme also converts (6E,10E)-geranyllinalool to (3E,7E)-4,8,12-trimethyltrideca-1,3,7,11-tetraene (see EC 1.14.14.58, trimethyltridecatetraene synthase).

Links to other databases:

References:

1.	Lee, S., Badieyan, S., Bevan, D.R., Herde, M., Gatz, C. and Tholl, D. Herbivore-induced and floral homoterpene volatiles are biosynthesized by a single P450 enzyme (CYP82G1) in Arabidopsis. Proc. Natl. Acad. Sci. USA 107 (2010) 21205–21210. [DOI] [PMID: 21088219]
2.	Richter, A., Schaff, C., Zhang, Z., Lipka, A.E., Tian, F., Kollner, T.G., Schnee, C., Preiss, S., Irmisch, S., Jander, G., Boland, W., Gershenzon, J., Buckler, E.S. and Degenhardt, J. Characterization of biosynthetic pathways for the production of the volatile homoterpenes DMNT and TMTT in Zea mays. Plant Cell 28 (2016) 2651–2665. [DOI] [PMID: 27662898]

[EC 1.14.14.59 created 2018]

1.14.14.60

Accepted name:

ferruginol monooxygenase

Reaction:

ferruginol + [reduced NADPH—hemoprotein reductase] + O₂ = 11-hydroxyferruginol + [oxidized NADPH—hemoprotein reductase] + H₂O

For diagram of carnosic acid, salviol and suginol diterpenoids biosynthesis, click here

Glossary:

ferruginol = abieta-8,11,13-trien-12-ol

Other name(s):

CYP76AH24; CYP76AH3

Systematic name:

ferruginol,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (11-hydroxyferruginol-forming)

Comments:

A cytochrome P-450 (heme-thiolate) protein isolated from the plants Salvia pomifera (apple sage) and Salvia miltiorrhiza (danshen). 11-Hydroxyferruginol is a precursor of carnosic acid, a potent antioxidant.

Links to other databases:

References:

1.	Ignea, C., Athanasakoglou, A., Ioannou, E., Georgantea, P., Trikka, F.A., Loupassaki, S., Roussis, V., Makris, A.M. and Kampranis, S.C. Carnosic acid biosynthesis elucidated by a synthetic biology platform. Proc. Natl. Acad. Sci. USA 113 (2016) 3681–3686. [DOI] [PMID: 26976595]
2.	Scheler, U., Brandt, W., Porzel, A., Rothe, K., Manzano, D., Bozic, D., Papaefthimiou, D., Balcke, G.U., Henning, A., Lohse, S., Marillonnet, S., Kanellis, A.K., Ferrer, A. and Tissier, A. Elucidation of the biosynthesis of carnosic acid and its reconstitution in yeast. Nat. Commun. 7:12942 (2016). [DOI] [PMID: 27703160]
3.	Guo, J., Ma, X., Cai, Y., Ma, Y., Zhan, Z., Zhou, Y.J., Liu, W., Guan, M., Yang, J., Cui, G., Kang, L., Yang, L., Shen, Y., Tang, J., Lin, H., Ma, X., Jin, B., Liu, Z., Peters, R.J., Zhao, Z.K. and Huang, L. Cytochrome P450 promiscuity leads to a bifurcating biosynthetic pathway for tanshinones. New Phytol. 210 (2016) 525–534. [DOI] [PMID: 26682704]

[EC 1.14.14.60 created 2018]

1.14.14.61

Accepted name:

carnosic acid synthase

Reaction:

11-hydroxyferruginol + 3 [reduced NADPH—hemoprotein reductase] + 3 O₂ = carnosic acid + 3 [oxidized NADPH—hemoprotein reductase] + 4 H₂O

For diagram of carnosic acid, salviol and suginol diterpenoids biosynthesis, click here

Glossary:

carnosic acid = 11,12-dihydroxyabieta-8,11,13-trien-20-oic acid

Other name(s):

CYP76AK6; CYP76AK7; CYP76AK8

Systematic name:

11-hydroxyferruginol,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase

Comments:

A cytochrome P-450 (heme-thiolate) protein isolated from the plants Salvia pomifera (apple sage), S. miltiorrhiza (red sage), S. fruticosa (Greek sage) and Rosmarinus officinalis (Rosemary).

Links to other databases:

References:

1.	Ignea, C., Athanasakoglou, A., Ioannou, E., Georgantea, P., Trikka, F.A., Loupassaki, S., Roussis, V., Makris, A.M. and Kampranis, S.C. Carnosic acid biosynthesis elucidated by a synthetic biology platform. Proc. Natl. Acad. Sci. USA 113 (2016) 3681–3686. [DOI] [PMID: 26976595]
2.	Scheler, U., Brandt, W., Porzel, A., Rothe, K., Manzano, D., Bozic, D., Papaefthimiou, D., Balcke, G.U., Henning, A., Lohse, S., Marillonnet, S., Kanellis, A.K., Ferrer, A. and Tissier, A. Elucidation of the biosynthesis of carnosic acid and its reconstitution in yeast. Nat. Commun. 7:12942 (2016). [DOI] [PMID: 27703160]

[EC 1.14.14.61 created 2018]

1.14.14.62

Accepted name:

salviol synthase

Reaction:

ferruginol + [reduced NADPH—hemoprotein reductase] + O₂ = salviol + [oxidized NADPH—hemoprotein reductase] + H₂O

For diagram of carnosic acid, salviol and suginol diterpenoids biosynthesis, click here

Glossary:

salviol = abieta-8,11,13-triene-2α,12-diol

Other name(s):

CYP71BE52

Systematic name:

ferruginol,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (salviol-forming)

Comments:

A cytochrome P-450 (heme-thiolate) protein isolated from the plant Salvia pomifera (apple sage).

Links to other databases:

References:

1.	Ignea, C., Athanasakoglou, A., Ioannou, E., Georgantea, P., Trikka, F.A., Loupassaki, S., Roussis, V., Makris, A.M. and Kampranis, S.C. Carnosic acid biosynthesis elucidated by a synthetic biology platform. Proc. Natl. Acad. Sci. USA 113 (2016) 3681–3686. [DOI] [PMID: 26976595]

[EC 1.14.14.62 created 2018]

1.14.14.63

Accepted name:

β-amyrin 16β-monooxygenase

Reaction:

β-amyrin + [reduced NADPH—hemoprotein reductase] + O₂ = maniladiol + [oxidized NADPH—hemoprotein reductase] + H₂O

For diagram of hydroxy-β-amyrin biosynthesis, click here

Glossary:

cochalic acid = 3β,16β-dihydroxyolean-12-en-28-oic acid
maniladiol = 16β-hydroxy-β-amyrin = olean-12-ene-3β,16β-diol

Other name(s):

CYP716A141

Systematic name:

β-amyrin,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (maniladiol-forming)

Comments:

A cytochrome P-450 (heme-thiolate) protein isolated from the plant Platycodon grandiflorus (baloon flower). The enzyme is also able to oxidize oleanolic acid to cochalic acid.

Links to other databases:

References:

Tamura, K., Teranishi, Y., Ueda, S., Suzuki, H., Kawano, N., Yoshimatsu, K., Saito, K., Kawahara, N., Muranaka, T. and Seki, H. Cytochrome P450 monooxygenase CYP716A141 is a unique β-amyrin C-16β oxidase Involved in triterpenoid saponin biosynthesis in Platycodon grandiflorus. Plant Cell Physiol. 58 (2017) 874–884. [DOI] [PMID: 28371833]

[EC 1.14.14.63 created 2018]

1.14.14.64

Accepted name:

β-amyrin 6β-monooxygenase

Reaction:

β-amyrin + [reduced NADPH—hemoprotein reductase] + O₂ = daturadiol + [oxidized NADPH—hemoprotein reductase] + H₂O

For diagram of hydroxy-β-amyrin biosynthesis, click here

Glossary:

daturadiol = 6β-hydroxy-β-amyrin = olean-12-ene-3β,6β-diol

Other name(s):

CYP716E26

Systematic name:

β-amyrin,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (daturadiol-forming)

Comments:

A cytochrome P-450 (heme-thiolate) protein isolated from the plant Solanum lycopersicum (tomato).

Links to other databases:

References:

1.	Yasumoto, S., Seki, H., Shimizu, Y., Fukushima, E.O. and Muranaka, T. Functional characterization of CYP716 family P450 enzymes in triterpenoid biosynthesis in tomato. Front. Plant Sci. 8:21 (2017). [DOI] [PMID: 28194155]

[EC 1.14.14.64 created 2018]

1.14.14.65

Accepted name:

sugiol synthase

Reaction:

ferruginol + 2 [reduced NADPH—hemoprotein reductase] + 2 O₂ = sugiol + 2 [oxidized NADPH—hemoprotein reductase] + 3 H₂O

For diagram of carnosic acid, salviol and suginol diterpenoids biosynthesis, click here

Glossary:

ferruginol = abieta-8,11,13-trien-12-ol
sugiol = 12-hydroxyabieta-8,11,13-trien-7-one

Other name(s):

CYP76AH3

Systematic name:

ferruginol,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (sugiol-forming)

Comments:

A cytochrome P-450 (heme-thiolate) protein isolated from the plant Salvia miltiorrhiza (danshen). The enzyme also oxidizes 11-hydroxyferruginol to 11-hydroxysugiol. It also oxidizes at C-12 of ferruginol (EC 1.14.14.60 ferruginol monooxygenase).

Links to other databases:

References:

Guo, J., Ma, X., Cai, Y., Ma, Y., Zhan, Z., Zhou, Y.J., Liu, W., Guan, M., Yang, J., Cui, G., Kang, L., Yang, L., Shen, Y., Tang, J., Lin, H., Ma, X., Jin, B., Liu, Z., Peters, R.J., Zhao, Z.K. and Huang, L. Cytochrome P450 promiscuity leads to a bifurcating biosynthetic pathway for tanshinones. New Phytol. 210 (2016) 525–534. [DOI] [PMID: 26682704]

[EC 1.14.14.65 created 2018]

1.14.14.66

Accepted name:

marmesin synthase

Reaction:

demethylsuberosin + [reduced NADPH—hemoprotein reductase] + O₂ = (+)-marmesin + [oxidized NADPH—hemoprotein reductase] + H₂O

For diagram of psoralen biosynthesis, click here

Glossary:

demethylsuberosin = 7-hydroxy-6-prenyl-1-benzopyran-2-one
(+)-marmesin = (S)-2-(2-hydroxypropan-2-yl)-2,3-dihydro-7H-furo[3,2-g]chromen-7-one

Systematic name:

demethylsuberosin,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase

Comments:

A P-450 monoxygenase involved in psoralen biosynthesis, see EC 1.14.14.141, psoralen synthase.

Links to other databases:

References:

1.	Hamerski, D. and Matern, U. Elicitor-induced biosynthesis of psoralens in Ammi majus L. suspension cultures. Microsomal conversion of demethylsuberosin into (+)marmesin and psoralen. Eur. J. Biochem. 171 (1988) 369–375. [PMID: 2828055]

[EC 1.14.14.66 created 2018]

1.14.14.67

Accepted name:

11-hydroxysugiol 20-monooxygenase

Reaction:

11-hydroxysugiol + [reduced NADPH—hemoprotein reductase] + O₂ = 11,20-dihydroxysugiol + [oxidized NADPH—hemoprotein reductase] + H₂O

For diagram of carnosic acid, salviol and suginol diterpenoids biosynthesis, click here

Glossary:

ferruginol = abieta-8,11,13-trien-12-ol
sugiol = 12-hydroxyabieta-8,11,13-trien-7-one

Other name(s):

CYP76AK1

Systematic name:

11-hydroxysugiol,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (11,20-dihydroxysugiol-forming)

Comments:

A cytochrome P-450 (heme-thiolate) protein isolated from the plant Salvia miltiorrhiza (danshen). The enzyme also oxidizes 11-hydroxyferruginol to 11,20-dihydroxyferruginol.

Links to other databases:

References:

[EC 1.14.14.67 created 2018]

1.14.14.68

Accepted name:

syn-pimaradiene 3-monooxygenase

Reaction:

9β-pimara-7,15-diene + [reduced NADPH—hemoprotein reductase] + O₂ = 9β-pimara-7,15-diene-3β-ol + [oxidized NADPH—hemoprotein reductase] + H₂O

For diagram of momilactone A biosynthesis, click here

Glossary:

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

Other name(s):

CYP701A8

Systematic name:

9β-pimara7,15-diene,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (9β-pimara-7,15-diene-3β-ol-forming)

Comments:

A cytochrome P-450 (heme-thiolate) protein isolated from rice, Oryza sativa.

Links to other databases:

References:

1.	Kitaoka, N., Wu, Y., Xu, M. and Peters, R.J. Optimization of recombinant expression enables discovery of novel cytochrome P450 activity in rice diterpenoid biosynthesis. Appl. Microbiol. Biotechnol. 99 (2015) 7549–7558. [DOI] [PMID: 25758958]

[EC 1.14.14.68 created 2018]

1.14.14.69

Accepted name:

ent-cassadiene hydroxylase

Reaction:

ent-cassa-12,15-diene + 3 [reduced NADPH—hemoprotein reductase] + 3 O₂ = ent-3β-hydroxycassa-12,15-dien-2-one + 3 [oxidized NADPH—hemoprotein reductase] + 4 H₂O (overall reaction)
(1a) ent-cassa-12,15-diene + [reduced NADPH—hemoprotein reductase] + O₂ = ent-cassa-12,15-dien-2β-ol + [oxidized NADPH—hemoprotein reductase] + H₂O
(1b) ent-cassa-12,15-dien-2β-ol + [reduced NADPH—hemoprotein reductase] + O₂ = ent-cassa-12,15-dien-2-one + [oxidized NADPH—hemoprotein reductase] + 2 H₂O
(1b′) ent-cassa-12,15-dien-2β-ol + [reduced NADPH—hemoprotein reductase] + O₂ = ent-cassa-12,15-diene-2β,3β-diol + [oxidized NADPH—hemoprotein reductase] + H₂O
(1c) ent-cassa-12,15-dien-2-one + [reduced NADPH—hemoprotein reductase] + O₂ = ent-3β-hydroxycassa-12,15-dien-2-one + [oxidized NADPH—hemoprotein reductase] + H₂O
(1c′) ent-cassa-12,15-diene-2β,3β-diol + [reduced NADPH—hemoprotein reductase] + O₂ = ent-3β-hydroxycassa-12,15-dien-2-one + [oxidized NADPH—hemoprotein reductase] + 2 H₂O

For diagram of ent-hydroxycassadiene biosynthesis, click here

Other name(s):

CYP71Z7

Systematic name:

ent-cassa-12,15-diene,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (ent-3β-hydroxycassa-12,15-dien-2-one-forming)

Comments:

A cytochrome P-450 (heme-thiolate) protein isolated from the plant Oryza sativa (rice) that is involved in phytocassanes biosynthesis. Depending on the order of activities, the enzyme may form either ent-cassa-12,15-dien-2-one or ent-cassa-12,15-diene-2β,3β-diol as an intermediate.

Links to other databases:

References:

1.	Kitaoka, N., Wu, Y., Xu, M. and Peters, R.J. Optimization of recombinant expression enables discovery of novel cytochrome P450 activity in rice diterpenoid biosynthesis. Appl. Microbiol. Biotechnol. 99 (2015) 7549–7558. [DOI] [PMID: 25758958]

[EC 1.14.14.69 created 2018]

1.14.15.24

Accepted name:

β-carotene 3-hydroxylase

Reaction:

β-carotene + 4 reduced ferredoxin [iron-sulfur] cluster + 2 H⁺ + 2 O₂ = zeaxanthin + 4 oxidized ferredoxin [iron-sulfur] cluster + 2 H₂O (overall reaction)
(1a) β-carotene + 2 reduced ferredoxin [iron-sulfur] cluster + H⁺ + O₂ = β-cryptoxanthin + 2 oxidized ferredoxin [iron-sulfur] cluster + H₂O
(1b) β-cryptoxanthin + 2 reduced ferredoxin [iron-sulfur] cluster + H⁺ + O₂ = zeaxanthin + 2 oxidized ferredoxin [iron-sulfur] cluster + H₂O

For diagram of lutein biosynthesis, click here and for diagram of zeaxanthin biosynthesis, click here

Other name(s):

β-carotene 3,3′-monooxygenase; CrtZ

Systematic name:

β-carotene,reduced ferredoxin [iron-sulfur] cluster:oxygen 3-oxidoreductase

Comments:

Requires ferredoxin and iron(II). Also acts on other carotenoids with a β-end group. In some species canthaxanthin is the preferred substrate.

Links to other databases:

References:

1.	Sun, Z., Gantt, E. and Cunningham, F.X., Jr. Cloning and functional analysis of the β-carotene hydroxylase of Arabidopsis thaliana. J. Biol. Chem. 271 (1996) 24349–24352. [DOI] [PMID: 8798688]
2.	Fraser, P.D., Miura, Y. and Misawa, N. In vitro characterization of astaxanthin biosynthetic enzymes. J. Biol. Chem. 272 (1997) 6128–6135. [DOI] [PMID: 9045623]
3.	Fraser, P.D., Shimada, H. and Misawa, N. Enzymic confirmation of reactions involved in routes to astaxanthin formation, elucidated using a direct substrate in vitro assay. Eur. J. Biochem. 252 (1998) 229–236. [DOI] [PMID: 9523693]
4.	Bouvier, F., Keller, Y., d'Harlingue, A. and Camara, B. Xanthophyll biosynthesis: molecular and functional characterization of carotenoid hydroxylases from pepper fruits (Capsicum annuum L.). Biochim. Biophys. Acta 1391 (1998) 320–328. [DOI] [PMID: 9555077]
5.	Linden, H. Carotenoid hydroxylase from Haematococcus pluvialis: cDNA sequence, regulation and functional complementation. Biochim. Biophys. Acta 1446 (1999) 203–212. [DOI] [PMID: 10524195]
6.	Zhu, C., Yamamura, S., Nishihara, M., Koiwa, H. and Sandmann, G. cDNAs for the synthesis of cyclic carotenoids in petals of Gentiana lutea and their regulation during flower development. Biochim. Biophys. Acta 1625 (2003) 305–308. [DOI] [PMID: 12591618]
7.	Choi, S.K., Matsuda, S., Hoshino, T., Peng, X. and Misawa, N. Characterization of bacterial β-carotene 3,3′-hydroxylases, CrtZ, and P₄₅₀ in astaxanthin biosynthetic pathway and adonirubin production by gene combination in Escherichia coli. Appl. Microbiol. Biotechnol. 72 (2006) 1238–1246. [DOI] [PMID: 16614859]

[EC 1.14.15.24 created 2011 as EC 1.14.13.129, transferred 2017 to EC 1.14.15.24]

1.14.15.25

Accepted name:

p-cymene methyl-monooxygenase

Reaction:

p-cymene + O₂ + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H⁺ = 4-isopropylbenzyl alcohol + 2 oxidized ferredoxin [iron-sulfur] cluster + H₂O

Glossary:

p-cymene = 4-methyl-1-(propan-2-yl)benzene

Other name(s):

cymAa (gene name); cymA (gene name); p-cymene methyl hydroxylase

Systematic name:

p-cymene,ferredoxin:oxygen oxidoreductase (methyl-hydroxylating)

Comments:

The enzyme, characterized from several Pseudomonas strains, initiates p-cymene catabolism through hydroxylation of the methyl group. The enzyme has a distinct preference for substrates containing at least an alkyl or heteroatom substituent at the para-position of toluene. The electrons are provided by a reductase (EC 1.18.1.3, ferredoxin—NAD⁺ reductase) that transfers electrons from NADH via FAD and an [2Fe-2S] cluster. In Pseudomonas chlororaphis the presence of a third component of unknown function greatly increases the activity. cf. EC 1.14.15.26, toluene methyl-monooxygenase.

Links to other databases:

References:

1.	Eaton, R.W. p-Cymene catabolic pathway in Pseudomonas putida F1: cloning and characterization of DNA encoding conversion of p-cymene to p-cumate. J. Bacteriol. 179 (1997) 3171–3180. [DOI] [PMID: 9150211]
2.	Dutta, T.K. and Gunsalus, I.C. Reductase gene sequences and protein structures: p-cymene methyl hydroxylase. Biochem. Biophys. Res. Commun. 233 (1997) 502–506. [DOI] [PMID: 9144566]
3.	Nishio, T., Patel, A., Wang, Y. and Lau, P.C. Biotransformations catalyzed by cloned p-cymene monooxygenase from Pseudomonas putida F1. Appl. Microbiol. Biotechnol. 55 (2001) 321–325. [PMID: 11341314]
4.	Dutta, T.K., Chakraborty, J., Roy, M., Ghosal, D., Khara, P. and Gunsalus, I.C. Cloning and characterization of a p-cymene monooxygenase from Pseudomonas chlororaphis subsp. aureofaciens. Res. Microbiol. 161 (2010) 876–882. [DOI] [PMID: 21035544]

[EC 1.14.15.25 created 2018]

1.14.15.26

Accepted name:

toluene methyl-monooxygenase

Reaction:

(1) toluene + O₂ + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H⁺ = benzyl alcohol + 2 oxidized ferredoxin [iron-sulfur] cluster + H₂O
(2) p-xylene + O₂ + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H⁺ = 4-methylbenzyl alcohol + 2 oxidized ferredoxin [iron-sulfur] cluster + H₂O
(3) m-xylene + O₂ + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H⁺ = 3-methylbenzyl alcohol + 2 oxidized ferredoxin [iron-sulfur] cluster + H₂O

Glossary:

toluene = methylbenzene
p-xylene = 1,4-dimethylbenzene
m-xylene = 1,3-dimethylbenzene

Other name(s):

xylM (gene names); ntnM (gene names)

Systematic name:

methylbenzene,ferredoxin:oxygen oxidoreductase (methyl-hydroxylating)

Comments:

The enzyme, characterized from several Pseudomonas strains, catalyses the first step in the degradation of toluenes and xylenes. It has a broad substrate specificity and is also active with substituted compounds, such as chlorotoluenes. The electrons are provided by a reductase (EC 1.18.1.3, ferredoxin—NAD⁺ reductase) that transfers electrons from NADH via FAD and an [2Fe-2S] cluster. The enzyme can also act on its products, producing gem-diols that spontaneously dehydrate to form aldehydes.

Links to other databases:

References:

1.	Suzuki, M., Hayakawa, T., Shaw, J.P., Rekik, M. and Harayama, S. Primary structure of xylene monooxygenase: similarities to and differences from the alkane hydroxylation system. J. Bacteriol. 173 (1991) 1690–1695. [DOI] [PMID: 1999388]
2.	Shaw, J.P. and Harayama, S. Purification and characterisation of the NADH:acceptor reductase component of xylene monooxygenase encoded by the TOL plasmid pWW0 of Pseudomonas putida mt-2. Eur. J. Biochem. 209 (1992) 51–61. [DOI] [PMID: 1327782]
3.	Brinkmann, U. and Reineke, W. Degradation of chlorotoluenes by in vivo constructed hybrid strains: problems of enzyme specificity, induction and prevention of meta-pathway. FEMS Microbiol. Lett. 75 (1992) 81–87. [PMID: 1526468]
4.	James, K.D. and Williams, P.A. ntn genes determining the early steps in the divergent catabolism of 4-nitrotoluene and toluene in Pseudomonas sp. strain TW3. J. Bacteriol. 180 (1998) 2043–2049. [PMID: 9555884]

[EC 1.14.15.26 created 2018]

1.14.19.53

Accepted name:

all-trans-retinol 3,4-desaturase

Reaction:

all-trans-retinol + 2 reduced adrenodoxin + 2 H⁺ + O₂ = all-trans-3,4-didehydroretinol + 2 oxidized adrenodoxin + 2 H₂O

For diagram of retinal and derivatives biosynthesis, click here

Other name(s):

CYP27C1 (gene name)

Systematic name:

all-trans-retinol,reduced adrenodoxin:oxygen 3,4-oxidoreductase

Comments:

A cytochrome P-450 (heme thiolate) enzyme found in vertebrates. The enzyme is also active with retinal and retinoic acid.

Links to other databases:

References:

1.	Enright, J.M., Toomey, M.B., Sato, S.Y., Temple, S.E., Allen, J.R., Fujiwara, R., Kramlinger, V.M., Nagy, L.D., Johnson, K.M., Xiao, Y., How, M.J., Johnson, S.L., Roberts, N.W., Kefalov, V.J., Guengerich, F.P. and Corbo, J.C. Cyp27c1 red-shifts the spectral sensitivity of photoreceptors by converting vitamin A₁ into A2. Curr. Biol. 25 (2015) 3048–3057. [DOI] [PMID: 26549260]
2.	Kramlinger, V.M., Nagy, L.D., Fujiwara, R., Johnson, K.M., Phan, T.T., Xiao, Y., Enright, J.M., Toomey, M.B., Corbo, J.C. and Guengerich, F.P. Human cytochrome P450 27C1 catalyzes 3,4-desaturation of retinoids. FEBS Lett. 590 (2016) 1304–1312. [DOI] [PMID: 27059013]

[EC 1.14.19.53 created 2018]

1.14.20.2

Transferred entry:

2,4-dihydroxy-1,4-benzoxazin-3-one-glucoside dioxygenase. Now EC 1.14.11.59, 2,4-dihydroxy-1,4-benzoxazin-3-one-glucoside dioxygenase

[EC 1.14.20.2 created 2012, deleted 2018]

1.14.99.42

Transferred entry:

zeaxanthin 7,8-dioxygenase. Now EC 1.13.11.84, crocetin dialdehyde synthase

[EC 1.14.99.42 created 2011, modified 2014, deleted 2017]

1.14.99.59

Accepted name:

tryptamine 4-monooxygenase

Reaction:

tryptamine + reduced acceptor + O₂ = 4-hydroxytryptamine + acceptor + H₂O

For diagram of psilocybin biosynthesis, click here

Glossary:

psilocybin = 3-[2-(dimethylamino)ethyl]-1H-indol-4-yl phosphate

Other name(s):

PsiH

Systematic name:

tryptamine,hydrogen-donor:oxygen oxidoreductase (4-hydroxylating)

Comments:

A cytochrome P-450 (heme-thiolate) protein isolated from the fungus Psilocybe cubensis. Involved in the biosynthesis of the psychoactive compound psilocybin.

Links to other databases:

References:

1.	Fricke, J., Blei, F. and Hoffmeister, D. Enzymatic synthesis of psilocybin. Angew. Chem. Int. Ed. Engl. 56 (2017) 12352–12355. [DOI] [PMID: 28763571]

[EC 1.14.99.59 created 2017]

*EC

2.1.1.294

Accepted name:

3-O-phospho-polymannosyl GlcNAc-diphospho-ditrans,octacis-undecaprenol 3-phospho-methyltransferase

Reaction:

S-adenosyl-L-methionine + 3-O-phospho-α-D-Man-(1→2)-α-D-Man-(1→2)-[α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→2)-α-D-Man-(1→2)]_n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol = S-adenosyl-L-homocysteine + 3-O-methylphospho-α-D-Man-(1→2)-α-D-Man-(1→2)-[α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→2)-α-D-Man-(1→2)]_n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol

Other name(s):

WbdD; S-adenosyl-L-methionine:3-O-phospho-α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)]_n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-α-diphospho-ditrans,octacis-undecaprenol 3-phospho-methyltransferase

Systematic name:

S-adenosyl-L-methionine:3-O-phospho-α-D-Man-(1→2)-α-D-Man-(1→2)-[α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→2)-α-D-Man-(1→2)]_n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol 3-phospho-methyltransferase

Comments:

The enzyme is involved in the biosynthesis of the polymannose O-polysaccharide in the outer leaflet of the membrane of Escherichia coli serotype O9a. O-Polysaccharide structures vary extensively because of differences in the number and type of sugars in the repeat unit. The dual kinase/methylase WbdD also catalyses the preceding phosphorylation of α-D-Man-(1→2)-α-D-Man-(1→2)-[α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→2)-α-D-Man-(1→2)]_n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol (cf. EC 2.7.1.181, polymannosyl GlcNAc-diphospho-ditrans,octacis-undecaprenol kinase).

Links to other databases:

References:

1.	Clarke, B.R., Cuthbertson, L. and Whitfield, C. Nonreducing terminal modifications determine the chain length of polymannose O antigens of Escherichia coli and couple chain termination to polymer export via an ATP-binding cassette transporter. J. Biol. Chem. 279 (2004) 35709–35718. [DOI] [PMID: 15184370]
2.	Clarke, B.R., Greenfield, L.K., Bouwman, C. and Whitfield, C. Coordination of polymerization, chain termination, and export in assembly of the Escherichia coli lipopolysaccharide O9a antigen in an ATP-binding cassette transporter-dependent pathway. J. Biol. Chem. 284 (2009) 30662–30672. [DOI] [PMID: 19734145]
3.	Clarke, B.R., Richards, M.R., Greenfield, L.K., Hou, D., Lowary, T.L. and Whitfield, C. In vitro reconstruction of the chain termination reaction in biosynthesis of the Escherichia coli O9a O-polysaccharide: the chain-length regulator, WbdD, catalyzes the addition of methyl phosphate to the non-reducing terminus of the growing glycan. J. Biol. Chem. 286 (2011) 41391–41401. [DOI] [PMID: 21990359]
4.	Liston, S.D., Clarke, B.R., Greenfield, L.K., Richards, M.R., Lowary, T.L. and Whitfield, C. Domain interactions control complex formation and polymerase specificity in the biosynthesis of the Escherichia coli O9a antigen. J. Biol. Chem. 290 (2015) 1075–1085. [DOI] [PMID: 25422321]

[EC 2.1.1.294 created 2014, modified 2018]

2.1.1.345

Accepted name:

psilocybin synthase

Reaction:

2 S-adenosyl-L-methionine + 4-hydroxytryptamine 4-phosphate = 2 S-adenosyl-L-homocysteine + psilocybin (overall reaction)
(1a) S-adenosyl-L-methionine + 4-hydroxytryptamine 4-phosphate = S-adenosyl-L-homocysteine + 4-hydroxy-N-methyltryptamine 4-phosphate
(1b) S-adenosyl-L-methionine + 4-hydroxy-N-methyltryptamine 4-phosphate = S-adenosyl-L-homocysteine + psilocybin

For diagram of psilocybin biosynthesis, click here

Glossary:

psilocybin = 3-[2-(dimethylamino)ethyl]-1H-indol-4-yl phosphate

Other name(s):

PsiM

Systematic name:

S-adenosyl-L-methionine:4-hydroxytryptamine-4-phosphate N,N-dimethyltransferase

Comments:

Isolated from the fungus Psilocybe cubensis. The product, psilocybin, is a psychoactive compound.

Links to other databases:

References:

1.	Fricke, J., Blei, F. and Hoffmeister, D. Enzymatic synthesis of psilocybin. Angew. Chem. Int. Ed. Engl. 56 (2017) 12352–12355. [DOI] [PMID: 28763571]

[EC 2.1.1.345 created 2017]

2.1.1.346

Accepted name:

U6 snRNA m⁶A methyltransferase

Reaction:

S-adenosyl-L-methionine + adenine in U6 snRNA = S-adenosyl-L-homocysteine + N⁶-methyladenine in U6 snRNA

Other name(s):

METTL16 (gene name)

Systematic name:

S-adenosyl-L-methionine:adenine in U6 snRNA methyltransferase

Comments:

This enzyme, found in vertebrates, methylates a specific adenine in a hairpin structure of snRNA. The effects of the binding of the methyltransferase to its substrate is important for the regulation of the activity of an isoform of EC 2.5.1.6, methionine adenosyltransferase, that produces S-adenosyl-L-methionine [1,2]. The enzyme also binds (and maybe methylates) the lncRNAs XIST and MALAT1 as well as a number of pre-mRNAs at specific positions often found in the intronic regions [2].

Links to other databases:

References:

1.	Pendleton, K.E., Chen, B., Liu, K., Hunter, O.V., Xie, Y., Tu, B.P. and Conrad, N.K. The U6 snRNA m⁶A methyltransferase METTL16 regulates SAM synthetase intron retention. Cell 169 (2017) 824–835.e14. [DOI] [PMID: 28525753]
2.	Warda, A.S., Kretschmer, J., Hackert, P., Lenz, C., Urlaub, H., Hobartner, C., Sloan, K.E. and Bohnsack, M.T. Human METTL16 is a N⁶-methyladenosine (m⁶A) methyltransferase that targets pre-mRNAs and various non-coding RNAs. EMBO Rep. 18 (2017) 2004–2014. [DOI] [PMID: 29051200]

[EC 2.1.1.346 created 2018]

2.1.1.347

Accepted name:

(+)-O-methylkolavelool synthase

Reaction:

S-adenosyl-L-methionine + (+)-kolavelool = S-adenosyl-L-homocysteine + (+)-O-methylkolavelool

For diagram of (+)-kolavenyl diphosphate derived diterpenoids, click here

Other name(s):

Haur_2147 (locus name)

Systematic name:

S-adenosyl-L-methionine:(+)-kolavelool O-methyltransferase

Comments:

Isolated from the bacterium Herpetosiphon aurantiacus.

Links to other databases:

References:

1.	Nakano, C., Oshima, M., Kurashima, N. and Hoshino, T. Identification of a new diterpene biosynthetic gene cluster that produces O-methylkolavelool in Herpetosiphon aurantiacus. ChemBioChem 16 (2015) 772–781. [DOI] [PMID: 25694050]

[EC 2.1.1.347 created 2018]

2.1.3.15

Accepted name:

acetyl-CoA carboxytransferase

Reaction:

[biotin carboxyl-carrier protein]-N⁶-carboxybiotinyl-L-lysine + acetyl-CoA = [biotin carboxyl-carrier protein]-N⁶-biotinyl-L-lysine + malonyl-CoA

Other name(s):

accAD (gene names)

Systematic name:

[biotin carboxyl-carrier protein]-N⁶-carboxybiotinyl-L-lysine:acetyl-CoA:carboxytransferase

Comments:

The enzyme catalyses the transfer of a carboxyl group carried on a biotinylated biotin carboxyl carrier protein (BCCP) to acetyl-CoA, forming malonyl-CoA. In some organisms this activity is part of a multi-domain polypeptide that includes the carrier protein and EC 6.3.4.14, biotin carboxylase (see EC 6.4.1.2, acetyl-CoA carboxylase). Some enzymes can also carboxylate propanonyl-CoA and butanoyl-CoA (cf. EC 6.4.1.3, propionyl-CoA carboxylase).

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9023-93-2

References:

1.	Bilder, P., Lightle, S., Bainbridge, G., Ohren, J., Finzel, B., Sun, F., Holley, S., Al-Kassim, L., Spessard, C., Melnick, M., Newcomer, M. and Waldrop, G.L. The structure of the carboxyltransferase component of acetyl-coA carboxylase reveals a zinc-binding motif unique to the bacterial enzyme. Biochemistry 45 (2006) 1712–1722. [DOI] [PMID: 16460018]
2.	Chuakrut, S., Arai, H., Ishii, M. and Igarashi, Y. Characterization of a bifunctional archaeal acyl coenzyme A carboxylase. J. Bacteriol. 185 (2003) 938–947. [DOI] [PMID: 12533469]

[EC 2.1.3.15 created 2017]

2.1 Transferring one-carbon groups

2.1.5 Methylenetransferases

2.1.5.1

Accepted name:

sesamin methylene transferase

Reaction:

(1) (+)-sesamin + tetrahydrofolate = (+)-demethylpiperitol + 5,10-methylenetetrahydrofolate
(2) (+)-demethylpiperitol + tetrahydrofolate = (+)-didemethylpinoresinol + 5,10-methylenetetrahydrofolate

For diagram of sesamin catabolism, click here

Glossary:

(+)-sesamin = 5,5′-[(1S,3aR,4S,6aR)-tetrahydro-1H,3H-furo[3,4-c]furan-1,4-diyl]bis(1,3-benzodioxole)
(+)-demethylpiperitol = 4-[(1S,3aR,4S,6aR)-4-(1,3-benzodioxol-5-yl)tetrahydro-1H,3H-furo[3,4-c]furan-1-yl]benzene-1,2-diol
(+)-didemethylpinoresinol = 4-[(1S,3aR,4S,6aR)-4-(3,4-dihydroxyphenyl)tetrahydro-1H,3H-furo[3,4-c]furan-1-yl]benzene-1,2-diol

Other name(s):

sesA (gene name)

Systematic name:

(+)-sesamin:tetrahydrofolate N-methylenetransferase

Comments:

This enzyme was characterized from the bacterium Sinomonas sp. No.22. It catalyses a cleavage of a methylene bridge, followed by the transfer of the methylene group to tetrahydrofolate. The enzyme is also active with (+)-episesamin, (–)-asarinin, (+)-sesaminol, (+)-sesamolin, and piperine.

Links to other databases:

References:

1.	Kumano, T., Fujiki, E., Hashimoto, Y. and Kobayashi, M. Discovery of a sesamin-metabolizing microorganism and a new enzyme. Proc. Natl. Acad. Sci. USA 113 (2016) 9087–9092. [DOI] [PMID: 27444012]

[EC 2.1.5.1 created 2018]

2.3.1.96

Deleted entry:

glycoprotein N-palmitoyltransferase

[EC 2.3.1.96 created 1989, deleted 2018]

2.3.1.128

Transferred entry:

ribosomal-protein-alanine N-acetyltransferase, now classified as EC 2.3.1.266, [ribosomal protein S18]-alanine N-acetyltransferase, and EC 2.3.1.267, [ribosomal protein S5]-alanine N-acetyltransferase.

[EC 2.3.1.128 created 1990, deleted 2018]

2.3.1.266

Accepted name:

[ribosomal protein bS18]-alanine N-acetyltransferase

Reaction:

acetyl-CoA + an N-terminal L-alanyl-[bS18 protein of 30S ribosome] = CoA + an N-terminal N-acetyl-L-alanyl-[bS18 protein of 30S ribosome]

Other name(s):

rimI (gene name)

Systematic name:

acetyl-CoA:N-terminal L-alanyl-[bS18 protein of 30S ribosome] N-acetyltransferase

Comments:

The enzyme, characterized from bacteria, is specific for protein bS18, a component of the 30S ribosomal subunit. cf. EC 2.3.1.267, [ribosomal protein uS5]-alanine N-acetyltransferase.

Links to other databases:

References:

1.	Isono, K. and Isono, S. Ribosomal protein modification in Escherichia coli. II. Studies of a mutant lacking the N-terminal acetylation of protein S18. Mol. Gen. Genet. 177 (1980) 645–651. [DOI] [PMID: 6991870]
2.	Yoshikawa, A., Isono, S., Sheback, A. and Isono, K. Cloning and nucleotide sequencing of the genes rimI and rimJ which encode enzymes acetylating ribosomal proteins S18 and S5 of Escherichia coli K12. Mol. Gen. Genet. 209 (1987) 481–488. [DOI] [PMID: 2828880]

[EC 2.3.1.266 created 1990 as EC 2.3.1.128, part transferred 2018 to EC 2.3.1.266, modified 2023]

2.3.1.267

Accepted name:

[ribosomal protein uS5]-alanine N-acetyltransferase

Reaction:

acetyl-CoA + an N-terminal L-alanyl-[uS5 protein of 30S ribosome] = CoA + an N-terminal N-acetyl-L-alanyl-[uS5 protein of 30S ribosome]

Other name(s):

rimJ (gene name)

Systematic name:

acetyl-CoA:N-terminal L-alanyl-[uS5 protein of 30S ribosome] N-acetyltransferase

Comments:

The enzyme, characterized from bacteria, is specific for protein uS5, a component of the 30S ribosomal subunit. It also plays a role in maturation of the 30S ribosomal subunit. cf. EC 2.3.1.266, [ribosomal protein bS18]-alanine N-acetyltransferase.

Links to other databases:

References:

1.	Yoshikawa, A., Isono, S., Sheback, A. and Isono, K. Cloning and nucleotide sequencing of the genes rimI and rimJ which encode enzymes acetylating ribosomal proteins S18 and S5 of Escherichia coli K12. Mol. Gen. Genet. 209 (1987) 481–488. [DOI] [PMID: 2828880]
2.	Roy-Chaudhuri, B., Kirthi, N., Kelley, T. and Culver, G.M. Suppression of a cold-sensitive mutation in ribosomal protein S5 reveals a role for RimJ in ribosome biogenesis. Mol. Microbiol. 68 (2008) 1547–1559. [DOI] [PMID: 18466225]
3.	Roy-Chaudhuri, B., Kirthi, N. and Culver, G.M. Appropriate maturation and folding of 16S rRNA during 30S subunit biogenesis are critical for translational fidelity. Proc. Natl. Acad. Sci. USA 107 (2010) 4567–4572. [DOI] [PMID: 20176963]

[EC 2.3.1.267 created 1990 as EC 2.3.1.128, part transferred 2018 to EC 2.3.1.267, modified 2023]

2.3.1.268

Accepted name:

ethanol O-acetyltransferase

Reaction:

ethanol + acetyl-CoA = ethyl acetate + CoA

Other name(s):

eat1 (gene name); ethanol acetyltransferase

Systematic name:

acetyl-CoA:ethanol O-acetyltransferase

Comments:

The enzyme, characterized from the yeast Wickerhamomyces anomalus, is responsible for most ethyl acetate synthesis in known ethyl acetate-producing yeasts. It is only distantly related to enzymes classified as EC 2.3.1.84, alcohol O-acetyltransferase. The enzyme also possesses thioesterase and esterase activities, which are inhibited by high ethanol concentrations.

Links to other databases:

References:

1.	Kruis, A.J., Levisson, M., Mars, A.E., van der Ploeg, M., Garces Daza, F., Ellena, V., Kengen, S.WM., van der Oost, J. and Weusthuis, R.A. Ethyl acetate production by the elusive alcohol acetyltransferase from yeast. Metab. Eng. 41 (2017) 92–101. [DOI] [PMID: 28356220]

[EC 2.3.1.268 created 2018]

*EC

2.3.2.26

Accepted name:

HECT-type E3 ubiquitin transferase

Reaction:

[E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-N⁶-ubiquitinyl-L-lysine (overall reaction)
(1a) [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [HECT-type E3 ubiquitin transferase]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [HECT-type E3 ubiquitin transferase]-S-ubiquitinyl-L-cysteine
(1b) [HECT-type E3 ubiquitin transferase]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-lysine = [HECT-type E3 ubiquitin transferase]-L-cysteine + [acceptor protein]-N⁶-ubiquitinyl-L-lysine

Glossary:

HECT protein domain = Homologous to the E6-AP Carboxyl Terminus protein domain

Other name(s):

HECT E3 ligase (misleading); ubiquitin transferase HECT-E3; S-ubiquitinyl-[HECT-type E3-ubiquitin transferase]-L-cysteine:acceptor protein ubiquitin transferase (isopeptide bond-forming)

Systematic name:

[E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine:[acceptor protein] ubiquitin transferase (isopeptide bond-forming)

Comments:

In the first step the enzyme transfers ubiquitin from the E2 ubiquitin-conjugating enzyme (EC 2.3.2.23) to a cysteine residue in its HECT domain (which is located in the C-terminal region), forming a thioester bond. In a subsequent step the enzyme transfers the ubiquitin to an acceptor protein, resulting in the formation of an isopeptide bond between the C-terminal glycine residue of ubiquitin and the ε-amino group of an L-lysine residue of the acceptor protein. cf. EC 2.3.2.27, RING-type E3 ubiquitin transferase and EC 2.3.2.31, RBR-type E3 ubiquitin transferase.

Links to other databases:

References:

1.	Maspero, E., Mari, S., Valentini, E., Musacchio, A., Fish, A., Pasqualato, S. and Polo, S. Structure of the HECT:ubiquitin complex and its role in ubiquitin chain elongation. EMBO Rep. 12 (2011) 342–349. [DOI] [PMID: 21399620]
2.	Metzger, M.B., Hristova, V.A. and Weissman, A.M. HECT and RING finger families of E3 ubiquitin ligases at a glance. J. Cell Sci. 125 (2012) 531–537. [DOI] [PMID: 22389392]

[EC 2.3.2.26 created 2015, modified 2017]

*EC

2.3.2.27

Accepted name:

RING-type E3 ubiquitin transferase

Reaction:

[E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-N⁶-ubiquitinyl-L-lysine

Glossary:

RING = Really Interesting New Gene

Other name(s):

RING E3 ligase (misleading); ubiquitin transferase RING E3; S-ubiquitinyl-[ubiquitin-conjugating E2 enzyme]-L-cysteine:acceptor protein ubiquitin transferase (isopeptide bond-forming, RING-type)

Systematic name:

[E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine:[acceptor protein] ubiquitin transferase (isopeptide bond-forming; RING-type)

Comments:

RING E3 ubiquitin transferases serve as mediators bringing the ubiquitin-charged E2 ubiquitin-conjugating enzyme (EC 2.3.2.23) and an acceptor protein together to enable the direct transfer of ubiquitin through the formation of an isopeptide bond between the C-terminal glycine residue of ubiquitin and the ε-amino group of an L-lysine residue of the acceptor protein. Unlike EC 2.3.2.26, HECT-type E3 ubiquitin transferase, the RING-E3 domain does not form a catalytic thioester intermediate with ubiquitin. Many members of the RING-type E3 ubiquitin transferase family are not able to bind a substrate directly, and form a complex with a cullin scaffold protein and a substrate recognition module (the complexes are named CRL for Cullin-RING-Ligase). In these complexes, the RING-type E3 ubiquitin transferase provides an additional function, mediating the transfer of a NEDD8 protein from a dedicated E2 carrier to the cullin protein (see EC 2.3.2.32, cullin-RING-type E3 NEDD8 transferase). cf. EC 2.3.2.31, RBR-type E3 ubiquitin transferase.

Links to other databases:

References:

1.	Eisele, F. and Wolf, D.H. Degradation of misfolded protein in the cytoplasm is mediated by the ubiquitin ligase Ubr1. FEBS Lett. 582 (2008) 4143–4146. [DOI] [PMID: 19041308]
2.	Metzger, M.B., Hristova, V.A. and Weissman, A.M. HECT and RING finger families of E3 ubiquitin ligases at a glance. J. Cell Sci. 125 (2012) 531–537. [DOI] [PMID: 22389392]
3.	Plechanovova, A., Jaffray, E.G., Tatham, M.H., Naismith, J.H. and Hay, R.T. Structure of a RING E3 ligase and ubiquitin-loaded E2 primed for catalysis. Nature 489 (2012) 115–120. [DOI] [PMID: 22842904]
4.	Pruneda, J.N., Littlefield, P.J., Soss, S.E., Nordquist, K.A., Chazin, W.J., Brzovic, P.S. and Klevit, R.E. Structure of an E3:E2~Ub complex reveals an allosteric mechanism shared among RING/U-box ligases. Mol. Cell 47 (2012) 933–942. [DOI] [PMID: 22885007]
5.	Metzger, M.B., Pruneda, J.N., Klevit, R.E. and Weissman, A.M. RING -type E3 ligases: master manipulators of E2 ubiquitin-conjugating enzymes and ubiquitination. Biochim. Biophys. Acta 1843 (2014) 47–60. [DOI] [PMID: 23747565]

[EC 2.3.2.27 created 2015, modified 2017]

2.3.2.31

Accepted name:

RBR-type E3 ubiquitin transferase

Reaction:

[E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-N⁶-ubiquitinyl-L-lysine (overall reaction)
(1a) [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [RBR-type E3 ubiquitin transferase]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [RBR-type E3 ubiquitin transferase]-S-ubiquitinyl-L-cysteine
(1b) [RBR-type E3 ubiquitin transferase]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-lysine = [RBR-type E3 ubiquitin transferase]-L-cysteine + [acceptor protein]-N⁶-ubiquitinyl-L-lysine

Glossary:

RBR = RING between RING
RING = Really Interesting New Gene

Systematic name:

[E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine:acceptor protein ubiquitin transferase (isopeptide bond-forming; RBR-type)

Comments:

RBR-type E3 ubiquitin transferases have two RING fingers separated by an internal motif (IBR, for In Between RING). The enzyme interacts with the CRL (Cullin-RING ubiquitin Ligase) complexes formed by certain RING-type E3 ubiquitin transferase (see EC 2.3.2.27), which include a neddylated cullin scaffold protein and a substrate recognition module. The RING1 domain binds an EC 2.3.2.23, E2 ubiquitin-conjugating enzyme, and transfers the ubiquitin that is bound to it to an internal cysteine residue in the RING2 domain, followed by the transfer of the ubiquitin from RING2 to the substrate [4]. Once the substrate has been ubiquitylated by the RBR-type ligase, it can be ubiqutylated further using ubiquitin carried directly on E2 enzymes, in a reaction catalysed by EC 2.3.2.27. Activity of the RBR-type enzyme is dependent on neddylation of the cullin protein in the CRL complex [2,4]. cf. EC 2.3.2.26, HECT-type E3 ubiquitin transferase, EC 2.3.2.27, RING-type E3 ubiquitin transferase, and EC 2.3.2.32, cullin-RING-type E3 NEDD8 transferase.

Links to other databases:

References:

1.	Wenzel, D.M., Lissounov, A., Brzovic, P.S. and Klevit, R.E. UBCH7 reactivity profile reveals parkin and HHARI to be RING/HECT hybrids. Nature 474 (2011) 105–108. [DOI] [PMID: 21532592]
2.	Kelsall, I.R., Duda, D.M., Olszewski, J.L., Hofmann, K., Knebel, A., Langevin, F., Wood, N., Wightman, M., Schulman, B.A. and Alpi, A.F. TRIAD1 and HHARI bind to and are activated by distinct neddylated Cullin-RING ligase complexes. EMBO J. 32 (2013) 2848–2860. [DOI] [PMID: 24076655]
3.	Duda, D.M., Olszewski, J.L., Schuermann, J.P., Kurinov, I., Miller, D.J., Nourse, A., Alpi, A.F. and Schulman, B.A. Structure of HHARI, a RING-IBR-RING ubiquitin ligase: autoinhibition of an Ariadne-family E3 and insights into ligation mechanism. Structure 21 (2013) 1030–1041. [DOI] [PMID: 23707686]
4.	Scott, D.C., Rhee, D.Y., Duda, D.M., Kelsall, I.R., Olszewski, J.L., Paulo, J.A., de Jong, A., Ovaa, H., Alpi, A.F., Harper, J.W. and Schulman, B.A. Two distinct types of E3 ligases work in unison to regulate substrate ubiquitylation. Cell 166 (2016) 1198–1214.e24. [DOI] [PMID: 27565346]

[EC 2.3.2.31 created 2017]

2.3.2.32

Accepted name:

cullin-RING-type E3 NEDD8 transferase

Reaction:

[E2 NEDD8-conjugating enzyme]-S-[NEDD8-protein]-yl-L-cysteine + [cullin]-L-lysine = [E2 NEDD8-conjugating enzyme]-L-cysteine + [cullin]-N⁶-[NEDD8-protein]-yl-L-lysine

Glossary:

NEDD = Neural-precursor-cell Expressed Developmentally Down-regulated protein

Other name(s):

RBX1 (gene name)

Systematic name:

[E2 NEDD8-conjugating enzyme]-S-[NEDD8-protein]-yl-L-cysteine:[cullin] [NEDD8-protein] transferase (isopeptide bond-forming; RING-type)

Comments:

Some RING-type E3 ubiquitin transferase (EC 2.3.2.27) are not able to bind a substrate protein directly. Instead, they form a complex with a cullin scaffold protein and a substrate recognition module, which is named CRL for Cullin-RING-Ligase. The cullin protein needs to be activated by the ubiquitin-like protein NEDD8 in a process known as neddylation. The transfer of NEDD8 from a NEDD8-specific E2 enzyme onto the cullin protein is a secondary function of the RING-type E3 ubiquitin transferase in the CRL complex. The process requires auxiliary factors that belong to the DCN1 (defective in cullin neddylation 1) family.

Links to other databases:

References:

1.	Kim, A.Y., Bommelje, C.C., Lee, B.E., Yonekawa, Y., Choi, L., Morris, L.G., Huang, G., Kaufman, A., Ryan, R.J., Hao, B., Ramanathan, Y. and Singh, B. SCCRO (DCUN1D1) is an essential component of the E3 complex for neddylation. J. Biol. Chem. 283 (2008) 33211–33220. [DOI] [PMID: 18826954]
2.	Kurz, T., Chou, Y.C., Willems, A.R., Meyer-Schaller, N., Hecht, M.L., Tyers, M., Peter, M. and Sicheri, F. Dcn1 functions as a scaffold-type E3 ligase for cullin neddylation. Mol. Cell 29 (2008) 23–35. [DOI] [PMID: 18206966]
3.	Scott, D.C., Monda, J.K., Grace, C.R., Duda, D.M., Kriwacki, R.W., Kurz, T. and Schulman, B.A. A dual E3 mechanism for Rub1 ligation to Cdc53. Mol. Cell 39 (2010) 784–796. [DOI] [PMID: 20832729]
4.	Scott, D.C., Sviderskiy, V.O., Monda, J.K., Lydeard, J.R., Cho, S.E., Harper, J.W. and Schulman, B.A. Structure of a RING E3 trapped in action reveals ligation mechanism for the ubiquitin-like protein NEDD8. Cell 157 (2014) 1671–1684. [DOI] [PMID: 24949976]
5.	Monda, J.K., Scott, D.C., Miller, D.J., Lydeard, J., King, D., Harper, J.W., Bennett, E.J. and Schulman, B.A. Structural conservation of distinctive N-terminal acetylation-dependent interactions across a family of mammalian NEDD8 ligation enzymes. Structure 21 (2013) 42–53. [DOI] [PMID: 23201271]

[EC 2.3.2.32 created 2017]

2.3.3.20

Accepted name:

acyl-CoA:acyl-CoA alkyltransferase

Reaction:

2 an acyl-CoA + H₂O = a (2R)-2-alkyl-3-oxoalkanoate + 2 CoA

Other name(s):

oleA (gene name)

Systematic name:

acyl-CoA:acyl-CoA alkyltransferase [(2R)-2-alkyl-3-oxoalkanoate-forming]

Comments:

The enzyme, found in certain bacterial species, catalyses a head-to-head non-decarboxylative Claisen condensation of two acyl-CoA molecules, resulting in formation of a 2-alkyl-3-oxoalkanoic acid. It is part of a pathway for the production of olefins.

Links to other databases:

References:

1.	Sukovich, D.J., Seffernick, J.L., Richman, J.E., Hunt, K.A., Gralnick, J.A. and Wackett, L.P. Structure, function, and insights into the biosynthesis of a head-to-head hydrocarbon in Shewanella oneidensis strain MR-1. Appl. Environ. Microbiol. 76 (2010) 3842–3849. [DOI] [PMID: 20418444]
2.	Frias, J.A., Richman, J.E., Erickson, J.S. and Wackett, L.P. Purification and characterization of OleA from Xanthomonas campestris and demonstration of a non-decarboxylative Claisen condensation reaction. J. Biol. Chem. 286 (2011) 10930–10938. [DOI] [PMID: 21266575]
3.	Goblirsch, B.R., Frias, J.A., Wackett, L.P. and Wilmot, C.M. Crystal structures of Xanthomonas campestris OleA reveal features that promote head-to-head condensation of two long-chain fatty acids. Biochemistry 51 (2012) 4138–4146. [DOI] [PMID: 22524624]
4.	Goblirsch, B.R., Jensen, M.R., Mohamed, F.A., Wackett, L.P. and Wilmot, C.M. Substrate trapping in crystals of the thiolase OleA identifies three channels that enable long chain olefin biosynthesis. J. Biol. Chem. 291 (2016) 26698–26706. [DOI] [PMID: 27815501]

[EC 2.3.3.20 created 2018]

2.4.1.348

Accepted name:

N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol 3-α-mannosyltransferase

Reaction:

GDP-α-D-mannose + N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = GDP + α-D-mannosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol

Other name(s):

WbdC

Systematic name:

GDP-α-D-mannose:N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol 3-α-mannosyltransferase (configuration-retaining)

Comments:

The enzyme is involved in the biosynthesis of the linker region of the polymannose O-polysaccharide in the outer leaflet of the membrane of Escherichia coli serotypes O8, O9 and O9a.

Links to other databases:

References:

Greenfield, L.K., Richards, M.R., Li, J., Wakarchuk, W.W., Lowary, T.L. and Whitfield, C. Biosynthesis of the polymannose lipopolysaccharide O-antigens from Escherichia coli serotypes O8 and O9a requires a unique combination of single- and multiple-active site mannosyltransferases. J. Biol. Chem. 287 (2012) 35078–35091. [DOI] [PMID: 22875852]

[EC 2.4.1.348 created 2017]

2.4.1.349

Accepted name:

mannosyl-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol 3-α-mannosyltransferase

Reaction:

2 GDP-α-D-mannose + α-D-mannosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = 2 GDP + α-D-mannosyl-(1→3)-α-D-mannosyl-(1→3)-α-D-mannosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol

Other name(s):

WbdB

Systematic name:

GDP-α-D-mannose:α-D-mannosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol 3-α-mannosyltransferase (configuration-retaining)

Comments:

The enzyme is involved in the biosynthesis of the linker region of the polymannose O-polysaccharide in the outer leaflet of the membrane of Escherichia coli serotypes O8, O9 and O9a. It has no activity with N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol (cf. EC 2.4.1.348, N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol 3-α-mannosyltransferase).

Links to other databases:

References:

[EC 2.4.1.349 created 2017]

2.4.1.350

Accepted name:

mogroside IE synthase

Reaction:

UDP-α-D-glucose + mogrol = mogroside IE + UDP

Glossary:

mogrol = (23R)-cucurbit-5-ene-3β,11α,23,25-tetraol

Other name(s):

UGT74AC1; mogrol C-3 hydroxyl glycosyltransferase

Systematic name:

UDP-α-D-glucose:mogrol 3-O-glucosyltransferase

Comments:

Isolated from the plant Siraitia grosvenorii (monk fruit).

Links to other databases:

References:

1.	Dai, L., Liu, C., Zhu, Y., Zhang, J., Men, Y., Zeng, Y. and Sun, Y. Functional characterization of cucurbitadienol synthase and triterpene glycosyltransferase involved in biosynthesis of mogrosides from Siraitia grosvenorii. Plant Cell Physiol. 56 (2015) 1172–1182. [DOI] [PMID: 25759326]

[EC 2.4.1.350 created 2017]

2.4.1.351

Accepted name:

rhamnogalacturonan I rhamnosyltransferase

Reaction:

UDP-β-L-rhamnose + α-D-galacturonosyl-[(1→2)-α-L-rhamnosyl-(1→4)-α-D-galacturonosyl]_n = UDP + [(1→2)-α-L-rhamnosyl-(1→4)-α-D-galacturonosyl]_n+1

Other name(s):

RRT; RG I rhamnosyltransferase

Systematic name:

UDP-β-L-rhamnose:rhamnogalacturonan I 4-rhamnosyltransferase (configuration-inverting)

Comments:

The enzyme, characterized from Vigna angularis (azuki beans), participates in the biosynthesis of rhamnogalacturonan type I. It does not require any metal ions, and prefers substrates with a degree of polymerization larger than 7.

Links to other databases:

References:

Uehara, Y., Tamura, S., Maki, Y., Yagyu, K., Mizoguchi, T., Tamiaki, H., Imai, T., Ishii, T., Ohashi, T., Fujiyama, K. and Ishimizu, T. Biochemical characterization of rhamnosyltransferase involved in biosynthesis of pectic rhamnogalacturonan I in plant cell wall. Biochem. Biophys. Res. Commun. 486 (2017) 130–136. [DOI] [PMID: 28283389]

[EC 2.4.1.351 created 2018]

2.4.1.352

Accepted name:

glucosylglycerate phosphorylase

Reaction:

2-O-(α-D-glucopyranosyl)-D-glycerate + phosphate = α-D-glucopyranose 1-phosphate + D-glycerate

Systematic name:

2-O-(α-D-glucopyranosyl)-D-glycerate:phosphate α-D-glucosyltransferase (configuration-retaining)

Comments:

The enzyme has been characterized from the bacterium Meiothermus silvanus.

Links to other databases:

References:

1.	Franceus, J., Pinel, D. and Desmet, T. Glucosylglycerate phosphorylase, an enzyme with novel specificity involved in compatible solute metabolism. Appl. Environ. Microbiol. 83 (2017) . [DOI] [PMID: 28754708]

[EC 2.4.1.352 created 2018]

*EC

2.5.1.98

Accepted name:

Rhizobium leguminosarum exopolysaccharide glucosyl ketal-pyruvate-transferase

Reaction:

phosphoenolpyruvate + [β-D-GlcA-(1→4)-2-O-Ac-β-D-GlcA-(1→4)-β-D-Glc-(1→4)-[3-O-(CH₃CH(OH)CH₂C(O))-4,6-CH₃(COO^-)C-β-D-Gal-(1→4)-β-D-Glc-(1→4)-β-D-Glc-(1→4)-β-D-Glc-(1→6)]-2(or 3)-O-Ac-α-D-Glc-(1→6)]_n = [β-D-GlcA-(1→4)-2-O-Ac-β-D-GlcA-(1→4)-β-D-Glc-(1→4)-[3-O-(CH₃CH(OH)CH₂C(O))-4,6-CH₃(COO^-)C-β-D-Gal-(1→3)-4,6-CH₃(COO^-)C-β-D-Glc-(1→4)-β-D-Glc-(1→4)-β-D-Glc-(1→6)]-2(or 3)-O-Ac-α-D-Glc-(1→6)]_n + phosphate

Other name(s):

PssM; 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(or 3)-O-Ac-D-Glc-α-(1→6)]_n 4,6-O-(1-carboxyethan-1,1-diyl)transferase

Systematic name:

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

Comments:

The enzyme is responsible for pyruvylation of the 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.

Links to other databases:

References:

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. [DOI] [PMID: 20233262]

[EC 2.5.1.98 created 2012, modified 2018]

2.5.1.99

Deleted entry:

all-trans-phytoene synthase. The activity was an artifact caused by photoisomerization of the product of EC 2.5.1.32, 15-cis-phytoene synthase.

[EC 2.5.1.99 created 2012, deleted 2018]

2.5.1.142

Accepted name:

nerylneryl diphosphate synthase

Reaction:

prenyl diphosphate + 3 (3-methylbut-3-en-1-yl diphosphate) = 3 diphosphate + nerylneryl diphosphate
(1a) prenyl diphosphate + 3-methylbut-3-en-1-yl diphosphate = diphosphate + neryl diphosphate
(1b) neryl diphosphate + 3-methylbut-3-en-1-yl diphosphate = diphosphate + (2Z,6Z)-farnesyl diphosphate
(1c) (2Z,6Z)-farnesyl diphosphate + 3-methylbut-3-en-1-yl diphosphate = diphosphate + nerylneryl diphosphate

For diagram of all-cis-polyprenyl diphosphate, click here

Glossary:

nerylneryl diphosphate = all-cis-tetraprenyl diphosphate

Other name(s):

CPT2; dimethylallyl-diphosphate:isopentenyl-diphosphate cistransferase (adding 3 isopentenyl units)

Systematic name:

prenyl-diphosphate:3-methylbut-3-en-1-yl-diphosphate cistransferase (adding 3 units of 3-methylbut-3-en-1-yl)

Comments:

Isolated from the plant Solanum lycopersicum (tomato).

Links to other databases:

References:

1.	Akhtar, T.A., Matsuba, Y., Schauvinhold, I., Yu, G., Lees, H.A., Klein, S.E. and Pichersky, E. The tomato cis-prenyltransferase gene family. Plant J. 73 (2013) 640–652. [DOI] [PMID: 23134568]
2.	Matsuba, Y., Zi, J., Jones, A.D., Peters, R.J. and Pichersky, E. Biosynthesis of the diterpenoid lycosantalonol via nerylneryl diphosphate in Solanum lycopersicum. PLoS One 10:e0119302 (2015). [DOI] [PMID: 25786135]

[EC 2.5.1.142 created 2017]

2.6.1.114

Accepted name:

8-demethyl-8-aminoriboflavin-5′-phosphate synthase

Reaction:

L-glutamate + FMN + O₂ + H₂O + 3 acceptor = 2-oxoglutarate + 8-amino-8-demethylriboflavin 5′-phosphate + CO₂ + 3 reduced acceptor (overall reaction)
(1a) FMN + O₂ = 8-demethyl-8-formylriboflavin 5′-phosphate + H₂O
(1b) 8-demethyl-8-formylriboflavin 5′-phosphate + H₂O + acceptor = 8-carboxy-8-demethylriboflavin 5′-phosphate + reduced acceptor
(1c) L-glutamate + 8-carboxy-8-demethylriboflavin 5′-phosphate + H₂O + 2 acceptor = 2-oxoglutarate + 8-amino-8-demethylriboflavin 5′-phosphate + CO₂ + 2 reduced acceptor

For diagram of roseoflavin biosynthesis, click here

Glossary:

roseoflavin = 8-demethyl-8-(dimethylamino)riboflavin

Other name(s):

rosB (gene name)

Systematic name:

L-glutamate:FMN aminotransferase (oxidizing, decarboxylating)

Comments:

The enzyme, characterized from the bacterium Streptomyces davawensis, has the activities of an oxidoreductase, a decarboxylase, and an aminotransferase. Its combined actions result in the replacement of a methyl substituent of one of the aromatic rings of FMN by an amino group, a step in the biosynthetic pathway of roseoflavin. The reaction requires thiamine for completion.

Links to other databases:

References:

1.	Schwarz, J., Konjik, V., Jankowitsch, F., Sandhoff, R. and Mack, M. Identification of the key enzyme of roseoflavin biosynthesis. Angew. Chem. Int. Ed. Engl. 55 (2016) 6103–6106. [DOI] [PMID: 27062037]
2.	Jhulki, I., Chanani, P.K., Abdelwahed, S.H. and Begley, T.P. A remarkable oxidative cascade that replaces the riboflavin C₈ methyl with an amino group during roseoflavin biosynthesis. J. Am. Chem. Soc. 138 (2016) 8324–8327. [DOI] [PMID: 27331868]
3.	Konjik, V., Brunle, S., Demmer, U., Vanselow, A., Sandhoff, R., Ermler, U. and Mack, M. The crystal structure of RosB: insights into the reaction mechanism of the first member of a family of flavodoxin-like enzymes. Angew. Chem. Int. Ed. Engl. 56 (2017) 1146–1151. [DOI] [PMID: 27981706]

[EC 2.6.1.114 created 2018]

*EC

2.7.1.181

Accepted name:

polymannosyl GlcNAc-diphospho-ditrans,octacis-undecaprenol kinase

Reaction:

ATP + α-D-Man-(1→2)-α-D-Man-(1→2)-[α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→2)-α-D-Man-(1→2)]_n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol = ADP + 3-O-phospho-α-D-Man-(1→2)-α-D-Man-(1→2)-[α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→2)-α-D-Man-(1→2)]_n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol

Other name(s):

WbdD; ATP:α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)]_n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol 3-phosphotransferase

Systematic name:

ATP:α-D-Man-(1→2)-α-D-Man-(1→2)-[α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→2)-α-D-Man-(1→2)]_n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol 3-phosphotransferase

Comments:

The enzyme is involved in the biosynthesis of the polymannose O-polysaccharide in the outer leaflet of the membrane of Escherichia coli serotype O9a. O-Polysaccharide structures vary extensively because of differences in the number and type of sugars in the repeat unit. The dual kinase/methylase WbdD also catalyses the methylation of 3-phospho-α-D-Man-(1→2)-α-D-Man-(1→2)-[α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→2)-α-D-Man-(1→2)]_n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol (cf. EC 2.1.1.294, 3-O-phospho-polymannosyl GlcNAc-diphospho-ditrans,octacis-undecaprenol 3-phospho-methyltransferase).

Links to other databases:

References:

1.	Clarke, B.R., Cuthbertson, L. and Whitfield, C. Nonreducing terminal modifications determine the chain length of polymannose O antigens of Escherichia coli and couple chain termination to polymer export via an ATP-binding cassette transporter. J. Biol. Chem. 279 (2004) 35709–35718. [DOI] [PMID: 15184370]
2.	Clarke, B.R., Greenfield, L.K., Bouwman, C. and Whitfield, C. Coordination of polymerization, chain termination, and export in assembly of the Escherichia coli lipopolysaccharide O9a antigen in an ATP-binding cassette transporter-dependent pathway. J. Biol. Chem. 284 (2009) 30662–30672. [DOI] [PMID: 19734145]
3.	Clarke, B.R., Richards, M.R., Greenfield, L.K., Hou, D., Lowary, T.L. and Whitfield, C. In vitro reconstruction of the chain termination reaction in biosynthesis of the Escherichia coli O9a O-polysaccharide: the chain-length regulator, WbdD, catalyzes the addition of methyl phosphate to the non-reducing terminus of the growing glycan. J. Biol. Chem. 286 (2011) 41391–41401. [DOI] [PMID: 21990359]
4.	Liston, S.D., Clarke, B.R., Greenfield, L.K., Richards, M.R., Lowary, T.L. and Whitfield, C. Domain interactions control complex formation and polymerase specificity in the biosynthesis of the Escherichia coli O9a antigen. J. Biol. Chem. 290 (2015) 1075–1085. [DOI] [PMID: 25422321]

[EC 2.7.1.181 created 2014, modified 2017]

2.7.1.222

Accepted name:

4-hydroxytryptamine kinase

Reaction:

ATP + 4-hydroxytryptamine = ADP + 4-hydroxytryptamine 4-phosphate

For diagram of psilocybin biosynthesis, click here

Glossary:

psilocybin = 3-[2-(dimethylamino)ethyl]-1H-indol-4-yl phosphate

Other name(s):

PsiK

Systematic name:

ATP:4-hydroxytryptamine 4-phosphotransferase

Comments:

Also acts on 4-hydroxy-L-tryptophan in vitro. Isolated from the fungus Psilocybe cubensis. Involved in the biosynthesis of the psychoactive compound psilocybin.

Links to other databases:

References:

1.	Fricke, J., Blei, F. and Hoffmeister, D. Enzymatic synthesis of psilocybin. Angew. Chem. Int. Ed. Engl. 56 (2017) 12352–12355. [DOI] [PMID: 28763571]

[EC 2.7.1.222 created 2017]

2.7.3.13

Accepted name:

glutamine kinase

Reaction:

ATP + L-glutamine + H₂O = AMP + phosphate + N⁵-phospho-L-glutamine

Systematic name:

ATP:L-glutamine N⁵-phosphotransferase

Comments:

The enzyme, characterized from the bacterium Campylobacter jejuni, is involved in formation of a unique O-methyl phosphoramidate modification on specific sugar residues within the bacterium’s capsular polysaccharides.

Links to other databases:

References:

Taylor, Z.W., Brown, H.A., Narindoshvili, T., Wenzel, C.Q., Szymanski, C.M., Holden, H.M. and Raushel, F.M. Discovery of a glutamine kinase required for the biosynthesis of the O-methyl phosphoramidate modifications found in the capsular polysaccharides of Campylobacter jejuni. J. Am. Chem. Soc. 139 (2017) 9463–9466. [DOI] [PMID: 28650156]

[EC 2.7.3.13 created 2017]

2.7.7.94

Transferred entry:

4-hydroxyphenylalkanoate adenylyltransferase. Now EC 6.2.1.51, 4-hydroxyphenylalkanoate adenylyltransferase FadD29

[EC 2.7.7.94 created 2016, deleted 2017]

2.7.9.6

Accepted name:

rifampicin phosphotransferase

Reaction:

ATP + rifampicin + H₂O = AMP + 21-phosphorifampicin + phosphate

For diagram of rifampicin, click here

Glossary:

rifampicin = rifampin = 3-[(4-methylpiperazin-1-yl)iminomethyl]rifamycin

Other name(s):

rifampin phosphotransferase; RPH

Systematic name:

ATP:rifampicin, water 21-O-phosphotransferase

Comments:

The enzyme, characterized from a diverse collection of Gram-positive bacteria, inactivates the antibiotic rifampicin by phosphorylating it at position 21. The enzyme comprises three domains: two substrate-binding domains (ATP-grasp and rifampicin-binding domains) and a smaller phosphate-carrying L-histidine swivel domain that transits between the spatially distinct substrate-binding sites during catalysis.

Links to other databases:

References:

1.	Spanogiannopoulos, P., Waglechner, N., Koteva, K. and Wright, G.D. A rifamycin inactivating phosphotransferase family shared by environmental and pathogenic bacteria. Proc. Natl. Acad. Sci. USA 111 (2014) 7102–7107. [DOI] [PMID: 24778229]
2.	Stogios, P.J., Cox, G., Spanogiannopoulos, P., Pillon, M.C., Waglechner, N., Skarina, T., Koteva, K., Guarne, A., Savchenko, A. and Wright, G.D. Rifampin phosphotransferase is an unusual antibiotic resistance kinase. Nat. Commun. 7:11343 (2016). [DOI] [PMID: 27103605]

[EC 2.7.9.6 created 2018]

*EC

2.8.1.2

Accepted name:

3-mercaptopyruvate sulfurtransferase

Reaction:

2-oxo-3-sulfanylpropanoate + reduced thioredoxin = pyruvate + hydrogen sulfide + oxidized thioredoxin (overall reaction)
(1a) 2-oxo-3-sulfanylpropanoate + [3-mercaptopyruvate sulfurtransferase]-L-cysteine = pyruvate + [3-mercaptopyruvate sulfurtransferase]-S-sulfanyl-L-cysteine
(1b) [3-mercaptopyruvate sulfurtransferase]-S-sulfanyl-L-cysteine + reduced thioredoxin = hydrogen sulfide + [3-mercaptopyruvate sulfurtransferase]-L-cysteine + oxidized thioredoxin

Glossary:

2-oxo-3-sulfanylpropanoate = 3-mercaptopyruvate (deprecated)

Other name(s):

β-mercaptopyruvate sulfurtransferase; TUM1 (gene name); MPST (gene name); 3-mercaptopyruvate:cyanide sulfurtransferase

Systematic name:

2-oxo-3-sulfanylpropanoate:sulfide sulfurtransferase

Comments:

The enzyme catalyses a transsulfuration reaction from 2-oxo-3-sulfanylpropanoate to an internal cysteine residue. In the presence of a dithiol such as reduced thioredoxin or dihydrolipoate, the sulfanyl sulfur is released as hydrogen sulfide. The enzyme participates in a sulfur relay process that leads to the 2-thiolation of some tRNAs and to protein urmylation by transferring sulfur between the NFS1 cysteine desulfurase (EC 2.8.1.7) and the MOCS3 sulfurtransferase (EC 2.8.1.11).

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9026-05-5

References:

1.	Fiedler, H. and Wood, J.L. Specificity studies on the β-mercaptopyruvate-cyanide transsulfuration system. J. Biol. Chem. 222 (1956) 387–397. [PMID: 13367011]
2.	Sörbo, B.H. Enzymic transfer of sulfur from mercaptopyruvate to sulfite or sulfinates. Biochem. Biophys. Acta 24 (1957) 324–329. [PMID: 13436433]
3.	Hylin, J.W. and Wood, J.L. Enzymatic formation of polysulfides from mercaptopyruvate. J. Biol. Chem. 234 (1959) 2141–2144. [PMID: 13673028]
4.	van den Hamer, C.J.A., Morell, A.G. and Scheinberg, H.I. A study of the copper content of β-mercaptopyruvate trans-sulfurase. J. Biol. Chem. 242 (1967) 2514–2516. [PMID: 6026243]
5.	Vachek, H. and Wood, J.L. Purification and properties of mercaptopyruvate sulfur transferase of Escherichia coli. Biochim. Biophys. Acta 258 (1972) 133–146. [DOI] [PMID: 4550801]
6.	Nagahara, N. and Katayama, A. Post-translational regulation of mercaptopyruvate sulfurtransferase via a low redox potential cysteine-sulfenate in the maintenance of redox homeostasis. J. Biol. Chem. 280 (2005) 34569–34576. [DOI] [PMID: 16107337]
7.	Shibuya, N., Tanaka, M., Yoshida, M., Ogasawara, Y., Togawa, T., Ishii, K. and Kimura, H. 3-Mercaptopyruvate sulfurtransferase produces hydrogen sulfide and bound sulfane sulfur in the brain. Antioxid Redox Signal 11 (2009) 703–714. [DOI] [PMID: 18855522]
8.	Mikami, Y., Shibuya, N., Kimura, Y., Nagahara, N., Ogasawara, Y. and Kimura, H. Thioredoxin and dihydrolipoic acid are required for 3-mercaptopyruvate sulfurtransferase to produce hydrogen sulfide. Biochem. J. 439 (2011) 479–485. [DOI] [PMID: 21732914]

[EC 2.8.1.2 created 1961, modified 2018]

3.1.1.103

Accepted name:

teichoic acid D-alanine hydrolase

Reaction:

[(4-D-Ala)-(2-GlcNAc)-Rib-ol-P]_n-[Gro-P]_m-β-D-ManNAc-(1→4)-α-D-GlcNAc-P-peptidoglycan + n H₂O = [(2-GlcNAc)-Rib-ol-P]_n-[Gro-P]_m-β-D-ManNAc-(1→4)-α-D-GlcNAc-P-peptidoglycan + n D-alanine

Glossary:

Rib-ol = ribitol

Other name(s):

fmtA (gene name)

Systematic name:

teichoic acid D-alanylhydrolase

Comments:

The enzyme, characterized from the bacterium Staphylococcus aureus, removes D-alanine groups from the teichoic acid produced by this organism, thus modulating the electrical charge of the bacterial surface. The activity greatly increases methicillin resistance in MRSA strains.

Links to other databases:

References:

1.	Komatsuzawa, H., Sugai, M., Ohta, K., Fujiwara, T., Nakashima, S., Suzuki, J., Lee, C.Y. and Suginaka, H. Cloning and characterization of the fmt gene which affects the methicillin resistance level and autolysis in the presence of triton X-100 in methicillin-resistant Staphylococcus aureus. Antimicrob. Agents Chemother. 41 (1997) 2355–2361. [PMID: 9371333]
2.	Qamar, A. and Golemi-Kotra, D. Dual roles of FmtA in Staphylococcus aureus cell wall biosynthesis and autolysis. Antimicrob. Agents Chemother. 56 (2012) 3797–3805. [DOI] [PMID: 22564846]
3.	Rahman, M.M., Hunter, H.N., Prova, S., Verma, V., Qamar, A. and Golemi-Kotra, D. The Staphylococcus aureus methicillin resistance factor FmtA is a D-amino esterase that acts on teichoic acids. MBio 7 (2016) e02070. [DOI] [PMID: 26861022]

[EC 3.1.1.103 created 2018]

3.2.1.206

Accepted name:

oleuropein β-glucosidase

Reaction:

oleuropein + H₂O = oleuropein aglycone + D-glucopyranose

Glossary:

oleuropein aglycone = methyl (2S,3E,4S)-4-{2-[2-(3,4-dihydroxyphenyl)ethoxy]-2-oxoethyl}-3-ethylidene-2-hydroxy-3,4-dihydro-2H-pyran-5-carboxylate
oleuropein = methyl (2R,3E,4S)-4-{2-[2-(3,4-dihydroxyphenyl)ethoxy]-2-oxoethyl}-3-ethylidene-2-(β-D-glucopyranosyloxy)-3,4-dihydro-2H-pyran-5-carboxylate
ligstroside = methyl (2S,3E,4S)-3-ethylidene-2-(β-D-glucopyranosyloxy)-4-{2-[2-(4-hydroxyphenyl)ethoxy]-2-oxoethyl}-3,4-dihydro-2H-pyran-5-carboxylate

Other name(s):

OeGLU (gene name)

Systematic name:

oleuropein 2-β-D-glucohydrolase

Comments:

Oleuropein is a glycosylated secoiridoid exclusively biosynthesized by members of the Oleaceae plant family where it is part of a defence system againt herbivores. The enzyme also hydrolyses ligstroside and demethyloleuropein.

Links to other databases:

References:

1.	Ciafardini, G., Marsilio, V., Lanza, B. and Pozzi, N. Hydrolysis of oleuropein by Lactobacillus plantarum strains associated with olive fermentation. Appl. Environ. Microbiol. 60 (1994) 4142–4147. [PMID: 16349442]
2.	Romero-Segura, C., Sanz, C. and Perez, A.G. Purification and characterization of an olive fruit β-glucosidase involved in the biosynthesis of virgin olive oil phenolics. J. Agric. Food Chem. 57 (2009) 7983–7988. [DOI] [PMID: 19689134]
3.	Gutierrez-Rosales, F., Romero, M.P., Casanovas, M., Motilva, M.J. and Minguez-Mosquera, M.I. β-Glucosidase involvement in the formation and transformation of oleuropein during the growth and development of olive fruits (Olea europaea L. cv. Arbequina) grown under different farming practices. J. Agric. Food Chem. 60 (2012) 4348–4358. [DOI] [PMID: 22475562]
4.	Koudounas, K., Banilas, G., Michaelidis, C., Demoliou, C., Rigas, S. and Hatzopoulos, P. A defence-related Olea europaea β-glucosidase hydrolyses and activates oleuropein into a potent protein cross-linking agent. J. Exp. Bot. 66 (2015) 2093–2106. [DOI] [PMID: 25697790]
5.	Koudounas, K., Thomopoulou, M., Michaelidis, C., Zevgiti, E., Papakostas, G., Tserou, P., Daras, G. and Hatzopoulos, P. The C-domain of oleuropein β-glucosidase assists in protein folding and sequesters the enzyme in nucleus. Plant Physiol. 174 (2017) 1371–1383. [DOI] [PMID: 28483880]

[EC 3.2.1.206 created 2017]

3.2.2.31

Accepted name:

adenine glycosylase

Reaction:

Hydrolyses free adenine bases from 7,8-dihydro-8-oxoguanine:adenine mismatched double-stranded DNA, leaving an apurinic site.

Other name(s):

mutY (gene name); A/G-specific adenine glycosylase

Systematic name:

adenine-DNA deoxyribohydrolase (adenine-releasing)

Comments:

The enzyme serves as a mismatch repair enzyme that works to correct 7,8-dihydro-8-oxoguanine:adenine mispairs that arise in DNA when error-prone synthesis occurs past 7,8-dihydro-8-oxoguanine (GO) lesions in DNA. The enzyme excises the adenine of the mispair, producing an apurinic site sensitive to AP endonuclease activity. After removing the undamaged adenine the enzyme remains bound to the site to prevent EC 3.2.2.23 (MutM) from removing the GO lesion, which could lead to a double strand break. In vitro the enzyme is also active with adenine:guanine, adenine:cytosine, and adenine:7,8-dihydro-8-oxoadenine (AO) mispairs, removing the adenine in all cases.

Links to other databases:

References:

1.	Au, K.G., Clark, S., Miller, J.H. and Modrich, P. Escherichia coli mutY gene encodes an adenine glycosylase active on G-A mispairs. Proc. Natl. Acad. Sci. USA 86 (1989) 8877–8881. [DOI] [PMID: 2682664]
2.	Michaels, M.L., Tchou, J., Grollman, A.P. and Miller, J.H. A repair system for 8-oxo-7,8-dihydrodeoxyguanine. Biochemistry 31 (1992) 10964–10968. [PMID: 1445834]

[EC 3.2.2.31 created 2018]

*EC

3.3.2.9

Accepted name:

microsomal epoxide hydrolase

Reaction:

(1) cis-stilbene oxide + H₂O = (1R,2R)-1,2-diphenylethane-1,2-diol
(2) 1-(4-methoxyphenyl)-N-methyl-N-[(3-methyloxetan-3-yl)methyl]methanamine + H₂O = 2-({[(4-methoxyphenyl)methyl](methyl)amino}methyl)-2-methylpropane-1,3-diol

Glossary:

oxirane = ethylene oxide = a 3-membered oxygen-containing ring
oxetane = 1,3-propylene oxide = a 4-membered oxygen-containing ring

Other name(s):

microsomal oxirane/oxetane hydrolase; epoxide hydratase (ambiguous); microsomal epoxide hydratase (ambiguous); epoxide hydrase; microsomal epoxide hydrase; arene-oxide hydratase (ambiguous); benzo[a]pyrene-4,5-oxide hydratase; benzo(a)pyrene-4,5-epoxide hydratase; aryl epoxide hydrase (ambiguous); cis-epoxide hydrolase; mEH; EPHX1 (gene name)

Systematic name:

cis-stilbene-oxide hydrolase

Comments:

This is a key hepatic enzyme that catalyses the hydrolytic ring opening of oxiranes (epoxides) and oxetanes to give the corresponding diols. The enzyme is involved in the metabolism of numerous substrates including the stereoselective hydrolytic ring opening of 7-oxabicyclo[4.1.0]hepta-2,4-dienes (arene oxides) to the corresponding trans-dihydrodiols. The reaction proceeds via a triad mechanism and involves the formation of an hydroxyalkyl-enzyme intermediate. Five epoxide-hydrolase enzymes have been identified in vertebrates to date: EC 3.3.2.6 (leukotriene-A₄ hydrolase), EC 3.3.2.7 (hepoxilin-epoxide hydrolase), EC 3.3.2.9 (microsomal epoxide hydrolase), EC 3.3.2.10 (soluble epoxide hydrolase) and EC 3.3.2.11 (cholesterol-5,6-oxide hydrolase).

Links to other databases:

References:

1.	Oesch, F. and Daly, J. Solubilization, purification, and properties of a hepatic epoxide hydrase. Biochim. Biophys. Acta 227 (1971) 692–697. [DOI] [PMID: 4998715]
2.	Jakoby, W.B. and Fjellstedt, T.A. Epoxidases. In: Boyer, P.D. (Ed.), The Enzymes, 3rd edn, vol. 7, Academic Press, New York, 1972, pp. 199–212.
3.	Oesch, F. Mammalian epoxide hydrases: inducible enzymes catalysing the inactivation of carcinogenic and cytotoxic metabolites derived from aromatic and olefinic compounds. Xenobiotica 3 (1973) 305–340. [DOI] [PMID: 4584115]
4.	Oesch, F. Purification and specificity of a human microsomal epoxide hydratase. Biochem. J. 139 (1974) 77–88. [PMID: 4463951]
5.	Lu, A.Y., Ryan, D., Jerina, D.M., Daly, J.W. and Levin, W. Liver microsomal expoxide hydrase. Solubilization, purification, and characterization. J. Biol. Chem. 250 (1975) 8283–8288. [PMID: 240858]
6.	Bellucci, G., Chiappe, C. and Ingrosso, G. Kinetics and stereochemistry of the microsomal epoxide hydrolase-catalyzed hydrolysis of cis-stilbene oxides. Chirality 6 (1994) 577–582. [DOI] [PMID: 7986671]
7.	Fretland, A.J. and Omiecinski, C.J. Epoxide hydrolases: biochemistry and molecular biology. Chem. Biol. Interact. 129 (2000) 41–59. [DOI] [PMID: 11154734]
8.	Morisseau, C. and Hammock, B.D. Epoxide hydrolases: mechanisms, inhibitor designs, and biological roles. Annu. Rev. Pharmacol. Toxicol. 45 (2005) 311–333. [DOI] [PMID: 15822179]
9.	Newman, J.W., Morisseau, C. and Hammock, B.D. Epoxide hydrolases: their roles and interactions with lipid metabolism. Prog. Lipid Res. 44 (2005) 1–51. [DOI] [PMID: 15748653]
10.	Toselli, F., Fredenwall, M., Svensson, P., Li, X.Q., Johansson, A., Weidolf, L. and Hayes, M.A. Oxetane substrates of human microsomal epoxide hydrolase. Drug Metab. Dispos. 45 (2017) 966–973. [DOI] [PMID: 28600384]

[EC 3.3.2.9 created 2006 (EC 3.3.2.3 created 1978, modified 1999, part incorporated 2006), modified 2017]

3.13.1.7

Accepted name:

carbonyl sulfide hydrolase

Reaction:

carbonyl sulfide + H₂O = hydrogen sulfide + CO₂

Other name(s):

COSase; COS hydrolase; cos (gene name)

Systematic name:

carbonyl sulfide hydrogen-sulfide-lyase (decarboxylating)

Comments:

The enzyme, characterized from the bacterium Thiobacillus thioparus, catalyses a step in the degradation pathway of thiocyanate. This activity is also catalysed by the archaeal EC 3.13.1.5, carbon disulfide lyase.

Links to other databases:

References:

Ogawa, T., Noguchi, K., Saito, M., Nagahata, Y., Kato, H., Ohtaki, A., Nakayama, H., Dohmae, N., Matsushita, Y., Odaka, M., Yohda, M., Nyunoya, H. and Katayama, Y. Carbonyl sulfide hydrolase from Thiobacillus thioparus strain THI115 is one of the β-carbonic anhydrase family enzymes. J. Am. Chem. Soc. 135 (2013) 3818–3825. [DOI] [PMID: 23406161]

[EC 3.13.1.7 created 2018]

4.1.1.105

Accepted name:

L-tryptophan decarboxylase

Reaction:

L-tryptophan = tryptamine + CO₂

For diagram of psilocybin biosynthesis, click here

Other name(s):

psiD (gene name); TDC (gene name)

Systematic name:

L-tryptophan carboxy-lyase

Comments:

The enzyme has been characterized from bacteria, plants, and fungi. Unlike EC 4.1.1.28, aromatic-L-amino-acid decarboxylase, this enzyme is specific for L-tryptophan.

Links to other databases:

References:

1.	Noe, W., Mollenschott, C. and Berlin, J. Tryptophan decarboxylase from Catharanthus roseus cell suspension cultures: purification, molecular and kinetic data of the homogenous protein. Plant Mol. Biol. 3 (1984) 281–288. [DOI] [PMID: 24310513]
2.	Buki, K.G., Vinh, D.Q. and Horvath, I. Partial purification and some properties of tryptophan decarboxylase from a Bacillus strain. Acta Microbiol Hung 32 (1985) 65–73. [PMID: 4036551]
3.	Nakazawa, H., Kumagai, H. and Yamada, H. Constitutive aromatic L-amino acid decarboxylase from Micrococcus percitreus. Biochem. Biophys. Res. Commun. 61 (1974) 75–82. [DOI] [PMID: 4441405]
4.	Lopez-Meyer, M. and Nessler, C.L. Tryptophan decarboxylase is encoded by two autonomously regulated genes in Camptotheca acuminata which are differentially expressed during development and stress. Plant J. 11 (1997) 1167–1175. [DOI] [PMID: 9225462]
5.	Fricke, J., Blei, F. and Hoffmeister, D. Enzymatic synthesis of psilocybin. Angew. Chem. Int. Ed. Engl. 56 (2017) 12352–12355. [DOI] [PMID: 28763571]

[EC 4.1.1.105 created 2017]

4.1.1.106

Accepted name:

fatty acid photodecarboxylase

Reaction:

a long-chain fatty acid + hν = a long-chain alkane + CO₂

Other name(s):

FAP (gene name)

Systematic name:

fatty acid carboxy-lyase (light-dependent, alkane-forming)

Comments:

This algal enzyme, characterized from the green algae Chlorella variabilis and Chlamydomonas reinhardtii, is dependent on blue light, which photooxidizes its FAD cofactor. The enzyme acts on fatty acids in the range of C₁₂ to C₂₂, with a higher efficiency for C₁₆ to C₁₇ chains, and forms an alkane product that is one carbon shorter than the substrate. The enzyme can also act on unsaturated fatty acids, forming the respective alkenes, but does not generate a new double bond.

Links to other databases:

References:

Sorigue, D., Legeret, B., Cuine, S., Blangy, S., Moulin, S., Billon, E., Richaud, P., Brugiere, S., Coute, Y., Nurizzo, D., Muller, P., Brettel, K., Pignol, D., Arnoux, P., Li-Beisson, Y., Peltier, G. and Beisson, F. An algal photoenzyme converts fatty acids to hydrocarbons. Science 357 (2017) 903–907. [DOI] [PMID: 28860382]

[EC 4.1.1.106 created 2017]

4.1.1.107

Accepted name:

3,4-dihydroxyphenylacetaldehyde synthase

Reaction:

L-dopa + O₂ + H₂O = 3,4-dihydroxyphenylacetaldehyde + CO₂ + NH₃ + H₂O₂

For diagram of phenylacetaldehyde, 4-hydroxyphenylacetaldehyde and 3,4-dihydroxyacetaldehyde biosynthesis, click here

Glossary:

L-dopa = 3,4-dihydroxyphenylalanine

Other name(s):

DHPAA synthase

Systematic name:

L-dopa carboxy-lyase (oxidative-deaminating)

Comments:

A pyridoxal 5′-phosphate protein. The enzyme, isolated from the mosquito Aedes aegypti, catalyses the production of 3,4-dihydroxylphenylacetaldehyde directly from L-dopa. Dopamine is not formed as an intermediate (cf. EC 4.1.1.28, aromatic-L-amino-acid decarboxylase). The enzyme is specific for L-dopa and does not react with other aromatic amino acids with the exception of a low activity with α-methyl-L-dopa.

Links to other databases:

References:

1.	Vavricka, C., Han, Q., Huang, Y., Erickson, S.M., Harich, K., Christensen, B.M. and Li, J. From L-dopa to dihydroxyphenylacetaldehyde: a toxic biochemical pathway plays a vital physiological function in insects. PLoS One 6:e16124 (2011). [DOI] [PMID: 21283636]

[EC 4.1.1.107 created 2017]

4.1.1.108

Accepted name:

4-hydroxyphenylacetaldehyde synthase

Reaction:

L-tyrosine + O₂ + H₂O = (4-hydroxyphenyl)acetaldehyde + CO₂ + NH₃ + H₂O₂

For diagram of phenylacetaldehyde, 4-hydroxyphenylacetaldehyde and 3,4-dihydroxyacetaldehyde biosynthesis, click here

Other name(s):

TYRDC-2 (gene name)

Systematic name:

L-tyrosine carboxy-lyase (oxidative-deaminating)

Comments:

A pyridoxal 5′-phosphate protein. The enzyme, isolated from the the plant Petroselinum crispum (parsley), catalyses the production of 4-hydroxyphenylacetaldehyde directly from L-tyrosine. Tyramine is not formed as an intermediate. The enzyme has a low activity with L-dopa (cf. EC 4.1.1.107, 3,4-dihydroxyphenylacetaldehyde synthase).

Links to other databases:

References:

1.	Torrens-Spence, M.P., Gillaspy, G., Zhao, B., Harich, K., White, R.H. and Li, J. Biochemical evaluation of a parsley tyrosine decarboxylase results in a novel 4-hydroxyphenylacetaldehyde synthase enzyme. Biochem. Biophys. Res. Commun. 418 (2012) 211–216. [DOI] [PMID: 22266321]
2.	Torrens-Spence, M.P., Liu, P., Ding, H., Harich, K., Gillaspy, G. and Li, J. Biochemical evaluation of the decarboxylation and decarboxylation-deamination activities of plant aromatic amino acid decarboxylases. J. Biol. Chem. 288 (2013) 2376–2387. [DOI] [PMID: 23204519]

[EC 4.1.1.108 created 2017]

4.1.1.109

Accepted name:

phenylacetaldehyde synthase

Reaction:

L-phenylalanine + O₂ + H₂O = phenylacetaldehyde + CO₂ + NH₃ + H₂O₂

For diagram of phenylacetaldehyde, 4-hydroxyphenylacetaldehyde and 3,4-dihydroxyacetaldehyde biosynthesis, click here

Other name(s):

PAAS (gene name)

Systematic name:

L-phenylalanine carboxy-lyase (oxidative-deaminating)

Comments:

A pyridoxal 5′-phosphate protein. The enzyme, isolated from the the plants Petunia hybrida and a Rosa hybrid, catalyses the production of phenylacetaldehyde directly from L-phenylalanine. The enzyme is specific for L-phenylalanine and does not accept other aromatic amino acids as substrates.

Links to other databases:

References:

Kaminaga, Y., Schnepp, J., Peel, G., Kish, C.M., Ben-Nissan, G., Weiss, D., Orlova, I., Lavie, O., Rhodes, D., Wood, K., Porterfield, D.M., Cooper, A.J., Schloss, J.V., Pichersky, E., Vainstein, A. and Dudareva, N. Plant phenylacetaldehyde synthase is a bifunctional homotetrameric enzyme that catalyzes phenylalanine decarboxylation and oxidation. J. Biol. Chem. 281 (2006) 23357–23366. [DOI] [PMID: 16766535]

[EC 4.1.1.109 created 2017]

4.1.99.23

Accepted name:

5-hydroxybenzimidazole synthase

Reaction:

5-amino-1-(5-phospho-β-D-ribosyl)imidazole + S-adenosyl-L-methionine + reduced acceptor = 5-hydroxybenzimidazole + 5′-deoxyadenosine + L-methionine + formate + NH₃ + phosphate + oxidized acceptor

For diagram of 5-hydroxybenzimidazole biosynthesis, click here

Other name(s):

bzaF (gene name); HBI synthase

Systematic name:

5-amino-1-(5-phospho-β-D-ribosyl)imidazole formate-lyase (5-hydroxybenzimidazole-forming)

Comments:

The enzyme, purified from bacteria, is part of the anaerobic pathway for cobalamin biosynthesis. It binds a [4Fe-4S] cluster that is coordinated by 3 cysteines and an exchangeable S-adenosyl-L-methionine molecule. The first stage of catalysis is reduction of the S-adenosyl-L-methionine to produce L-methionine and a 5′-deoxyadenosin-5′-yl radical that is crucial for the conversion of the substrate.

Links to other databases:

References:

1.	Mehta, A.P., Abdelwahed, S.H., Fenwick, M.K., Hazra, A.B., Taga, M.E., Zhang, Y., Ealick, S.E. and Begley, T.P. Anaerobic 5-hydroxybenzimidazole formation from aminoimidazole ribotide: an unanticipated intersection of thiamin and vitamin B₁₂ biosynthesis. J. Am. Chem. Soc. 137 (2015) 10444–10447. [DOI] [PMID: 26237670]
2.	Hazra, A.B., Han, A.W., Mehta, A.P., Mok, K.C., Osadchiy, V., Begley, T.P. and Taga, M.E. Anaerobic biosynthesis of the lower ligand of vitamin B₁₂. Proc. Natl. Acad. Sci. USA 112 (2015) 10792–10797. [DOI] [PMID: 26246619]

[EC 4.1.99.23 created 2017]

*EC

4.2.3.141

Accepted name:

sclareol synthase

Reaction:

(13E)-8α-hydroxylabd-13-en-15-yl diphosphate + H₂O = sclareol + diphosphate

For diagram of hydroxylabdenyl diphosphate derived diterpenoids, click here

Glossary:

sclareol = (13R)-labd-14-ene-8α,13-diol
(13E)-8α-hydroxylabd-13-en-15-yl diphosphate = 8-hydroxycopalyl diphosphate

Other name(s):

Systematic name:

(13E)-8α-hydroxylabd-13-en-15-yl-diphosphate-lyase (sclareol-forming)

Comments:

Isolated from the plant Salvia sclarea (clary sage). Originally thought to be synthesized in one step from geranylgeranyl diphosphate it is now known to require two enzymes, EC 4.2.1.133, copal-8-ol diphosphate synthase and EC 4.2.3.141, sclareol synthase. Sclareol is used in perfumery.

Links to other databases:

References:

Caniard, A., Zerbe, P., Legrand, S., Cohade, A., Valot, N., Magnard, J.L., Bohlmann, J. and Legendre, L. Discovery and functional characterization of two diterpene synthases for sclareol biosynthesis in Salvia sclarea (L.) and their relevance for perfume manufacture. BMC Plant Biol. 12:119 (2012). [DOI] [PMID: 22834731]

[EC 4.2.3.141 created 2013, modified 2017]

4.2.3.195

Accepted name:

rhizathalene A synthase

Reaction:

geranylgeranyl diphosphate = rhizathalene A + diphosphate

For diagram of miscellaneous diterpenoid biosynthesis, click here

Other name(s):

TPS08 (gene name)

Systematic name:

geranygeranyl-diphosphate diphosphate-lyase (rhizathalene A-forming)

Comments:

The enzyme was identified in the roots of the plant Arabidopsis thaliana (thale cress). The product is a semivolatile diterpene that acts as a local antifeedant in belowground direct defense against root-feeding insects.

Links to other databases:

References:

Vaughan, M.M., Wang, Q., Webster, F.X., Kiemle, D., Hong, Y.J., Tantillo, D.J., Coates, R.M., Wray, A.T., Askew, W., O'Donnell, C., Tokuhisa, J.G. and Tholl, D. Formation of the unusual semivolatile diterpene rhizathalene by the Arabidopsis class I terpene synthase TPS08 in the root stele is involved in defense against belowground herbivory. Plant Cell 25 (2013) 1108–1125. [DOI] [PMID: 23512856]

[EC 4.2.3.195 created 2017]

4.99.1.12

Accepted name:

pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel chelatase

Reaction:

Ni(II)-pyridinium-3,5-bisthiocarboxylate mononucleotide = pyridinium-3,5-bisthiocarboxylate mononucleotide + Ni²⁺

Other name(s):

LarC; P2TMN nickel chelatase

Systematic name:

Ni(II)-pyridinium-3,5-bisthiocarboxylate mononucleotide nickel-lyase (pyridinium-3,5-bisthiocarboxylate-mononucleotide-forming)

Comments:

This enzyme, found in Lactobacillus plantarum, is involved in the biosynthesis of a nickel-pincer cofactor. It catalyses the insertion of Ni²⁺ into the cofactor forming a covalent bond between a carbon atom and the nickel atom.

Links to other databases:

References:

1.	Desguin, B., Goffin, P., Viaene, E., Kleerebezem, M., Martin-Diaconescu, V., Maroney, M.J., Declercq, J.P., Soumillion, P. and Hols, P. Lactate racemase is a nickel-dependent enzyme activated by a widespread maturation system. Nat. Commun. 5:3615 (2014). [DOI] [PMID: 24710389]
2.	Desguin, B., Soumillion, P., Hols, P. and Hausinger, R.P. Nickel-pincer cofactor biosynthesis involves LarB-catalyzed pyridinium carboxylation and LarE-dependent sacrificial sulfur insertion. Proc. Natl. Acad. Sci. USA 113 (2016) 5598–5603. [DOI] [PMID: 27114550]

[EC 4.99.1.12 created 2017]

5.1.3.39

Deleted entry:

L-erythrulose 4-phosphate epimerase. The activity has been shown not to take place.

[EC 5.1.3.39 created 2016, deleted 2018]

*EC

5.3.3.8

Accepted name:

Δ³-Δ²-enoyl-CoA isomerase

Reaction:

(1) a (3Z)-alk-3-enoyl-CoA = a (2E)-alk-2-enoyl-CoA
(2) a (3E)-alk-3-enoyl-CoA = a (2E)-alk-2-enoyl-CoA

For diagram of Benzoyl-CoA catabolism, click here

Other name(s):

ECI (gene name); dodecenoyl-CoA isomerase; dodecenoyl-CoA Δ-isomerase; Δ³-cis-Δ²-trans-enoyl-CoA isomerase; acetylene-allene isomerase; dodecenoyl-CoA Δ³-cis-Δ²-trans-isomerase; dodecenoyl-CoA (3Z)-(2E)-isomerase

Systematic name:

(3Z/3E)-alk-3-enoyl-CoA (2E)-isomerase

Comments:

The enzyme participates in the β-oxidation of fatty acids with double bonds at an odd position. Processing of these substrates via the β-oxidation system results in intermediates with a cis- or trans-double bond at position C₃, which cannot be processed further by the regular enzymes of the β-oxidation system. This enzyme isomerizes the bond to a trans bond at position C₂, which can be processed further. The reaction rate is ten times higher for the (3Z) isomers than for (3E) isomers. The enzyme can also catalyse the isomerization of 3-acetylenic fatty acyl thioesters to 2,3-dienoyl fatty acyl thioesters.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 62213-29-0

References:

1.	Stoffel, W., Ditzer, R. and Caesar, H. Der Stoffwechsel der ungesättigten Fettsäuren. III. Zur β-Oxydation der Mono- und Polyenfettsäuren. Der Mechanismus der enzymatischen Reaktionen an Δ³cis-Enoyl-CoA-Verbindungen. Hoppe-Seyler's Z. Physiol. Chem. 339 (1964) 167–181. [PMID: 5830064]
2.	Stoffel, W. and Ecker, W. Δ³-cis,-Δ²-trans-Enoyl-CoA isomerase from rat liver mitochondria. Methods Enzymol. 14 (1969) 99–105.
3.	Stoffel, W. and Grol, M. Purification and properties of 3-cis-2-trans-enoyl-CoA isomerase (dodecenoyl-CoA Δ-isomerase) from rat liver mitochondria. Hoppe-Seyler's Z. Physiol. Chem. 359 (1978) 1777–1782. [PMID: 738702]
4.	Miesowicz, F.M. and Bloch, K. Purification of hog liver isomerase. Mechanism of isomerization of 3-alkenyl and 3-alkynyl thioesters. J. Biol. Chem. 254 (1979) 5868–5877. [PMID: 376522]
5.	Engeland, K. and Kindl, H. Purification and characterization of a plant peroxisomal Δ²,Δ³-enoyl-CoA isomerase acting on 3-cis-enoyl-CoA and 3-trans-enoyl-CoA. Eur. J. Biochem. 196 (1991) 699–705. [DOI] [PMID: 2013292]
6.	Geisbrecht, B.V., Zhang, D., Schulz, H. and Gould, S.J. Characterization of PECI, a novel monofunctional Δ³, Δ²-enoyl-CoA isomerase of mammalian peroxisomes. J. Biol. Chem. 274 (1999) 21797–21803. [DOI] [PMID: 10419495]
7.	Zhang, D., Yu, W., Geisbrecht, B.V., Gould, S.J., Sprecher, H. and Schulz, H. Functional characterization of Δ³,Δ²-enoyl-CoA isomerases from rat liver. J. Biol. Chem. 277 (2002) 9127–9132. [DOI] [PMID: 11781327]
8.	Goepfert, S., Vidoudez, C., Tellgren-Roth, C., Delessert, S., Hiltunen, J.K. and Poirier, Y. Peroxisomal Δ³,Δ²-enoyl CoA isomerases and evolution of cytosolic paralogues in embryophytes. Plant J. 56 (2008) 728–742. [DOI] [PMID: 18657232]

[EC 5.3.3.8 created 1978, modified 1980, modified 2018]

5.3.3.21

Accepted name:

Δ^3,5-Δ^2,4-dienoyl-CoA isomerase

Reaction:

a (3E,5Z)-alka-3,5-dienoyl-CoA = a (2E,4E)-alka-2,4-dienoyl-CoA

Other name(s):

3,5-tetradecadienoyl-CoA isomerase; DCI1 (gene name)

Systematic name:

(3E,5Z)-alka-3,5-dienoyl-CoA Δ^3,5-Δ^2,4 isomerase

Comments:

The enzyme participates in an alternative degradation route of fatty acids with cis-double bonds on odd-number carbons such as oleate and linoleate. The main physiological substrate is (3E,5Z)-tetradeca-3,5-dienoyl-CoA, but other (3E,5Z)-dienoyl-CoAs with varying carbon chain lengths are also substrates.

Links to other databases:

References:

1.	Filppula, S.A., Yagi, A.I., Kilpelainen, S.H., Novikov, D., FitzPatrick, D.R., Vihinen, M., Valle, D. and Hiltunen, J.K. Δ^3,5-Δ^2,4-dienoyl-CoA isomerase from rat liver. Molecular characterization. J. Biol. Chem. 273 (1998) 349–355. [DOI] [PMID: 9417087]
2.	Modis, Y., Filppula, S.A., Novikov, D.K., Norledge, B., Hiltunen, J.K. and Wierenga, R.K. The crystal structure of dienoyl-CoA isomerase at 1.5 Å resolution reveals the importance of aspartate and glutamate sidechains for catalysis. Structure 6 (1998) 957–970. [DOI] [PMID: 9739087]
3.	Geisbrecht, B.V., Schulz, K., Nau, K., Geraghty, M.T., Schulz, H., Erdmann, R. and Gould, S.J. Preliminary characterization of Yor180Cp: identification of a novel peroxisomal protein of saccharomyces cerevisiae involved in fatty acid metabolism. Biochem. Biophys. Res. Commun. 260 (1999) 28–34. [DOI] [PMID: 10381339]
4.	Gurvitz, A., Mursula, A.M., Yagi, A.I., Hartig, A., Ruis, H., Rottensteiner, H. and Hiltunen, J.K. Alternatives to the isomerase-dependent pathway for the β-oxidation of oleic acid are dispensable in Saccharomyces cerevisiae. Identification of YOR180c/DCI1 encoding peroxisomal Δ(3,5)-Δ(2,4)-dienoyl-CoA isomerase. J. Biol. Chem. 274 (1999) 24514–24521. [DOI] [PMID: 10455114]
5.	Zhang, D., Liang, X., He, X.Y., Alipui, O.D., Yang, S.Y. and Schulz, H. Δ^3,5,Δ^2,4-dienoyl-CoA isomerase is a multifunctional isomerase. A structural and mechanistic study. J. Biol. Chem. 276 (2001) 13622–13627. [DOI] [PMID: 11278886]
6.	Goepfert, S., Vidoudez, C., Rezzonico, E., Hiltunen, J.K. and Poirier, Y. Molecular identification and characterization of the Arabidopsis Δ^3,5,Δ^2,4-dienoyl-coenzyme A isomerase, a peroxisomal enzyme participating in the β-oxidation cycle of unsaturated fatty acids. Plant Physiol. 138 (2005) 1947–1956. [DOI] [PMID: 16040662]

[EC 5.3.3.21 created 2018]

6.2.1.51

Accepted name:

4-hydroxyphenylalkanoate adenylyltransferase FadD29

Reaction:

(1) ATP + 17-(4-hydroxyphenyl)heptadecanoate + holo-[(phenol)carboxyphthiodiolenone synthase] = AMP + diphosphate + 17-(4-hydroxyphenyl)heptadecanoyl-[(phenol)carboxyphthiodiolenone synthase]
(1a) ATP + 17-(4-hydroxyphenyl)heptadecanoate = diphosphate + 17-(4-hydroxyphenyl)heptadecanoyl-adenylate
(1b) 17-(4-hydroxyphenyl)heptadecanoyl-adenylate + holo-[(phenol)carboxyphthiodiolenone synthase] = AMP + 17-(4-hydroxyphenyl)heptadecanoyl-[(phenol)carboxyphthiodiolenone synthase]
(2) ATP + 19-(4-hydroxyphenyl)nonadecanoate + holo-[(phenol)carboxyphthiodiolenone synthase] = AMP + diphosphate + 19-(4-hydroxyphenyl)nonadecanoyl-[(phenol)carboxyphthiodiolenone synthase]
(2a) ATP + 19-(4-hydroxyphenyl)nonadecanoate = diphosphate + 19-(4-hydroxyphenyl)nonadecanoyl-adenylate
(2b) 19-(4-hydroxyphenyl)nonadecanoyl-adenylate + holo-[(phenol)carboxyphthiodiolenone synthase] = AMP + 19-(4-hydroxyphenyl)nonadecanoyl-[(phenol)carboxyphthiodiolenone synthase]

Other name(s):

fadD29 (gene name); 4-hydroxyphenylalkanoate adenylase

Systematic name:

4-hydroxyphenylalkanoate:holo-[(phenol)carboxyphthiodiolenone synthase] ligase

Comments:

The mycobacterial enzyme participates in the biosynthesis of phenolphthiocerols. Following the substrate’s activation by adenylation, it is transferred to an acyl-carrier protein domain within the enzyme, from which it is transferred to the phenolphthiocerol/phthiocerol polyketide synthase.

Links to other databases:

References:

1.	Simeone, R., Leger, M., Constant, P., Malaga, W., Marrakchi, H., Daffe, M., Guilhot, C. and Chalut, C. Delineation of the roles of FadD22, FadD26 and FadD29 in the biosynthesis of phthiocerol dimycocerosates and related compounds in Mycobacterium tuberculosis. FEBS J. 277 (2010) 2715–2725. [DOI] [PMID: 20553505]
2.	Vergnolle, O., Chavadi, S.S., Edupuganti, U.R., Mohandas, P., Chan, C., Zeng, J., Kopylov, M., Angelo, N.G., Warren, J.D., Soll, C.E. and Quadri, L.E. Biosynthesis of cell envelope-associated phenolic glycolipids in Mycobacterium marinum. J. Bacteriol. 197 (2015) 1040–1050. [DOI] [PMID: 25561717]

[EC 6.2.1.51 created 2016 as EC 2.7.7.94, transferred 2017 to EC 6.2.1.51]

6.2.1.52

Accepted name:

L-firefly luciferin—CoA ligase

Reaction:

ATP + L-firefly luciferin + CoA = AMP + diphosphate + L-firefly luciferyl-CoA

Glossary:

L-firefly luciferin = (R)-4,5-dihydro-2-(6-hydroxy-1,3-benzothiazol-2-yl)thiazole-4-carboxylate

Other name(s):

LUC

Systematic name:

(R)-4,5-dihydro-2-(6-hydroxy-1,3-benzothiazol-2-yl)thiazole-4-carboxylate:CoA ligase (AMP-forming)

Comments:

This is an alternative activity of the firefly luciferase (EC 1.13.12.7), which the enzyme exhibits under normal conditions only when acting on the L-enantiomer of its substrate. The D-isomer can act as a substrate for the CoA—ligase activity in vitro only under low oxygen conditions that are not found in vivo. The activation of L-firefly luciferin to a CoA ester is a step in a recycling pathway that results in its epimerization to the D enantiomer, which is the only substrate whose oxygenation results in light emission.

Links to other databases:

References:

1.	Fraga, H., Esteves da Silva, J.C. and Fontes, R. Identification of luciferyl adenylate and luciferyl coenzyme a synthesized by firefly luciferase. ChemBioChem 5 (2004) 110–115. [DOI] [PMID: 14695520]
2.	Nakamura, M., Maki, S., Amano, Y., Ohkita, Y., Niwa, K., Hirano, T., Ohmiya, Y. and Niwa, H. Firefly luciferase exhibits bimodal action depending on the luciferin chirality. Biochem. Biophys. Res. Commun. 331 (2005) 471–475. [DOI] [PMID: 15850783]
3.	Viviani, V.R., Scorsato, V., Prado, R.A., Pereira, J.G., Niwa, K., Ohmiya, Y. and Barbosa, J.A. The origin of luciferase activity in Zophobas mealworm AMP/CoA-ligase (protoluciferase): luciferin stereoselectivity as a switch for the oxygenase activity. Photochem Photobiol Sci 9 (2010) 1111–1119. [DOI] [PMID: 20526507]
4.	Maeda, J., Kato, D.I., Okuda, M., Takeo, M., Negoro, S., Arima, K., Ito, Y. and Niwa, K. Biosynthesis-inspired deracemizative production of D-luciferin by combining luciferase and thioesterase. Biochim. Biophys. Acta 1861 (2017) 2112–2118. [DOI] [PMID: 28454735]

[EC 6.2.1.52 created 2017]

6.3.2.52

Accepted name:

jasmonoyl—L-amino acid ligase

Reaction:

ATP + jasmonate + an L-amino acid = AMP + diphosphate + a jasmonoyl-L-amino acid

Other name(s):

JAR1 (gene name); JAR4 (gene name); JAR6 (gene name); jasmonoyl—L-amino acid synthetase

Systematic name:

jasmonate:L-amino acid ligase

Comments:

Two jasmonoyl-L-amino acid synthetases have been described from Nicotiana attenuata [3] and one from Arabidopsis thaliana [1]. The N. attenuata enzymes generate jasmonoyl-L-isoleucine, jasmonoyl-L-leucine, and jasmonoyl-L-valine. The enzyme from A. thaliana could catalyse the addition of many different amino acids to jasmonate in vitro [1,4,5]. While the abundant form of jasmonate in plants is (–)-jasmonate, the active form of jasmonoyl-L-isoleucine is (+)-7-iso-jasmonoyl-L-isoleucine.

Links to other databases: