The Enzyme Database

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

Proposed Changes to the Enzyme List

The entries below are proposed additions and amendments to the Enzyme Nomenclature list. They were prepared for the NC-IUBMB by Kristian Axelsen, Richard Cammack, Ron Caspi, Masaaki Kotera, Andrew McDonald, Gerry Moss, Dietmar Schomburg, Ida Schomburg and Keith Tipton. Comments and suggestions on these draft entries should be sent to Dr Andrew McDonald (Department of Biochemistry, Trinity College Dublin, Dublin 2, Ireland). The date on which an enzyme will be made official is appended after the EC number. To prevent confusion please do not quote new EC numbers until they are incorporated into the main list.

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


Contents

EC 1.1.1.422 pseudoephedrine dehydrogenase
EC 1.1.1.423 ephedrine dehydrogenase
EC 1.1.98.7 serine-type anaerobic sulfatase-maturating enzyme
*EC 1.3.8.11 cyclohexane-1-carbonyl-CoA dehydrogenase (electron-transfer flavoprotein)
EC 1.8.98.7 cysteine-type anaerobic sulfatase-maturating enzyme
EC 1.11.1.15 transferred
EC 1.11.1.24 thioredoxin-dependent peroxiredoxin
EC 1.11.1.25 glutaredoxin-dependent peroxiredoxin
EC 1.11.1.26 NADH-dependent peroxiredoxin
EC 1.11.1.27 glutathione-dependent peroxiredoxin
EC 1.11.1.28 lipoyl-dependent peroxiredoxin
EC 1.11.1.29 mycoredoxin-dependent peroxiredoxin
*EC 1.14.16.5 alkylglycerol monooxygenase
*EC 1.14.16.6 mandelate 4-monooxygenase
*EC 1.14.17.1 dopamine β-monooxygenase
EC 1.14.18.12 2-hydroxy fatty acid dioxygenase
*EC 1.16.1.8 [methionine synthase] reductase
*EC 1.17.1.8 4-hydroxy-tetrahydrodipicolinate reductase
EC 1.17.99.8 limonene dehydrogenase
*EC 1.20.4.1 arsenate reductase (glutathione/glutaredoxin)
*EC 2.4.2.42 UDP-D-xylose:β-D-glucoside α-1,3-D-xylosyltransferase
*EC 2.7.1.8 glucosamine kinase
*EC 2.7.1.147 ADP-specific glucose/glucosamine kinase
EC 2.7.2.17 [amino group carrier protein]-L-2-aminoadipate 6-kinase
*EC 2.7.7.2 FAD synthase
EC 2.8.3.26 succinyl-CoA:mesaconate CoA transferase
EC 2.9.1.3 tRNA 2-selenouridine synthase
EC 3.1.3.108 nocturnin
EC 3.1.27.3 transferred
EC 3.2.1.44 transferred
*EC 3.2.1.155 xyloglucan-specific endo-processive β-1,4-glucanase
EC 3.2.1.211 endo-(1→3)-fucoidanase
EC 3.2.1.212 endo-(1→4)-fucoidanase
EC 3.2.1.213 galactan exo-1,6-β-galactobiohydrolase (non-reducing end)
EC 3.4.17.24 tubulin-glutamate carboxypeptidase
EC 3.6.1.73 inosine/xanthosine triphosphatase
EC 3.7.1.26 2,4-didehydro-3-deoxy-L-rhamnonate hydrolase
EC 3.13.1.9 S-inosyl-L-homocysteine hydrolase
EC 4.1.2.41 transferred
EC 4.1.2.61 feruloyl-CoA hydratase/lyase
*EC 4.2.1.96 4a-hydroxytetrahydrobiopterin dehydratase
EC 4.2.1.101 transferred
EC 4.2.2.27 pectin monosaccharide-lyase
*EC 4.3.3.7 4-hydroxy-tetrahydrodipicolinate synthase
EC 4.6.1.24 ribonuclease T1
EC 4.6.1.25 bacteriophage T4 restriction endoribonuclease RegB
EC 6.2.1.62 3,4-dihydroxybenzoate—[aryl-carrier protein] ligase
EC 6.2.1.63 L-arginine—[L-arginyl-carrier protein] ligase
*EC 7.1.1.7 quinol oxidase (electrogenic, proton-motive force generating)


EC 1.1.1.422 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: pseudoephedrine dehydrogenase
Reaction: (+)-(1S,2S)-pseudoephedrine + NAD+ = (S)-2-methylamino-1-phenylpropan-1-one + NADH + H+
Other name(s): PseDH
Systematic name: (+)-(1S,2S)-pseudoephedrine:NAD+ 1-oxoreductase
Comments: The enzyme, characterized from the bacterium Arthrobacter sp. TS-15, acts on a broad range of different aryl-alkyl ketones, such as haloketones, ketoamines, diketones, and ketoesters. It accepts various types of aryl groups including phenyl-, pyridyl-, thienyl-, and furyl-rings, but the presence of an aromatic ring is essential for the activity. In addition, the presence of a functional group on the alkyl chain, such as an amine, a halogen, or a ketone, is also crucial. The enzyme exhibits a strict anti-Prelog enantioselectivity. When acting on diketones, it catalyses the reduction of only the keto group closest to the ring, with no further reduction to the diol. cf. EC 1.1.1.423, ephedrine dehydrogenase.
References:
1.  Shanati, T., Lockie, C., Beloti, L., Grogan, G. and Ansorge-Schumacher, M.B. Two enantiocomplementary ephedrine dehydrogenases from Arthrobacter sp. TS-15 with broad substrate specificity. ACS Catal. 9 (2019) 6202–6211.
2.  Shanati, T., Ansorge-Schumacher, M. Enzymes and methods for the stereoselective reduction of carbonyl compounds, oxidation and stereoselective reductive amination - for the enantioselective preparation of alcohol amine compounds. (2019) Patent WO2019002459.
[EC 1.1.1.422 created 2020]
 
 
EC 1.1.1.423 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: ephedrine dehydrogenase
Reaction: (–)-(1R,2S)-ephedrine + NAD+ = (S)-2-methylamino-1-phenylpropan-1-one + NADH + H+
Other name(s): EDH
Systematic name: (–)-(1R,2S)-ephedrine:NAD+ 1-oxoreductase
Comments: The enzyme, characterized from the bacterium Arthrobacter sp. TS-15, acts on a broad range of different aryl-alkyl ketones, such as haloketones, ketoamines, diketones, and ketoesters. It accepts various types of aryl groups including phenyl-, pyridyl-, thienyl-, and furyl-rings, but the presence of an aromatic ring is essential for the activity. In addition, the presence of a functional group on the alkyl chain, such as an amine, a halogen, or a ketone, is also crucial. The enzyme exhibits a strict Prelog enantioselectivity. When acting on diketones, it catalyses the reduction of only the keto group closest to the ring, with no further reduction to the diol. cf. EC 1.1.1.422, pseudoephedrine dehydrogenase.
References:
1.  Shanati, T., Lockie, C., Beloti, L., Grogan, G. and Ansorge-Schumacher, M.B. Two enantiocomplementary ephedrine dehydrogenases from Arthrobacter sp. TS-15 with broad substrate specificity. ACS Catal. 9 (2019) 6202–6211.
2.  Shanati, T., Ansorge-Schumacher, M. Enzymes and methods for the stereoselective reduction of carbonyl compounds, oxidation and stereoselective reductive amination - for the enantioselective preparation of alcohol amine compounds. (2019) Patent WO2019002459.
[EC 1.1.1.423 created 2020]
 
 
EC 1.1.98.7 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: serine-type anaerobic sulfatase-maturating enzyme
Reaction: S-adenosyl-L-methionine + a [sulfatase]-L-serine = a [sulfatase]-3-oxo-L-alanine + 5′-deoxyadenosine + L-methionine
Glossary: 3-oxo-L-alanine = (S)-formylglycine = (S)-Cα-formylglycine = FGly
Other name(s): atsB (gene name)
Systematic name: [sulfatase]-L-serine:S-adenosyl-L-methionine oxidoreductase (3-oxo-L-alanine-forming)
Comments: A bacterial radical S-adenosyl-L-methionine (AdoMet) enzyme that contains three [4Fe-4S] clusters. The enzyme, found in some bacteria, activates a type I sulfatase enzyme (EC 3.1.6.1) by converting a conserved L-serine residue in the active site to a unique 3-oxo-L-alanine residue that is essential for the sulfatase activity. While the enzyme from Klebsiella pneumoniae is specific for L-serine, the enzyme from Clostridium perfringens can also act on L-cysteine, see EC 1.8.98.7, cysteine-type anaerobic sulfatase-maturating enzyme.
References:
1.  Szameit, C., Miech, C., Balleininger, M., Schmidt, B., von Figura, K. and Dierks, T. The iron sulfur protein AtsB is required for posttranslational formation of formylglycine in the Klebsiella sulfatase. J. Biol. Chem. 274 (1999) 15375–15381. [PMID: 10336424]
2.  Fang, Q., Peng, J. and Dierks, T. Post-translational formylglycine modification of bacterial sulfatases by the radical S-adenosylmethionine protein AtsB. J. Biol. Chem. 279 (2004) 14570–14578. [PMID: 14749327]
3.  Grove, T.L., Lee, K.H., St Clair, J., Krebs, C. and Booker, S.J. In vitro characterization of AtsB, a radical SAM formylglycine-generating enzyme that contains three [4Fe-4S] clusters. Biochemistry 47 (2008) 7523–7538. [PMID: 18558715]
[EC 1.1.98.7 created 2020]
 
 
*EC 1.3.8.11 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: cyclohexane-1-carbonyl-CoA dehydrogenase (electron-transfer flavoprotein)
Reaction: cyclohexane-1-carbonyl-CoA + electron-transfer flavoprotein = cyclohex-1-ene-1-carbonyl-CoA + reduced electron-transfer flavoprotein
Other name(s): aliB (gene name); cyclohexane-1-carbonyl-CoA dehydrogenase (ambiguous)
Systematic name: cyclohexane-1-carbonyl-CoA:electron transfer flavoprotein oxidoreductase
Comments: Contains FAD. The enzyme, characterized from the strict anaerobic bacterium Syntrophus aciditrophicus, is involved in production of cyclohexane-1-carboxylate, a byproduct produced by that organism during fermentation of benzoate and crotonate to acetate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Pelletier, D.A. and Harwood, C.S. 2-Hydroxycyclohexanecarboxyl coenzyme A dehydrogenase, an enzyme characteristic of the anaerobic benzoate degradation pathway used by Rhodopseudomonas palustris. J. Bacteriol. 182 (2000) 2753–2760. [PMID: 10781543]
2.  Kung, J.W., Seifert, J., von Bergen, M. and Boll, M. Cyclohexanecarboxyl-coenzyme A (CoA) and cyclohex-1-ene-1-carboxyl-CoA dehydrogenases, two enzymes involved in the fermentation of benzoate and crotonate in Syntrophus aciditrophicus. J. Bacteriol. 195 (2013) 3193–3200. [DOI] [PMID: 23667239]
[EC 1.3.8.11 created 2013, modified 2020]
 
 
EC 1.8.98.7 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: cysteine-type anaerobic sulfatase-maturating enzyme
Reaction: S-adenosyl-L-methionine + a [sulfatase]-L-cysteine + H2O = a [sulfatase]-3-oxo-L-alanine + 5′-deoxyadenosine + L-methionine + hydrogen sulfide
Glossary: 3-oxo-L-alanine = formylglycine = Cα-formylglycine = FGly
Other name(s): anSME; Cys-type anaerobic sulfatase-maturating enzyme; anaerobic sulfatase maturase
Systematic name: [sulfatase]-L-cysteine:S-adenosyl-L-methionine oxidoreductase (3-oxo-L-alanine-forming)
Comments: A radical S-adenosylmethionine (AdoMet) enzyme that contains three [4Fe-4S] clusters. The enzyme, found in some bacteria, activates a type I sulfatase enzyme (EC 3.1.6.1) by converting a conserved L-cysteine residue in the active site to a unique 3-oxo-L-alanine residue that is essential for the sulfatase activity. Some enzymes can also act on L-serine, see EC 1.1.98.7, serine-type anaerobic sulfatase-maturating enzyme and EC 1.8.3.7, formylglycine-generating enzyme.
References:
1.  Berteau, O., Guillot, A., Benjdia, A. and Rabot, S. A new type of bacterial sulfatase reveals a novel maturation pathway in prokaryotes. J. Biol. Chem. 281 (2006) 22464–22470. [PMID: 16766528]
2.  Benjdia, A., Subramanian, S., Leprince, J., Vaudry, H., Johnson, M.K. and Berteau, O. Anaerobic sulfatase-maturating enzymes, first dual substrate radical S-adenosylmethionine enzymes. J. Biol. Chem. 283 (2008) 17815–17826. [PMID: 18408004]
3.  Benjdia, A., Leprince, J., Sandstrom, C., Vaudry, H. and Berteau, O. Mechanistic investigations of anaerobic sulfatase-maturating enzyme: direct Cβ H-atom abstraction catalyzed by a radical AdoMet enzyme. J. Am. Chem. Soc. 131 (2009) 8348–8349. [PMID: 19489556]
4.  Benjdia, A., Subramanian, S., Leprince, J., Vaudry, H., Johnson, M.K. and Berteau, O. Anaerobic sulfatase-maturating enzyme--a mechanistic link with glycyl radical-activating enzymes. FEBS J. 277 (2010) 1906–1920. [PMID: 20218986]
5.  Grove, T.L., Ahlum, J.H., Qin, R.M., Lanz, N.D., Radle, M.I., Krebs, C. and Booker, S.J. Further characterization of Cys-type and Ser-type anaerobic sulfatase maturating enzymes suggests a commonality in the mechanism of catalysis. Biochemistry 52 (2013) 2874–2887. [PMID: 23477283]
[EC 1.8.98.7 created 2020]
 
 
EC 1.11.1.15 – public review until 19 March 2020 [Last modified: 2020-02-20 08:08:21]
Transferred entry: peroxiredoxin. Now described by EC 1.11.1.24, thioredoxin-dependent peroxiredoxin; EC 1.11.1.25, glutaredoxin-dependent peroxiredoxin; EC 1.11.1.26, NADH-dependent peroxiredoxin; EC 1.11.1.27, glutathione-dependent peroxiredoxin; EC 1.11.1.28, lipoyl-dependent peroxiredoxin; and EC 1.11.1.29, mycoredoxin-dependent peroxiredoxin.
[EC 1.11.1.15 created 2004, deleted 2020]
 
 
EC 1.11.1.24 – public review until 16 March 2020 [Last modified: 2020-02-18 05:35:12]
Accepted name: thioredoxin-dependent peroxiredoxin
Reaction: thioredoxin + ROOH = thioredoxin disulfide + H2O + ROH
For diagram of reaction, click here and for mechanism, click here
Other name(s): thioredoxin peroxidase; bcp (gene name); tpx (gene name); PrxQ
Systematic name: thioredoxin:hydroperoxide oxidoreductase
Comments: Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant proteins. They can be divided into three classes: typical 2-Cys, atypical 2-Cys and 1-Cys peroxiredoxins [4]. The peroxidase reaction comprises two steps centred around a redox-active cysteine called the peroxidatic cysteine. All three peroxiredoxin classes have the first step in common, in which the peroxidatic cysteine attacks the peroxide substrate and is oxidized to S-hydroxycysteine (a sulfenic acid) (see mechanism). The second step of the peroxidase reaction, the regeneration of cysteine from S-hydroxycysteine, distinguishes the three peroxiredoxin classes. For typical 2-Cys Prxs, in the second step, the peroxidatic S-hydroxycysteine from one subunit is attacked by the ‘resolving’ cysteine located in the C-terminus of the second subunit, to form an intersubunit disulfide bond, which is then reduced by one of several cell-specific thiol-containing reductants completing the catalytic cycle. In the atypical 2-Cys Prxs, both the peroxidatic cysteine and its resolving cysteine are in the same polypeptide, so their reaction forms an intrachain disulfide bond. The 1-Cys Prxs conserve only the peroxidatic cysteine, so its regeneration involves direct interaction with a reductant molecule. Thioredoxin-dependent peroxiredoxins are the most common. They have been reported from archaea, bacteria, fungi, plants, and animals.
References:
1.  Kang, S.W., Chae, H.Z., Seo, M.S., Kim, K., Baines, I.C. and Rhee, S.G. Mammalian peroxiredoxin isoforms can reduce hydrogen peroxide generated in response to growth factors and tumor necrosis factor-α. J. Biol. Chem. 273 (1998) 6297–6302. [PMID: 9497357]
2.  Kong, W., Shiota, S., Shi, Y., Nakayama, H. and Nakayama, K. A novel peroxiredoxin of the plant Sedum lineare is a homologue of Escherichia coli bacterioferritin co-migratory protein (Bcp). Biochem. J. 351 (2000) 107–114. [PMID: 10998352]
3.  Jeong, W., Cha, M.K. and Kim, I.H. Thioredoxin-dependent hydroperoxide peroxidase activity of bacterioferritin comigratory protein (BCP) as a new member of the thiol-specific antioxidant protein (TSA)/alkyl hydroperoxide peroxidase C (AhpC) family. J. Biol. Chem. 275 (2000) 2924–2930. [PMID: 10644761]
4.  Wood, Z.A., Schröder, E., Harris, J.R. and Poole, L.B. Structure, mechanism and regulation of peroxiredoxins. Trends Biochem. Sci. 28 (2003) 32–40. [DOI] [PMID: 12517450]
5.  Jeon, S.J. and Ishikawa, K. Characterization of novel hexadecameric thioredoxin peroxidase from Aeropyrum pernix K1. J. Biol. Chem. 278 (2003) 24174–24180. [PMID: 12707274]
6.  Perez-Perez, M.E., Mata-Cabana, A., Sanchez-Riego, A.M., Lindahl, M. and Florencio, F.J. A comprehensive analysis of the peroxiredoxin reduction system in the cyanobacterium Synechocystis sp. strain PCC 6803 reveals that all five peroxiredoxins are thioredoxin dependent. J. Bacteriol. 191 (2009) 7477–7489. [PMID: 19820102]
[EC 1.11.1.24 created 1983 as EC 1.11.1.15, part transferred 2020 to EC 1.11.1.24]
 
 
EC 1.11.1.25 – public review until 16 March 2020 [Last modified: 2020-02-18 05:35:32]
Accepted name: glutaredoxin-dependent peroxiredoxin
Reaction: glutaredoxin + ROOH = glutaredoxin disulfide + H2O + ROH
For diagram of reaction, click here and for mechanism, click here
Other name(s): PRXIIB (gene name)
Systematic name: glutaredoxin:hydroperoxide oxidoreductase
Comments: Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant proteins. They can be divided into three classes: typical 2-Cys, atypical 2-Cys and 1-Cys peroxiredoxins [2]. The peroxidase reaction comprises two steps centred around a redox-active cysteine called the peroxidatic cysteine. All three peroxiredoxin classes have the first step in common, in which the peroxidatic cysteine attacks the peroxide substrate and is oxidized to S-hydroxycysteine (a sulfenic acid) (see mechanism). The second step of the peroxidase reaction, the regeneration of cysteine from S-hydroxycysteine, distinguishes the three peroxiredoxin classes. For typical 2-Cys Prxs, in the second step, the peroxidatic S-hydroxycysteine from one subunit is attacked by the ‘resolving’ cysteine located in the C-terminus of the second subunit, to form an intersubunit disulfide bond, which is then reduced by one of several cell-specific thiol-containing reductants completing the catalytic cycle. In the atypical 2-Cys Prxs, both the peroxidatic cysteine and its resolving cysteine are in the same polypeptide, so their reaction forms an intrachain disulfide bond. To recycle the disulfide, known atypical 2-Cys Prxs appear to use thioredoxin as an electron donor. The 1-Cys Prxs conserve only the peroxidatic cysteine, so its regeneration involves direct interaction with a reductant molecule. Glutaredoxin-dependent peroxiredoxins have been reported from bacteria, fungi, plants, and animals. These enzymes are often able to use an alternative reductant such as thioredoxin or glutathione.
References:
1.  Rouhier, N., Gelhaye, E. and Jacquot, J.P. Glutaredoxin-dependent peroxiredoxin from poplar: protein-protein interaction and catalytic mechanism. J. Biol. Chem. 277 (2002) 13609–13614. [PMID: 11832487]
2.  Wood, Z.A., Schröder, E., Harris, J.R. and Poole, L.B. Structure, mechanism and regulation of peroxiredoxins. Trends Biochem. Sci. 28 (2003) 32–40. [DOI] [PMID: 12517450]
3.  Pedrajas, J.R., Padilla, C.A., McDonagh, B. and Barcena, J.A. Glutaredoxin participates in the reduction of peroxides by the mitochondrial 1-CYS peroxiredoxin in Saccharomyces cerevisiae. Antioxid Redox Signal 13 (2010) 249–258. [PMID: 20059400]
4.  Hanschmann, E.M., Lonn, M.E., Schutte, L.D., Funke, M., Godoy, J.R., Eitner, S., Hudemann, C. and Lillig, C.H. Both thioredoxin 2 and glutaredoxin 2 contribute to the reduction of the mitochondrial 2-Cys peroxiredoxin Prx3. J. Biol. Chem. 285 (2010) 40699–40705. [PMID: 20929858]
5.  Lim, J.G., Bang, Y.J. and Choi, S.H. Characterization of the Vibrio vulnificus 1-Cys peroxiredoxin Prx3 and regulation of its expression by the Fe-S cluster regulator IscR in response to oxidative stress and iron starvation. J. Biol. Chem. 289 (2014) 36263–36274. [PMID: 25398878]
6.  Couturier, J., Prosper, P., Winger, A.M., Hecker, A., Hirasawa, M., Knaff, D.B., Gans, P., Jacquot, J.P., Navaza, A., Haouz, A. and Rouhier, N. In the absence of thioredoxins, what are the reductants for peroxiredoxins in Thermotoga maritima. Antioxid Redox Signal 18 (2013) 1613–1622. [PMID: 22866991]
[EC 1.11.1.25 created 1983 as EC 1.11.1.15, part transferred 2020 to EC 1.11.1.25]
 
 
EC 1.11.1.26 – public review until 16 March 2020 [Last modified: 2020-02-18 05:35:47]
Accepted name: NADH-dependent peroxiredoxin
Reaction: NADH + ROOH + H+ = NAD+ + H2O + ROH
For diagram of reaction, click here and for mechanism, click here
Other name(s): ahpC (gene name); ahpF (gene name); alkyl hydroperoxide reductase
Systematic name: NADH:hydroperoxide oxidoreductase
Comments: Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant proteins. They can be divided into three classes: typical 2-Cys, atypical 2-Cys and 1-Cys peroxiredoxins [1]. The peroxidase reaction comprises two steps centred around a redox-active cysteine called the peroxidatic cysteine. All three peroxiredoxin classes have the first step in common, in which the peroxidatic cysteine attacks the peroxide substrate and is oxidized to S-hydroxycysteine (a sulfenic acid) (see mechanism). The second step of the peroxidase reaction, the regeneration of cysteine from S-hydroxycysteine, distinguishes the three peroxiredoxin classes. For typical 2-Cys Prxs, in the second step, the peroxidatic S-hydroxycysteine from one subunit is attacked by the ‘resolving’ cysteine located in the C-terminus of the second subunit, to form an intersubunit disulfide bond, which is then reduced by one of several cell-specific thiol-containing reductants completing the catalytic cycle. In the atypical 2-Cys Prxs, both the peroxidatic cysteine and its resolving cysteine are in the same polypeptide, so their reaction forms an intrachain disulfide bond. The 1-Cys Prxs conserve only the peroxidatic cysteine, so its regeneration involves direct interaction with a reductant molecule. This bacterial peroxiredoxin differs from most other forms by comprising two types of subunits. One subunit (AhpC) is a typical 2-Cys peroxiredoxin. Following the reduction of the substrate, one AhpC subunit forms a disulfide bond with an identical unit. The disulfide bond is reduced by the second type of subunit (AhpF). This second subunit is a flavin-containing protein that uses electrons from NADH to reduce the cysteine residues on the AhpC subunits back to their active state.
References:
1.  Wood, Z.A., Schröder, E., Harris, J.R. and Poole, L.B. Structure, mechanism and regulation of peroxiredoxins. Trends Biochem. Sci. 28 (2003) 32–40. [DOI] [PMID: 12517450]
2.  Dip, P.V., Kamariah, N., Subramanian Manimekalai, M.S., Nartey, W., Balakrishna, A.M., Eisenhaber, F., Eisenhaber, B. and Gruber, G. Structure, mechanism and ensemble formation of the alkylhydroperoxide reductase subunits AhpC and AhpF from Escherichia coli. Acta Crystallogr. D Biol. Crystallogr. 70 (2014) 2848–2862. [PMID: 25372677]
3.  Nartey, W., Basak, S., Kamariah, N., Manimekalai, M.S., Robson, S., Wagner, G., Eisenhaber, B., Eisenhaber, F. and Gruber, G. NMR studies reveal a novel grab and release mechanism for efficient catalysis of the bacterial 2-Cys peroxiredoxin machinery. FEBS J. 282 (2015) 4620–4638. [PMID: 26402142]
[EC 1.11.1.26 created 1983 as EC 1.11.1.15, part transferred 2020 to EC 1.11.1.26]
 
 
EC 1.11.1.27 – public review until 16 March 2020 [Last modified: 2020-02-20 09:11:02]
Accepted name: glutathione-dependent peroxiredoxin
Reaction: 2 glutathione + ROOH = glutathione disulfide + H2O + ROH
For diagram of reaction, click here and for mechanism, click here
Other name(s): PRDX6 (gene name); prx3 (gene name)
Systematic name: glutathione:hydroperoxide oxidoreductase
Comments: Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant proteins. They can be divided into three classes: typical 2-Cys, atypical 2-Cys and 1-Cys peroxiredoxins [1]. The peroxidase reaction comprises two steps centred around a redox-active cysteine called the peroxidatic cysteine. All three peroxiredoxin classes have the first step in common, in which the peroxidatic cysteine attacks the peroxide substrate and is oxidized to S-hydroxycysteine (a sulfenic acid) (see mechanism). The second step of the peroxidase reaction, the regeneration of cysteine from S-hydroxycysteine, distinguishes the three peroxiredoxin classes. For typical 2-Cys Prxs, in the second step, the peroxidatic S-hydroxycysteine from one subunit is attacked by the ‘resolving’ cysteine located in the C-terminus of the second subunit, to form an intersubunit disulfide bond, which is then reduced by one of several cell-specific thiol-containing reductants completing the catalytic cycle. In the atypical 2-Cys Prxs, both the peroxidatic cysteine and its resolving cysteine are in the same polypeptide, so their reaction forms an intrachain disulfide bond. The 1-Cys Prxs conserve only the peroxidatic cysteine, so its regeneration involves direct interaction with a reductant molecule. Glutathione-dependent peroxiredoxins have been reported from bacteria and animals, and appear to be 1-Cys enzymes. The mechanism for the mammalian PRDX6 enzyme involves heterodimerization of the enzyme with π-glutathione S-transferase, followed by glutathionylation of the oxidized cysteine residue. Subsequent dissociation of the heterodimer yields glutathionylated peroxiredoxin, which is restored to the active form via spontaneous reduction by a second glutathione molecule.
References:
1.  Wood, Z.A., Schröder, E., Harris, J.R. and Poole, L.B. Structure, mechanism and regulation of peroxiredoxins. Trends Biochem. Sci. 28 (2003) 32–40. [DOI] [PMID: 12517450]
2.  Pauwels, F., Vergauwen, B., Vanrobaeys, F., Devreese, B. and Van Beeumen, J.J. Purification and characterization of a chimeric enzyme from Haemophilus influenzae Rd that exhibits glutathione-dependent peroxidase activity. J. Biol. Chem. 278 (2003) 16658–16666. [PMID: 12606554]
3.  Manevich, Y., Feinstein, S.I. and Fisher, A.B. Activation of the antioxidant enzyme 1-CYS peroxiredoxin requires glutathionylation mediated by heterodimerization with π GST. Proc. Natl. Acad. Sci. USA 101 (2004) 3780–3785. [PMID: 15004285]
4.  Greetham, D. and Grant, C.M. Antioxidant activity of the yeast mitochondrial one-Cys peroxiredoxin is dependent on thioredoxin reductase and glutathione in vivo. Mol. Cell Biol. 29 (2009) 3229–3240. [PMID: 19332553]
5.  Lim, J.G., Bang, Y.J. and Choi, S.H. Characterization of the Vibrio vulnificus 1-Cys peroxiredoxin Prx3 and regulation of its expression by the Fe-S cluster regulator IscR in response to oxidative stress and iron starvation. J. Biol. Chem. 289 (2014) 36263–36274. [PMID: 25398878]
[EC 1.11.1.27 created 1983 as EC 1.11.1.15, part transferred 2020 to EC 1.11.1.27]
 
 
EC 1.11.1.28 – public review until 16 March 2020 [Last modified: 2020-02-18 05:37:00]
Accepted name: lipoyl-dependent peroxiredoxin
Reaction: a [lipoyl-carrier protein]-N6-[(R)-dihydrolipoyl]-L-lysine + ROOH = a [lipoyl-carrier protein]-N6-lipoyl-L-lysine + H2O + ROH
For diagram of reaction, click here and for mechanism, click here
Other name(s): Ohr; ahpC (gene name); ahpD (gene name)
Systematic name: lipoyl:hydroperoxide oxidoreductase
Comments: Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant proteins. They can be divided into three classes: typical 2-Cys, atypical 2-Cys and 1-Cys peroxiredoxins [2]. The peroxidase reaction comprises two steps centred around a redox-active cysteine called the peroxidatic cysteine. All three peroxiredoxin classes have the first step in common, in which the peroxidatic cysteine attacks the peroxide substrate and is oxidized to S-hydroxycysteine (a sulfenic acid) (see mechanism). The second step of the peroxidase reaction, the regeneration of cysteine from S-hydroxycysteine, distinguishes the three peroxiredoxin classes. For typical 2-Cys Prxs, in the second step, the peroxidatic S-hydroxycysteine from one subunit is attacked by the ‘resolving’ cysteine located in the C-terminus of the second subunit, to form an intersubunit disulfide bond, which is then reduced by one of several cell-specific thiol-containing reductants completing the catalytic cycle. In the atypical 2-Cys Prxs, both the peroxidatic cysteine and its resolving cysteine are in the same polypeptide, so their reaction forms an intrachain disulfide bond. The 1-Cys Prxs conserve only the peroxidatic cysteine, so its regeneration involves direct interaction with a reductant molecule. Two types of lipoyl-dependent peroxiredoxins have been reported from bacteria. One type is the AhpC/AhpD system, originally described from Mycobacterium tuberculosis. In that system, AhpC catalyses reduction of the substrate, resulting in an intramolecular disulfide. AhpD then forms an intermolecular disulfide crosslink with AhpC, reducing it back to active state. AhpD is reduced in turn by lipoylated proteins. The second type, which has been characterized in Xylella fastidiosa, consists of only one type of subunit, which interacts directly with lipoylated proteins.
References:
1.  Hillas, P.J., del Alba, F.S., Oyarzabal, J., Wilks, A. and Ortiz De Montellano, P.R. The AhpC and AhpD antioxidant defense system of Mycobacterium tuberculosis. J. Biol. Chem. 275 (2000) 18801–18809. [PMID: 10766746]
2.  Wood, Z.A., Schröder, E., Harris, J.R. and Poole, L.B. Structure, mechanism and regulation of peroxiredoxins. Trends Biochem. Sci. 28 (2003) 32–40. [DOI] [PMID: 12517450]
3.  Koshkin, A., Nunn, C.M., Djordjevic, S. and Ortiz de Montellano, P.R. The mechanism of Mycobacterium tuberculosis alkylhydroperoxidase AhpD as defined by mutagenesis, crystallography, and kinetics. J. Biol. Chem. 278 (2003) 29502–29508. [PMID: 12761216]
4.  Koshkin, A., Knudsen, G.M. and Ortiz De Montellano, P.R. Intermolecular interactions in the AhpC/AhpD antioxidant defense system of Mycobacterium tuberculosis. Arch. Biochem. Biophys. 427 (2004) 41–47. [PMID: 15178486]
5.  Shi, S. and Ehrt, S. Dihydrolipoamide acyltransferase is critical for Mycobacterium tuberculosis pathogenesis. Infect. Immun. 74 (2006) 56–63. [PMID: 16368957]
6.  Cussiol, J.R., Alegria, T.G., Szweda, L.I. and Netto, L.E. Ohr (organic hydroperoxide resistance protein) possesses a previously undescribed activity, lipoyl-dependent peroxidase. J. Biol. Chem. 285 (2010) 21943–21950. [PMID: 20463026]
[EC 1.11.1.28 created 1983 as EC 1.11.1.15, part transferred 2020 to EC 1.11.1.28]
 
 
EC 1.11.1.29 – public review until 16 March 2020 [Last modified: 2020-02-18 05:37:16]
Accepted name: mycoredoxin-dependent peroxiredoxin
Reaction: mycoredoxin + ROOH = mycoredoxin disulfide + H2O + ROH
For diagram of reaction, click here and for mechanism, click here
Other name(s): ahpE (gene name)
Systematic name: mycoredoxin:hydroperoxide oxidoreductase
Comments: Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant proteins. They can be divided into three classes: typical 2-Cys, atypical 2-Cys and 1-Cys peroxiredoxins [1]. The peroxidase reaction comprises two steps centred around a redox-active cysteine called the peroxidatic cysteine. All three peroxiredoxin classes have the first step in common, in which the peroxidatic cysteine attacks the peroxide substrate and is oxidized to S-hydroxycysteine (a sulfenic acid) (see mechanism). The second step of the peroxidase reaction, the regeneration of cysteine from S-hydroxycysteine, distinguishes the three peroxiredoxin classes. For typical 2-Cys Prxs, in the second step, the peroxidatic S-hydroxycysteine from one subunit is attacked by the ‘resolving’ cysteine located in the C-terminus of the second subunit, to form an intersubunit disulfide bond, which is then reduced by one of several cell-specific thiol-containing reductants completing the catalytic cycle. In the atypical 2-Cys Prxs, both the peroxidatic cysteine and its resolving cysteine are in the same polypeptide, so their reaction forms an intrachain disulfide bond. The 1-Cys Prxs conserve only the peroxidatic cysteine, so its regeneration involves direct interaction with a reductant molecule. Mycoredoxin-dependent enzymes are found in Mycobacteria. Following the reduction of the substrate, the sulfenic acid derivative of the peroxidatic cysteine forms a protein mixed disulfide with the N-terminal cysteine of mycoredoxin, which is then reduced by the C-terminal cysteine of mycoredoxin, restoring the peroxiredoxin to active state and resulting in an intra-protein disulfide in mycoredoxin. The disulfide is eventually reduced by mycothiol.
References:
1.  Wood, Z.A., Schröder, E., Harris, J.R. and Poole, L.B. Structure, mechanism and regulation of peroxiredoxins. Trends Biochem. Sci. 28 (2003) 32–40. [DOI] [PMID: 12517450]
2.  Hugo, M., Turell, L., Manta, B., Botti, H., Monteiro, G., Netto, L.E., Alvarez, B., Radi, R. and Trujillo, M. Thiol and sulfenic acid oxidation of AhpE, the one-cysteine peroxiredoxin from Mycobacterium tuberculosis: kinetics, acidity constants, and conformational dynamics. Biochemistry 48 (2009) 9416–9426. [PMID: 19737009]
3.  Hugo, M., Van Laer, K., Reyes, A.M., Vertommen, D., Messens, J., Radi, R. and Trujillo, M. Mycothiol/mycoredoxin 1-dependent reduction of the peroxiredoxin AhpE from Mycobacterium tuberculosis. J. Biol. Chem. 289 (2014) 5228–5239. [PMID: 24379404]
4.  Kumar, A., Balakrishna, A.M., Nartey, W., Manimekalai, M.SS. and Gruber, G. Redox chemistry of Mycobacterium tuberculosis alkylhydroperoxide reductase E (AhpE): Structural and mechanistic insight into a mycoredoxin-1 independent reductive pathway of AhpE via mycothiol. Free Radic. Biol. Med. 97 (2016) 588–601. [PMID: 27417938]
5.  Pedre, B., van Bergen, L.A., Pallo, A., Rosado, L.A., Dufe, V.T., Molle, I.V., Wahni, K., Erdogan, H., Alonso, M., Proft, F.D. and Messens, J. The active site architecture in peroxiredoxins: a case study on Mycobacterium tuberculosis AhpE. Chem. Commun. (Camb.) 52 (2016) 10293–10296. [PMID: 27471753]
[EC 1.11.1.29 created 1983 as EC 1.11.1.15, part transferred 2020 to EC 1.11.1.29]
 
 
*EC 1.14.16.5 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: alkylglycerol monooxygenase
Reaction: 1-O-alkyl-sn-glycerol + a 5,6,7,8-tetrahydropteridine + O2 = 1-O-(1-hydroxyalkyl)-sn-glycerol + a 4a-hydroxy-5,6,7,8-tetrahydropteridine
Other name(s): glyceryl-ether monooxygenase; glyceryl-ether cleaving enzyme; glyceryl ether oxygenase; glyceryl etherase; O-alkylglycerol monooxygenase
Systematic name: 1-alkyl-sn-glycerol,tetrahydrobiopteridine:oxygen oxidoreductase
Comments: The enzyme cleaves alkylglycerols, but does not cleave alkenylglycerols (plasmalogens). Requires non-heme iron [7], reduced glutathione and phospholipids for full activity. The product spontaneously breaks down to form a fatty aldehyde and glycerol. The co-product, 4a-hydroxytetrahydropteridine, is rapidly dehydrated to 6,7-dihydropteridine, either spontaneously or by EC 4.2.1.96, 4a-hydroxytetrahydrobiopterin dehydratase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37256-82-9
References:
1.  Ishibashi, T. and Imai, Y. Solubilization and partial characterization of alkylglycerol monooxygenase from rat liver microsomes. Eur. J. Biochem. 132 (1983) 23–27. [DOI] [PMID: 6840084]
2.  Pfleger, E.C., Piantadosi, C. and Snyder, F. The biocleavage of isomeric glyceryl ethers by soluble liver enzymes in a variety of species. Biochim. Biophys. Acta 144 (1967) 633–648. [DOI] [PMID: 4383918]
3.  Snyder, F., Malone, B. and Piantadosi, C. Tetrahydropteridine-dependent cleavage enzyme for O-alkyl lipids: substrate specificity. Biochim. Biophys. Acta 316 (1973) 259–265. [DOI] [PMID: 4355017]
4.  Soodsma, J.F., Piantadosi, C. and Snyder, F. Partial characterization of the alkylglycerol cleavage enzyme system of rat liver. J. Biol. Chem. 247 (1972) 3923–3929. [PMID: 4402391]
5.  Tietz, A., Lindberg, M. and Kennedy, E.P. A new pteridine-requiring enzyme system for the oxidation of glyceryl ethers. J. Biol. Chem. 239 (1964) 4081–4090. [PMID: 14247652]
6.  Taguchi, H. and Armarego, W.L. Glyceryl-ether monooxygenase [EC 1.14.16.5]. A microsomal enzyme of ether lipid metabolism. Med. Res. Rev. 18 (1998) 43–89. [DOI] [PMID: 9436181]
7.  Watschinger, K., Keller, M.A., Hermetter, A., Golderer, G., Werner-Felmayer, G. and Werner, E.R. Glyceryl ether monooxygenase resembles aromatic amino acid hydroxylases in metal ion and tetrahydrobiopterin dependence. Biol. Chem. 390 (2009) 3–10. [DOI] [PMID: 19007315]
8.  Werner, E.R., Hermetter, A., Prast, H., Golderer, G. and Werner-Felmayer, G. Widespread occurrence of glyceryl ether monooxygenase activity in rat tissues detected by a novel assay. J. Lipid Res. 48 (2007) 1422–1427. [DOI] [PMID: 17303893]
[EC 1.14.16.5 created 1972 as EC 1.14.99.17, transferred 1976 to EC 1.14.16.5, modified 2010, modified 2020]
 
 
*EC 1.14.16.6 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: mandelate 4-monooxygenase
Reaction: (S)-2-hydroxy-2-phenylacetate + a 5,6,7,8-tetrahydropteridine + O2 = (S)-4-hydroxymandelate + a 4a-hydroxy-5,6,7,8-tetrahydropteridine
Glossary: (S)-4-hydroxymandelate = (S)-2-hydroxy-2-(4-hydroxyphenyl)acetate
Other name(s): L-mandelate 4-hydroxylase; mandelic acid 4-hydroxylase
Systematic name: (S)-2-hydroxy-2-phenylacetate,tetrahydropteridine:oxygen oxidoreductase (4-hydroxylating)
Comments: Requires Fe2+. The enzyme has been characterized from the bacterium Pseudomonas putida. The 4a-hydroxytetrahydropteridine formed can dehydrate to 6,7-dihydropteridine, both spontaneously and by the action of EC 4.2.1.96, 4a-hydroxytetrahydrobiopterin dehydratase. The 6,7-dihydropteridine must be enzymically reduced back to tetrahydropteridine, by EC 1.5.1.34, 6,7-dihydropteridine reductase, before it slowly rearranges into the more stable but inactive compound 7,8-dihydropteridine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 39459-82-0
References:
1.  Bhat, S.G. and Vaidyanathan, C.S. Purifications and properties of L-mandelate-4-hydroxylase from Pseudomonas convexa. Arch. Biochem. Biophys. 176 (1976) 314–323. [DOI] [PMID: 9909]
[EC 1.14.16.6 created 1984, modified 2020]
 
 
*EC 1.14.17.1 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: dopamine β-monooxygenase
Reaction: dopamine + 2 ascorbate + O2 = noradrenaline + 2 monodehydroascorbate + H2O
For diagram of dopa biosynthesis, click here
Glossary: dopamine = 4-(2-aminoethyl)benzene-1,2-diol
Other name(s): dopamine β-hydroxylase; MDBH (membrane-associated dopamine β-monooxygenase); SDBH (soluble dopamine β-monooxygenase); dopamine-B-hydroxylase; 3,4-dihydroxyphenethylamine β-oxidase; 4-(2-aminoethyl)pyrocatechol β-oxidase; dopa β-hydroxylase; dopamine β-oxidase; dopamine hydroxylase; phenylamine β-hydroxylase; (3,4-dihydroxyphenethylamine)β-mono-oxygenase; DβM (gene name)
Systematic name: dopamine,ascorbate:oxygen oxidoreductase (β-hydroxylating)
Comments: A copper protein. The enzyme, found in animals, binds two copper ions with distinct roles during catalysis. Stimulated by fumarate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9013-38-1
References:
1.  Levin, E.Y., Levenberg, B. and Kaufman, S. The enzymatic conversion of 3,4-dihydroxyphenylethylamine to norepinephrine. J. Biol. Chem. 235 (1960) 2080–2086. [PMID: 14416204]
2.  Friedman, S. and Kaufman, S. 3,4-Dihydroxyphenylethylamine β-hydroxylase. Physical properties, copper content, and role of copper in the catalytic activity. J. Biol. Chem. 240 (1965) 4763–4773. [PMID: 5846992]
3.  Skotland, T. and Ljones, T. Direct spectrophotometric detection of ascorbate free radical formed by dopamine β-monooxygenase and by ascorbate oxidase. Biochim. Biophys. Acta 630 (1980) 30–35. [PMID: 7388045]
4.  Evans, J.P., Ahn, K. and Klinman, J.P. Evidence that dioxygen and substrate activation are tightly coupled in dopamine β-monooxygenase. Implications for the reactive oxygen species. J. Biol. Chem. 278 (2003) 49691–49698. [PMID: 12966104]
[EC 1.14.17.1 created 1965 as EC 1.14.2.1, transferred 1972 to EC 1.14.17.1, modified 2020]
 
 
EC 1.14.18.12 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: 2-hydroxy fatty acid dioxygenase
Reaction: a (2R)-2-hydroxy Cn-fatty acid + O2 = a Cn-1-fatty acid + H2O + CO2
Other name(s): MPO1 (gene name)
Systematic name: 2-hydroxy fatty acid:oxygen oxidoreductase (CO2,H2O-forming)
Comments: Requires Fe(II). The enzyme, characterized from yeast, is involved in phytosphingosine metabolism. The reaction is mediated by iron(IV) peroxide and results in the release of a water molecule and a carbon dioxide molecule, shortening the substrate by a single carbon atom and forming an odd-numbered fatty acid. Both oxygen atoms of the original carboxylate group are released - one as the leaving water molecule, the other as one of the oxygens of the carbon dioxide molecule. The two oxygen atoms in the newly-formed carboxylate originate from the 2-hydroxy group and from molecular oxygen, respectively. The other oxygen atom of the molecular oxygen is incorporated into the leaving CO2 molecule. The enzyme from the yeast Saccharomyces cerevisiae is active at least toward C14 to C26 2-hydroxy fatty acids, but not against C8 2-hydroxy fatty acid.
References:
1.  Kondo, N., Ohno, Y., Yamagata, M., Obara, T., Seki, N., Kitamura, T., Naganuma, T. and Kihara, A. Identification of the phytosphingosine metabolic pathway leading to odd-numbered fatty acids. Nat. Commun. 5:5338 (2014). [PMID: 25345524]
2.  Seki, N., Mori, K., Kitamura, T., Miyamoto, M. and Kihara, A. Yeast Mpo1 is a novel dioxygenase that catalyzes the α-oxidation of a 2-hydroxy fatty acid in an Fe2+-dependent manner. Mol. Cell Biol. 39:e00428-18 (2019). [DOI] [PMID: 30530523]
[EC 1.14.18.12 created 2020]
 
 
*EC 1.16.1.8 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: [methionine synthase] reductase
Reaction: 2 [methionine synthase]-methylcob(III)alamin + 2 S-adenosyl-L-homocysteine + NADP+ = 2 [methionine synthase]-cob(II)alamin + NADPH + H+ + 2 S-adenosyl-L-methionine
For diagram of reaction, click here
Other name(s): methionine synthase cob(II)alamin reductase (methylating); methionine synthase reductase; [methionine synthase]-cobalamin methyltransferase (cob(II)alamin reducing); [methionine synthase]-methylcob(I)alamin,S-adenosylhomocysteine:NADP+ oxidoreductase
Systematic name: [methionine synthase]-methylcob(III)alamin,S-adenosyl-L-homocysteine:NADP+ oxidoreductase
Comments: In humans, the enzyme is a flavoprotein containing FAD and FMN. The substrate of the enzyme is the inactivated cobalt(II) form of EC 2.1.1.13, methionine synthase. Electrons are transferred from NADPH to FAD to FMN. Defects in this enzyme lead to hereditary hyperhomocysteinemia.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 207004-87-3
References:
1.  Leclerc, D., Wilson, A., Dumas, R., Gafuik, C., Song, D., Watkins, D., Heng, H.H.Q., Rommens, J.M., Scherer, S.W., Rosenblatt, D.S., Gravel, R.A. Cloning and mapping of a cDNA for methionine synthase reductase, a flavoprotein defective in patients with homocystinuria. Proc. Natl. Acad. Sci. USA 95 (1998) 3059–3064. [DOI] [PMID: 9501215]
2.  Olteanu, H. and Banerjee, R. Human methionine synthase reductase, a soluble P-450 reductase-like dual flavoprotein, is sufficient for NADPH-dependent methionine synthase activation. J. Biol. Chem. 276 (2001) 35558–35563. [DOI] [PMID: 11466310]
3.  Olteanu, H., Munson, T. and Banerjee, R. Differences in the efficiency of reductive activation of methionine synthase and exogenous electron acceptors between the common polymorphic variants of human methionine synthase reductase. Biochemistry 41 (2002) 13378–13385. [DOI] [PMID: 12416982]
[EC 1.16.1.8 created 1999 as EC 2.1.1.135, transferred 2003 to EC 1.16.1.8, modified 2020]
 
 
*EC 1.17.1.8 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: 4-hydroxy-tetrahydrodipicolinate reductase
Reaction: (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)+ + H2O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H + H+
For diagram of lysine biosynthesis (early stages), click here
Glossary: (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate = (2S)-2,3,4,5-tetrahydrodipicolinate
Other name(s): dihydrodipicolinate reductase (incorrect); dihydrodipicolinic acid reductase (incorrect); 2,3,4,5-tetrahydrodipicolinate:NAD(P)+ oxidoreductase (incorrect); dapB (gene name)
Systematic name: (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate:NAD(P)+ 4-oxidoreductase
Comments: The substrate of the enzyme was initially thought to be (S)-2,3-dihydrodipicolinate [1], and the enzyme was classified accordingly as EC 1.3.1.26, dihydrodipicolinate reductase. Later studies of the enzyme from the bacterium Escherichia coli have suggested that the actual substrate of the enzyme is (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate, and that its activity includes a dehydration step [2], and thus the enzyme has been reclassified as 4-hydroxy-tetrahydrodipicolinate reductase. However, the identity of the substrate is still controversial, as more recently it has been suggested that it may be (S)-2,3-dihydrodipicolinate after all [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Farkas, W. and Gilvarg, C. The reduction step in diaminopimelic acid biosynthesis. J. Biol. Chem. 240 (1965) 4717–4722. [PMID: 4378965]
2.  Devenish, S.R., Blunt, J.W. and Gerrard, J.A. NMR studies uncover alternate substrates for dihydrodipicolinate synthase and suggest that dihydrodipicolinate reductase is also a dehydratase. J. Med. Chem. 53 (2010) 4808–4812. [DOI] [PMID: 20503968]
3.  Karsten, W.E., Nimmo, S.A., Liu, J. and Chooback, L. Identification of 2,3-dihydrodipicolinate as the product of the dihydrodipicolinate synthase reaction from Escherichia coli. Arch. Biochem. Biophys. 653 (2018) 50–62. [PMID: 29944868]
[EC 1.17.1.8 created 1976 as EC 1.3.1.26, transferred 2013 to EC 1.17.1.8, modified 2020]
 
 
EC 1.17.99.8 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: limonene dehydrogenase
Reaction: (1) (S)-limonene + H2O + acceptor = (–)-perillyl alcohol + reduced acceptor
(2) (R)-limonene + H2O + acceptor = (+)-perillyl alcohol + reduced acceptor
Glossary: limonene = 1-methyl-4-(prop-1-en-2-yl)cyclohex-1-ene
perillyl alcohol = [4-(prop-1-en-2-yl)cyclohex-1-en-1-yl]methanol
(–)-perillyl alcohol = (S)-perillyl alcohol = [(4S)-4-(prop-1-en-2-yl)cyclohex-1-en-1-yl]methanol
(+)-perillyl alcohol = (R)-perillyl alcohol = [(4R)-4-(prop-1-en-2-yl)cyclohex-1-en-1-yl]methanol
(–)-limonene = (S)-limonene = (4S)-1-methyl-4-(prop-1-en-2-yl)cyclohexene
(+)-limonene = (R)-limonene = (4R)-1-methyl-4-(prop-1-en-2-yl)cyclohexene
Other name(s): ctmAB (gene names)
Systematic name: limonene:acceptor oxidoreductase (7-hydroxylating)
Comments: Contains FAD. The enzyme, characterized from the bacterium Castellaniella defragrans 65Phen, hydroxylates the R- and S-enantiomers at a similar rate. The in vivo electron acceptor may be a heterodimeric electron transfer flavoprotein (ETF).
References:
1.  Petasch, J., Disch, E.M., Markert, S., Becher, D., Schweder, T., Huttel, B., Reinhardt, R. and Harder, J. The oxygen-independent metabolism of cyclic monoterpenes in Castellaniella defragrans 65Phen. BMC Microbiol. 14:164 (2014). [PMID: 24952578]
2.  Puentes-Cala, E., Liebeke, M., Markert, S. and Harder, J. Limonene dehydrogenase hydroxylates the allylic methyl group of cyclic monoterpenes in the anaerobic terpene degradation by Castellaniella defragrans. J. Biol. Chem. 293 (2018) 9520–9529. [PMID: 29716998]
[EC 1.17.99.8 created 2020]
 
 
*EC 1.20.4.1 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: arsenate reductase (glutathione/glutaredoxin)
Reaction: arsenate + glutathione + glutaredoxin = arsenite + a glutaredoxin-glutathione disulfide + H2O
For diagram of arsenate catabolism, click here
Other name(s): ArsC (ambiguous); arsenate:glutaredoxin oxidoreductase; arsenate reductase (glutaredoxin)
Systematic name: arsenate:glutathione/glutaredoxin oxidoreductase
Comments: The enzyme is part of a system for detoxifying arsenate. The substrate binds to a catalytic cysteine residue, forming a covalent thiolate—As(V) intermediate. A tertiary intermediate is then formed between the arsenic, the enzyme’s cysteine, and a glutathione cysteine. This intermediate is reduced by glutaredoxin, which forms a dithiol with the glutathione, leading to the dissociation of arsenite. Thus reduction of As(V) is mediated by three cysteine residues: one in ArsC, one in glutathione, and one in glutaredoxin. Although the arsenite formed is more toxic than arsenate, it can be extruded from some bacteria by EC 7.3.2.7, arsenite-transporting ATPase; in other organisms, arsenite can be methylated by EC 2.1.1.137, arsenite methyltransferase, in a pathway that produces non-toxic organoarsenical compounds. cf. EC 1.20.4.4, arsenate reductase (thioredoxin).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, UM-BBD, CAS registry number: 146907-46-2
References:
1.  Gladysheva, T., Liu, J.Y. and Rosen, B.P. His-8 lowers the pKa of the essential Cys-12 residue of the ArsC arsenate reductase of plasmid R773. J. Biol. Chem. 271 (1996) 33256–33260. [DOI] [PMID: 8969183]
2.  Gladysheva, T.B., Oden, K.L. and Rosen, B.P. Properties of the arsenate reductase of plasmid R773. Biochemistry 33 (1994) 7288–7293. [PMID: 8003492]
3.  Holmgren, A. and Aslund, F. Glutaredoxin. Methods Enzymol. 252 (1995) 283–292. [DOI] [PMID: 7476363]
4.  Krafft, T. and Macy, J.M. Purification and characterization of the respiratory arsenate reductase of Chrysiogenes arsenatis. Eur. J. Biochem. 255 (1998) 647–653. [DOI] [PMID: 9738904]
5.  Martin, J.L. Thioredoxin - a fold for all reasons. Structure 3 (1995) 245–250. [DOI] [PMID: 7788290]
6.  Radabaugh, T.R. and Aposhian, H.V. Enzymatic reduction of arsenic compounds in mammalian systems: reduction of arsenate to arsenite by human liver arsenate reductase. Chem. Res. Toxicol. 13 (2000) 26–30. [DOI] [PMID: 10649963]
7.  Sato, T. and Kobayashi, Y. The ars operon in the skin element of Bacillus subtilis confers resistance to arsenate and arsenite. J. Bacteriol. 180 (1998) 1655–1661. [PMID: 9537360]
8.  Shi, J., Vlamis-Gardikas, V., Aslund, F., Holmgren, A. and Rosen, B.P. Reactivity of glutaredoxins 1, 2, and 3 from Escherichia coli shows that glutaredoxin 2 is the primary hydrogen donor to ArsC-catalyzed arsenate reduction. J. Biol. Chem. 274 (1999) 36039–36042. [DOI] [PMID: 10593884]
9.  Mukhopadhyay, R. and Rosen, B.P. Arsenate reductases in prokaryotes and eukaryotes. Environ Health Perspect 110 Suppl 5 (2002) 745–748. [PMID: 12426124]
10.  Messens, J. and Silver, S. Arsenate reduction: thiol cascade chemistry with convergent evolution. J. Mol. Biol. 362 (2006) 1–17. [PMID: 16905151]
[EC 1.20.4.1 created 2000 as EC 1.97.1.5, transferred 2001 to EC 1.20.4.1, modified 2015, modified 2019, modified 2020]
 
 
*EC 2.4.2.42 – public review until 16 March 2020 [Last modified: 2020-02-19 05:47:04]
Accepted name: UDP-D-xylose:β-D-glucoside α-1,3-D-xylosyltransferase
Reaction: UDP-α-D-xylose + [protein with EGF-like domain]-3-O-(β-D-glucosyl)-L-serine = UDP + [protein with EGF-like domain]-3-O-[α-D-xylosyl-(1→3)-β-D-glucosyl]-L-serine
Other name(s): β-glucoside α-1,3-xylosyltransferase; UDP-α-D-xylose:β-D-glucoside 3-α-D-xylosyltransferase; GXYLT1 (gene name); GXYLT2 (gene name)
Systematic name: UDP-α-D-xylose:[protein with EGF-like domain]-3-O-(β-D-glucosyl)-L-serine 3-α-D-xylosyltransferase (configuration-retaining)
Comments: The enzyme, found in animals and insects, is involved in the biosynthesis of the α-D-xylosyl-(1→3)-α-D-xylosyl-(1→3)-β-D-glucosyl trisaccharide on epidermal growth factor-like (EGF-like) domains [2,3]. When present on Notch proteins, the trisaccharide functions as a modulator of the signalling activity of this protein.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Omichi, K., Aoki, K., Minamida, S. and Hase, S. Presence of UDP-D-xylose: β-D-glucoside α-1,3-D-xylosyltransferase involved in the biosynthesis of the Xyl α 1-3Glc β-Ser structure of glycoproteins in the human hepatoma cell line HepG2. Eur. J. Biochem. 245 (1997) 143–146. [DOI] [PMID: 9128735]
2.  Ishimizu, T., Sano, K., Uchida, T., Teshima, H., Omichi, K., Hojo, H., Nakahara, Y. and Hase, S. Purification and substrate specificity of UDP-D-xylose:β-D-glucoside α-1,3-D-xylosyltransferase involved in the biosynthesis of the Xyl α1-3Xyl α1-3Glc β1-O-Ser on epidermal growth factor-like domains. J. Biochem. 141 (2007) 593–600. [DOI] [PMID: 17317689]
3.  Sethi, M.K., Buettner, F.F., Krylov, V.B., Takeuchi, H., Nifantiev, N.E., Haltiwanger, R.S., Gerardy-Schahn, R. and Bakker, H. Identification of glycosyltransferase 8 family members as xylosyltransferases acting on O-glucosylated notch epidermal growth factor repeats. J. Biol. Chem. 285 (2010) 1582–1586. [PMID: 19940119]
[EC 2.4.2.42 created 2010, modified 2020]
 
 
*EC 2.7.1.8 – public review until 16 March 2020 [Last modified: 2020-02-17 12:42:26]
Accepted name: glucosamine kinase
Reaction: ATP + D-glucosamine = ADP + D-glucosamine 6-phosphate
Glossary: D-glucosamine 6-phosphate = 2-amino-2-deoxy-D-glucose 6-phosphate
Other name(s): glucosamine kinase (phosphorylating); ATP:2-amino-2-deoxy-D-glucose-6-phosphotransferase; aminodeoxyglucose kinase; ATP:D-glucosamine phosphotransferase
Systematic name: ATP:D-glucosamine 6-phosphotransferase
Comments: The enzyme is specific for glucosamine and has only a minor activity with D-glucose. Two unrelated enzymes with this activity have been described. One type was studied in the bacterium Vibrio cholerae, where it participates in a chitin degradation pathway. The other type has been described from actinobacteria, where it is involved in the incorporation of environmental glucosamine into antibiotic biosynthesis pathways. cf. EC 2.7.1.147, ADP-specific glucose/glucosamine kinase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9031-90-7
References:
1.  Bueding, E. and MacKinnon, J.A. Hexokinases of Schistosoma mansoni. J. Biol. Chem. 215 (1955) 495–506. [PMID: 13242546]
2.  Park, J.K., Wang, L.X. and Roseman, S. Isolation of a glucosamine-specific kinase, a unique enzyme of Vibrio cholerae. J. Biol. Chem. 277 (2002) 15573–15578. [DOI] [PMID: 11850417]
3.  Manso, J.A., Nunes-Costa, D., Macedo-Ribeiro, S., Empadinhas, N. and Pereira, P.J.B. Molecular fingerprints for a novel enzyme family in actinobacteria with glucosamine kinase activity. MBio 10:e00239-19 (2019). [PMID: 31088917]
[EC 2.7.1.8 created 1961, modified 2014, modified 2020]
 
 
*EC 2.7.1.147 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: ADP-specific glucose/glucosamine kinase
Reaction: (1) ADP + D-glucose = AMP + D-glucose 6-phosphate
(2) ADP + D-glucosamine = AMP + D-glucosamine 6-phosphate
Other name(s): ADP-specific glucokinase; ADP-dependent glucokinase
Systematic name: ADP:D-glucose/D-glucosamine 6-phosphotransferase
Comments: Requires Mg2+. The enzyme, characterized from a number of hyperthermophilic archaeal species, is highly specific for ADP. No activity is detected when ADP is replaced by ATP, GDP, phosphoenolpyruvate, diphosphate or polyphosphate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 173585-07-4
References:
1.  Kengen, S.W., Tuininga, J.E., de Bok, F.A., Stams, A.J. and de Vos, W.M. Purification and characterization of a novel ADP-dependent glucokinase from the hyperthermophilic archaeon Pyrococcus furiosus. J. Biol. Chem. 270 (1995) 30453–30457. [DOI] [PMID: 8530474]
2.  Koga, S., Yoshioka, I., Sakuraba, H., Takahashi, M., Sakasegawa, S., Shimizu, S. and Ohshima, T. Biochemical characterization, cloning, and sequencing of ADP-dependent (AMP-forming) glucokinase from two hyperthermophilic archaea, Pyrococcus furiosus and Thermococcus litoralis. J. Biochem. 128 (2000) 1079–1085. [PMID: 11098152]
3.  Aslam, M., Takahashi, N., Matsubara, K., Imanaka, T., Kanai, T. and Atomi, H. Identification of the glucosamine kinase in the chitinolytic pathway of Thermococcus kodakarensis. J. Biosci. Bioeng. 125:S1389-1723( (2018). [PMID: 29146530]
[EC 2.7.1.147 created 2001, modified 2020]
 
 
EC 2.7.2.17 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: [amino group carrier protein]-L-2-aminoadipate 6-kinase
Reaction: ATP + an [amino group carrier protein]-C-terminal-N-(1,4-dicarboxybutan-1-yl)-L-glutamine = ADP + phosphate + an [amino group carrier protein]-C-terminal-N-(1-carboxy-5-phosphooxy-5-oxopentan-1-yl)-L-glutamine
Other name(s): lysZ (gene name)
Systematic name: [amino group carrier protein]-C-terminal-N-(1,4-dicarboxybutan-1-yl)-L-glutamine 5-O-kinase
Comments: The enzyme participates in an L-lysine biosynthetric pathway in certain species of bacteria and archaea.
References:
1.  Nishida, H., Nishiyama, M., Kobashi, N., Kosuge, T., Hoshino, T. and Yamane, H. A prokaryotic gene cluster involved in synthesis of lysine through the amino adipate pathway: a key to the evolution of amino acid biosynthesis. Genome Res. 9 (1999) 1175–1183. [PMID: 10613839]
2.  Horie, A., Tomita, T., Saiki, A., Kono, H., Taka, H., Mineki, R., Fujimura, T., Nishiyama, C., Kuzuyama, T. and Nishiyama, M. Discovery of proteinaceous N-modification in lysine biosynthesis of Thermus thermophilus. Nat. Chem. Biol. 5 (2009) 673–679. [DOI] [PMID: 19620981]
3.  Ouchi, T., Tomita, T., Horie, A., Yoshida, A., Takahashi, K., Nishida, H., Lassak, K., Taka, H., Mineki, R., Fujimura, T., Kosono, S., Nishiyama, C., Masui, R., Kuramitsu, S., Albers, S.V., Kuzuyama, T. and Nishiyama, M. Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus. Nat. Chem. Biol. 9 (2013) 277–283. [DOI] [PMID: 23434852]
[EC 2.7.2.17 created 2020]
 
 
*EC 2.7.7.2 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: FAD synthase
Reaction: ATP + FMN = diphosphate + FAD
For diagram of FAD biosynthesis, click here
Other name(s): FAD pyrophosphorylase; riboflavin mononucleotide adenylyltransferase; adenosine triphosphate-riboflavin mononucleotide transadenylase; adenosine triphosphate-riboflavine mononucleotide transadenylase; riboflavin adenine dinucleotide pyrophosphorylase; riboflavine adenine dinucleotide adenylyltransferase; flavin adenine dinucleotide synthetase; FADS; FMN adenylyltransferase; FAD synthetase (misleading)
Systematic name: ATP:FMN adenylyltransferase
Comments: Requires Mg2+ and is highly specific for ATP as phosphate donor [5]. The cofactors FMN and FAD participate in numerous processes in all organisms, including mitochondrial electron transport, photosynthesis, fatty-acid oxidation, and metabolism of vitamin B6, vitamin B12 and folates [3]. While monofunctional FAD synthetase is found in eukaryotes and in some prokaryotes, most prokaryotes have a bifunctional enzyme that exhibits both this activity and that of EC 2.7.1.26, riboflavin kinase [3,5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9026-37-3
References:
1.  Giri, K.V., Rao, N.A., Cama, H.R. and Kumar, S.A. Studies on flavinadenine dinucleotide-synthesizing enzyme in plants. Biochem. J. 75 (1960) 381–386. [PMID: 13828163]
2.  Schrecker, A.W. and Kornberg, A. Reversible enzymatic synthesis of flavin-adenine dinucleotide. J. Biol. Chem. 182 (1950) 795–803. [PMID: 19994476]
3.  Sandoval, F.J. and Roje, S. An FMN hydrolase is fused to a riboflavin kinase homolog in plants. J. Biol. Chem. 280 (2005) 38337–38345. [DOI] [PMID: 16183635]
4.  Oka, M. and McCormick, D.B. Complete purification and general characterization of FAD synthetase from rat liver. J. Biol. Chem. 262 (1987) 7418–7422. [PMID: 3034893]
5.  Brizio, C., Galluccio, M., Wait, R., Torchetti, E.M., Bafunno, V., Accardi, R., Gianazza, E., Indiveri, C. and Barile, M. Over-expression in Escherichia coli and characterization of two recombinant isoforms of human FAD synthetase. Biochem. Biophys. Res. Commun. 344 (2006) 1008–1016. [DOI] [PMID: 16643857]
[EC 2.7.7.2 created 1961, modified 2007, modified 2020]
 
 
EC 2.8.3.26 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: succinyl-CoA:mesaconate CoA transferase
Reaction: succinyl-CoA + mesaconate = 2-methylfumaryl-CoA + succinate
Glossary: 2-methylfumaryl-CoA = (E)-3-carboxy-2-methylprop-2-enoyl-CoA
mesaconate = 2-methylbut-2-enedioic acid
Other name(s): mct (gene name)
Systematic name: succinyl-CoA:mesaconate CoA transferase
Comments: The enzyme participates in the methylaspartate cycle, an anaplerotic pathway that operates in some members of the haloarchaea and forms malate from acetyl-CoA.
References:
1.  Khomyakova, M., Bukmez, O., Thomas, L.K., Erb, T.J. and Berg, I.A. A methylaspartate cycle in haloarchaea. Science 331 (2011) 334–337. [PMID: 21252347]
2.  Borjian, F., Johnsen, U., Schonheit, P. and Berg, I.A. Succinyl-CoA:mesaconate CoA-transferase and mesaconyl-CoA hydratase, enzymes of the methylaspartate cycle in Haloarcula hispanica. Front. Microbiol. 8:1683 (2017). [PMID: 28932214]
[EC 2.8.3.26 created 2020]
 
 
EC 2.9.1.3 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: tRNA 2-selenouridine synthase
Reaction: selenophosphate + geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA + H2O = 5-methylaminomethyl-2-selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol + diphosphate + phosphate (overall reaction)
(1a) geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA = 5-methylaminomethyl-2-(S-geranyl)thiouridine34 in tRNA + diphosphate
(1b) selenophosphate + 5-methylaminomethyl-2-(S-geranyl)thiouridine34 in tRNA = 5-methylaminomethyl-2-(Se-phospho)selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol
(1c) 5-methylaminomethyl-2-(Se-phospho)selenouridine34 in tRNA + H2O = 5-methylaminomethyl-2-selenouridine34 in tRNA + phosphate
Other name(s): selU (gene name); mnmH (gene name); ybbB (gene name); sufY (gene name)
Systematic name: geranyl diphosphate/selenophosphate:tRNA 5-methylaminomethyl-2-thiouridine34 geranyl/selenophosphatetransferase
Comments: This bacterial enzyme converts 5-methylaminomethyl-2-uridine and 5-carboxymethylaminomethyl-2-uridine to the respective selenouridine forms in a two-step process that involves geranylation and subsequent phosphoselenation of the resulting geranylated intermediates. The resultant seleno-phosphorylated uridine intermediates further react with a water molecule to release a phosphate anion and 2-selenouridine tRNA. The enzyme contains a rhodanese domain.
References:
1.  Bartos, P., Maciaszek, A., Rosinska, A., Sochacka, E. and Nawrot, B. Transformation of a wobble 2-thiouridine to 2-selenouridine via S-geranyl-2-thiouridine as a possible cellular pathway. Bioorg. Chem. 56 (2014) 49–53. [PMID: 24971911]
2.  Jager, G., Chen, P. and Bjork, G.R. Transfer RNA bound to mnmh protein is enriched with geranylated tRNA—a possible intermediate in its selenation. PLoS One 11:e0153488 (2016). [PMID: 27073879]
3.  Sierant, M., Leszczynska, G., Sadowska, K., Komar, P., Radzikowska-Cieciura, E., Sochacka, E. and Nawrot, B. Escherichia coli tRNA 2-selenouridine synthase (SelU) converts S2U-RNA to Se2U-RNA via S-geranylated-intermediate. FEBS Lett. 592 (2018) 2248–2258. [PMID: 29862510]
[EC 2.9.1.3 created 2020]
 
 
EC 3.1.3.108 – public review until 16 March 2020 [Last modified: 2020-02-19 09:44:51]
Accepted name: nocturnin
Reaction: (1) NADPH + H2O = NADH + phosphate
(2) NADP+ + H2O = NAD+ + phosphate
Other name(s): NOCT (gene name); nocturnin (curled); MJ0109 (gene name); NADP phosphatase; NADPase
Systematic name: NADPH 2′-phosphohydrolase
Comments: The mammalian mitochondrial enzyme is a rhythmically expressed protein that regulates metabolism under the control of circadian clock. It has a slight preference for NADPH over NADP+. The archaeal enzyme, identified in Methanocaldococcus jannaschii, is bifunctional acting as NAD+ kinase (EC 2.7.1.23) and NADP+ phosphatase with a slight preference for NADP+ over NADPH.
References:
1.  Kawai, S. and Murata, K. Structure and function of NAD kinase and NADP phosphatase: key enzymes that regulate the intracellular balance of NAD(H) and NADP(H). Biosci. Biotechnol. Biochem. 72 (2008) 919–930. [DOI] [PMID: 18391451]
2.  Abshire, E.T., Chasseur, J., Bohn, J.A., Del Rizzo, P.A., Freddolino, P.L., Goldstrohm, A.C. and Trievel, R.C. The structure of human nocturnin reveals a conserved ribonuclease domain that represses target transcript translation and abundance in cells. Nucleic Acids Res. 46 (2018) 6257–6270. [PMID: 29860338]
3.  Estrella, M.A., Du, J. and Korennykh, A. Crystal structure of human nocturnin catalytic domain. Sci. Rep. 8:16294 (2018). [PMID: 30389976]
4.  Estrella, M.A., Du, J., Chen, L., Rath, S., Prangley, E., Chitrakar, A., Aoki, T., Schedl, P., Rabinowitz, J. and Korennykh, A. The metabolites NADP+ and NADPH are the targets of the circadian protein nocturnin (curled). Nat. Commun. 10:2367 (2019). [PMID: 31147539]
[EC 3.1.3.108 created 2020]
 
 
EC 3.1.27.3 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Transferred entry: ribonuclease T1. Now EC 4.6.1.24, ribonuclease T1, since the primary reaction is that of a lyase
[EC 3.1.27.3 created 1961 as EC 3.1.4.8, transferred 1965 to EC 2.7.7.26, reinstated 1972 as EC 3.1.4.8, transferred 1978 to EC 3.1.27.3, deleted 2020]
 
 
EC 3.2.1.44 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Transferred entry: fucoidanase. Now EC 3.2.1.211, endo-(13)-fucoidanase and EC 3.2.1.212, endo-(14)-fucoidanase
[EC 3.2.1.44 created 1972, deleted 2020]
 
 
*EC 3.2.1.155 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: xyloglucan-specific endo-processive β-1,4-glucanase
Reaction: Hydrolysis of (1→4)-D-glucosidic linkages in xyloglucans so as to successively remove oligosaccharides from the newly-formed chain end after endo-initiation on a polymer molecule
Other name(s): Cel74A; [(1→6)-α-D-xylo]-(1→4)-β-D-glucan exo-glucohydrolase (ambiguous); xyloglucan-specific exo-β-1,4-glucanase (ambiguous)
Systematic name: [(1→6)-α-D-xylo]-(1→4)-β-D-glucan endo-processive glucohydrolase
Comments: The enzyme removes branched oligosaccharides, containing preferentially four glucoside residues in the main chain, from xyloglucan molecules in a processive manner after the initial endo-type attack on a polysaccharide [1-5]. Hydrolysis occurs at either the unsubstituted D-glucopyranose residue in the main backbone and/or the D-glucopyranose residue bearing a xylosyl group [1-5]. The enzyme does not display activity, or shows very low activity, towards other β-D-glucans [1,2,4,5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 1000598-79-7
References:
1.  Grishutin, S.G., Gusakov, A.V., Markov, A.V., Ustinov, B.B., Semenova, M.V. and Sinitsyn, A.P. Specific xyloglucanases as a new class of polysaccharide-degrading enzymes. Biochim. Biophys. Acta 1674 (2004) 268–281. [DOI] [PMID: 15541296]
2.  Ichinose, H., Araki, Y., Michikawa, M., Harazono, K., Yaoi, K., Karita, S. and Kaneko, S. Characterization of an endo-processive-type xyloglucanase having a β-1,4-glucan-binding module and an endo-type xyloglucanase from Streptomyces avermitilis. Appl. Environ. Microbiol. 78 (2012) 7939–7945. [PMID: 22941084]
3.  Matsuzawa, T., Saito, Y. and Yaoi, K. Key amino acid residues for the endo-processive activity of GH74 xyloglucanase. FEBS Lett. 588 (2014) 1731–1738. [PMID: 24657616]
4.  Arnal, G., Stogios, P.J., Asohan, J., Skarina, T., Savchenko, A. and Brumer, H. Structural enzymology reveals the molecular basis of substrate regiospecificity and processivity of an exemplar bacterial glycoside hydrolase family 74 endo-xyloglucanase. Biochem. J. 475 (2018) 3963–3978. [PMID: 30463871]
5.  Arnal, G., Stogios, P.J., Asohan, J., Attia, M.A., Skarina, T., Viborg, A.H., Henrissat, B., Savchenko, A. and Brumer, H. Substrate specificity, regiospecificity, and processivity in glycoside hydrolase family 74. J. Biol. Chem. 294 (2019) 13233–13247. [PMID: 31324716]
6.  Gusakov, A.V. Additional sequence and structural characterization of an endo-processive GH74 xyloglucanase from Myceliophthora thermophila and the revision of the EC 3.2.1.155 entry. Biochim. Biophys. Acta. 1864:129511 (2020). [PMID: 31911243]
[EC 3.2.1.155 created 2005, withdrawn at public-review stage, modified and reinstated 2006, modified 2020]
 
 
EC 3.2.1.211 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: endo-(1→3)-fucoidanase
Reaction: endohydrolysis of (1→3)-α-L-fucoside linkages in fucan
Other name(s): α-L-fucosidase (incorrect); poly(1,3-α-L-fucoside-2/4-sulfate) glycanohydrolase
Systematic name: poly[(1→3)-α-L-fucoside-2/4-sulfate] glycanohydrolase
Comments: The enzyme specifically hydrolyses (1→3)-α-L-fucoside linkages in fucan. Fucans are found mainly in different species of seaweed and are sulfated polysaccharides with a backbone of (1→3)-linked or alternating (1→3)- and (1→4)-linked α-L-fucopyranosyl residues. In the literature, the sulfated polysaccharides are often called fucoidans. Fucoidans include polysaccharides with a relatively low proportion of fucose and some polysaccharides that have a backbone composed of other saccharides with fucose in the branching side chains. The sulfation of the α-L-fucopyranosyl residues may occur at positions 2 and 4. The enzyme degrades fucan to sulfated α-L-fucooligosaccharides but neither L-fucose nor small fucooligosaccharides are produced.
References:
1.  Thanassi, N.M. and Nakada, H.I. Enzymic degradation of fucoidan by enzymes from the hepatopancreas of abalone, Halotus species. Arch. Biochem. Biophys. 118 (1967) 172–177.
2.  Bakunina, I.Iu, Nedashkovskaia, O.I., Alekseeva, S.A., Ivanova, E.P., Romanenko, L.A., Gorshkova, N.M., Isakov, V.V., Zviagintseva, T.N. and Mikhailov, V.V. [Degradation of fucoidan by the marine proteobacterium Pseudoalteromonas citrea] Mikrobiologiia 71 (2002) 49–55. [PMID: 11910806] (in Russian)
3.  Berteau, O. and Mulloy, B. Sulfated fucans, fresh perspectives: structures, functions, and biological properties of sulfated fucans and an overview of enzymes active toward this class of polysaccharide. Glycobiology 13 (2003) 29R–40R. [PMID: 12626402]
4.  Bilan, M.I., Kusaykin, M.I., Grachev, A.A., Tsvetkova, E.A., Zvyagintseva, T.N., Nifantiev, N.E. and Usov, A.I. Effect of enzyme preparation from the marine mollusk Littorina kurila on fucoidan from the brown alga Fucus distichus. Biochemistry (Mosc.) 70 (2005) 1321–1326. [PMID: 16417453]
[EC 3.2.1.211 created 1972 as EC 3.2.1.44, part transferred 2020 to EC 3.2.1.211 ]
 
 
EC 3.2.1.212 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: endo-(1→4)-fucoidanase
Reaction: endohydrolysis of (1→4)-α-L-fucoside linkages in fucan
Other name(s): α-L-fucosidase (incorrect); poly(1,4-α-L-fucoside-2/3-sulfate) glycanohydrolase
Systematic name: poly[(1→4)-α-L-fucoside-2/3-sulfate] glycanohydrolase
Comments: The enzyme specifically hydrolyses (1→4)-α-L-fucoside linkages in fucan. Fucans are found mainly in different species of seaweed and are sulfated polysaccharides with a backbone of (1→3)-linked or alternating (1→3)- and (1→4)-linked α-L-fucopyranosyl residues. In the literature, the sulfated polysaccharides are often called fucoidans. Fucoidans include polysaccharides with a relatively low proportion of fucose and some polysaccharides that have a backbone composed of other saccharides with fucose in the branching side chains. The sulfation of the α-L-fucopyranosyl residues may occur at positions 2 and 3. The enzyme degrades fucan to sulfated α-L-fucooligosaccharides but neither L-fucose nor small fucooligosaccharides are produced.
References:
1.  Thanassi, N.M. and Nakada, H.I. Enzymic degradation of fucoidan by enzymes from the hepatopancreas of abalone, Halotus species. Arch. Biochem. Biophys. 118 (1967) 172–177.
2.  Berteau, O. and Mulloy, B. Sulfated fucans, fresh perspectives: structures, functions, and biological properties of sulfated fucans and an overview of enzymes active toward this class of polysaccharide. Glycobiology 13 (2003) 29R–40R. [PMID: 12626402]
3.  Descamps, V., Colin, S., Lahaye, M., Jam, M., Richard, C., Potin, P., Barbeyron, T., Yvin, J.C. and Kloareg, B. Isolation and culture of a marine bacterium degrading the sulfated fucans from marine brown algae. Mar Biotechnol (NY) 8 (2006) 27–39. [PMID: 16222488]
4.  Kim, W.J., Kim, S.M., Lee, Y.H., Kim, H.G., Kim, H.K., Moon, S.H., Suh, H.H., Jang, K.H. and Park, Y.I. Isolation and characterization of marine bacterial strain degrading fucoidan from Korean Undaria pinnatifida Sporophylls. J. Microbiol. Biotechnol. 18 (2008) 616–623. [PMID: 18467852]
5.  Silchenko, A.S., Kusaykin, M.I., Kurilenko, V.V., Zakharenko, A.M., Isakov, V.V., Zaporozhets, T.S., Gazha, A.K. and Zvyagintseva, T.N. Hydrolysis of fucoidan by fucoidanase isolated from the marine bacterium, Formosa algae. Mar. Drugs 11 (2013) 2413–2430. [PMID: 23852092]
6.  Silchenko, A.S., Kusaykin, M.I., Zakharenko, A.M., Menshova, R.V., Khanh, H.H.N., Dmitrenok, P.S., Isakov, V.V., Zvyagintseva, T.N. Endo-1,4-fucoidanase from vietnamese marine mollusk Lambis sp. which producing sulphated fucooligosaccharides. J. Mol. Catal. B 102 (2014) 154–160.
7.  Silchenko, A.S., Ustyuzhanina, N.E., Kusaykin, M.I., Krylov, V.B., Shashkov, A.S., Dmitrenok, A.S., Usoltseva, R.V., Zueva, A.O., Nifantiev, N.E. and Zvyagintseva, T.N. Expression and biochemical characterization and substrate specificity of the fucoidanase from Formosa algae. Glycobiology 27 (2017) 254–263. [PMID: 28031251]
[EC 3.2.1.212 created 1972 as EC 3.2.1.44, part transferred 2020 to EC 3.2.1.212]
 
 
EC 3.2.1.213 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: galactan exo-1,6-β-galactobiohydrolase (non-reducing end)
Reaction: Hydrolysis of (1→6)-β-D-galactosidic linkages in arabinogalactan proteins and (1→3):(1→6)-β-galactans to yield (1→6)-β-galactobiose as the final product.
Other name(s): exo-β-1,6-galactobiohydrolase; 1,6Gal (gene name)
Systematic name: exo-β-(1→6)-galactobiohydrolase (non-reducing end)
Comments: The enzyme, characterized from the bacterium Bifidobacterium longum, specifically hydrolyses (1→6)-β-galactobiose from the non-reducing terminal of (1→6)-β-D-galactooligosaccharides with a degree of polymerization (DP) of 3 or higher, using an exo mode of action. The enzyme cannot hydrolyse α-L-arabinofuranosylated (1→6)-β-galactans (as found in arabinogalactans) and does not act on (1→3)-β-D- or (1→4)-β-D-galactans. cf. EC 3.2.1.164, galactan endo-1,6-β-galactosidase.
References:
1.  Fujita, K., Sakamoto, A., Kaneko, S., Kotake, T., Tsumuraya, Y. and Kitahara, K. Degradative enzymes for type II arabinogalactan side chains in Bifidobacterium longum subsp. longum. Appl. Microbiol. Biotechnol. 103 (2019) 1299–1310. [PMID: 30564851]
[EC 3.2.1.213 created 2020]
 
 
EC 3.4.17.24 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: tubulin-glutamate carboxypeptidase
Reaction: This is a subfamily of enzymes that cleave C-terminal and/or side chain amino acids from tubulins. The dual-specificity enzymes can cleave both α- and γ-linked L-glutamate from tubulins, removing the posttranslationally added polyglutamyl side chains from the C-terminal regions. In addition, the enzyme removes two glutamate residues from the C-terminus of β-tubulin and detyrosinated α-tubulin (from which the C-terminal L-tyrosine has been removed by EC 3.4.17.17, tubulinyl-Tyr carboxypeptidase). The latter is cleaved to δ2-tubulin and further to δ3-tubulin.
Other name(s): cytosolic carboxypeptidase 1; cytosolic carboxypeptidase 5; CCP1; CCP5; Agtpbp1 (gene name); AGBL5 (gene name)
References:
1.  Rogowski, K., van Dijk, J., Magiera, M.M., Bosc, C., Deloulme, J.C., Bosson, A., Peris, L., Gold, N.D., Lacroix, B., Bosch Grau, M., Bec, N., Larroque, C., Desagher, S., Holzer, M., Andrieux, A., Moutin, M.J. and Janke, C. A family of protein-deglutamylating enzymes associated with neurodegeneration. Cell 143 (2010) 564–578. [PMID: 21074048]
2.  Kimura, Y., Kurabe, N., Ikegami, K., Tsutsumi, K., Konishi, Y., Kaplan, O.I., Kunitomo, H., Iino, Y., Blacque, O.E. and Setou, M. Identification of tubulin deglutamylase among Caenorhabditis elegans and mammalian cytosolic carboxypeptidases (CCPs). J. Biol. Chem. 285 (2010) 22936–22941. [PMID: 20519502]
3.  Berezniuk, I., Vu, H.T., Lyons, P.J., Sironi, J.J., Xiao, H., Burd, B., Setou, M., Angeletti, R.H., Ikegami, K. and Fricker, L.D. Cytosolic carboxypeptidase 1 is involved in processing α- and β-tubulin. J. Biol. Chem. 287 (2012) 6503–6517. [PMID: 22170066]
4.  Berezniuk, I., Lyons, P.J., Sironi, J.J., Xiao, H., Setou, M., Angeletti, R.H., Ikegami, K. and Fricker, L.D. Cytosolic carboxypeptidase 5 removes α- and γ-linked glutamates from tubulin. J. Biol. Chem. 288 (2013) 30445–30453. [PMID: 24022482]
5.  Pathak, N., Austin-Tse, C.A., Liu, Y., Vasilyev, A. and Drummond, I.A. Cytoplasmic carboxypeptidase 5 regulates tubulin glutamylation and zebrafish cilia formation and function. Mol. Biol. Cell 25 (2014) 1836–1844. [PMID: 24743595]
[EC 3.4.17.24 created 2020]
 
 
EC 3.6.1.73 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: inosine/xanthosine triphosphatase
Reaction: (1) inosine 5′-triphosphate + H2O = inosine 5′-diphosphate + phosphate
(2) xanthosine 5′-triphosphate + H2O = xanthosine 5′-diphosphate + phosphate
Glossary: inosine 5′-triphosphate = ITP
xanthosine 5′-triphosphate = XTP
Other name(s): yjjX (gene name)
Systematic name: inosine/xanthosine 5′-triphosphate phosphohydrolase
Comments: The enzyme, characterized from the bacterium Escherichia coli, preferentially hydrolyses inosine triphosphate and xanthosine triphosphate, which are formed by oxidative deamination damage. By hydrolysing these damaged nucleotides, the enzyme prevents their incorporation into RNA.
References:
1.  Zheng, J., Singh, V.K. and Jia, Z. Identification of an ITPase/XTPase in Escherichia coli by structural and biochemical analysis. Structure 13 (2005) 1511–1520. [PMID: 16216582]
[EC 3.6.1.73 created 2020]
 
 
EC 3.7.1.26 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: 2,4-didehydro-3-deoxy-L-rhamnonate hydrolase
Reaction: 2,4-didehydro-3-deoxy-L-rhamnonate + H2O = pyruvate + (S)-lactate
Other name(s): L-2,4-diketo-3-deoxyrhamnonate hydrolase; lra6 (gene name)
Systematic name: 2,4-didehydro-3-deoxy-L-rhamnonate hydrolase
Comments: The enzyme, characterized from the bacterium Sphingomonas sp. SKA58, participates in an L-rhamnose degradation pathway.
References:
1.  Watanabe, S. and Makino, K. Novel modified version of nonphosphorylated sugar metabolism - an alternative L-rhamnose pathway of Sphingomonas sp. FEBS J. 276 (2009) 1554–1567. [DOI] [PMID: 19187228]
[EC 3.7.1.26 created 2020]
 
 
EC 3.13.1.9 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: S-inosyl-L-homocysteine hydrolase
Reaction: S-inosyl-L-homocysteine + H2O = inosine + L-homocysteine
Other name(s): SIHH
Systematic name: S-inosyl-L-homocysteine hydrolase (inosine-forming)
Comments: The enzyme, characterized from the methanogenic archaeon Methanocaldococcus jannaschii, binds an NAD+ cofactor. It participates in an alternative pathway for the regeneration of S-adenosyl-L-methionine from S-adenosyl-L-homocysteine that involves the deamination of the latter to S-inosyl-L-homocysteine.
References:
1.  Miller, D., Xu, H. and White, R.H. S-inosyl-L-homocysteine hydrolase, a novel enzyme involved in S-adenosyl-L-methionine recycling. J. Bacteriol. 197 (2015) 2284–2291. [PMID: 25917907]
[EC 3.13.1.9 created 2020]
 
 
EC 4.1.2.41 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Transferred entry: vanillin synthase. Now included with EC 4.1.2.61, feruloyl-CoA hydratase/lyase
[EC 4.1.2.41 created 2000, deleted 2019]
 
 
EC 4.1.2.61 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: feruloyl-CoA hydratase/lyase
Reaction: feruloyl-CoA + H2O = vanillin + acetyl-CoA (overall reaction)
(1a) feruloyl-CoA + H2O = 3-hydroxy-3-(4-hydroxy-3-methoxyphenyl)propanoyl-CoA
(1b) 3-hydroxy-3-(4-hydroxy-3-methoxyphenyl)propanoyl-CoA = vanillin + acetyl-CoA
Other name(s): hydroxycinnamoyl-CoA hydratase lyase; enoyl-CoA hydratase/aldolase; HCHL; ferB (gene name); couA (gene name)
Systematic name: feruloyl-CoA hydro-lyase/vanillin-lyase (acetyl-CoA-forming)
Comments: The enzyme is a member of the enoyl-CoA hydratase/isomerase superfamily. It catalyses a two-step process involving first the hydration of the double bond of feruloyl-CoA and then the cleavage of the resultant β-hydroxy thioester by retro-aldol reaction. (E)-caffeoyl-CoA and (E)-4-coumaroyl-CoA are also substrates.
References:
1.  Pometto, A.L. and Crawford, D.L. Whole-cell bioconversion of vanillin to vanillic acid by Streptomyces viridosporus. Appl. Environ. Microbiol. 45 (1983) 1582–1585. [PMID: 6870241]
2.  Narbad, A. and Gasson, M.J. Metabolism of ferulic acid via vanillin using a novel CoA-dependent pathway in a newly-isolated strain of Pseudomonas fluorescens. Microbiology 144 (1998) 1397–1405. [DOI] [PMID: 9611814]
3.  Gasson, M.J., Kitamura, Y., McLauchlan, W.R., Narbad, A., Parr, A.J., Parsons, E.L., Payne, J., Rhodes, M.J. and Walton, N.J. Metabolism of ferulic acid to vanillin. A bacterial gene of the enoyl-SCoA hydratase/isomerase superfamily encodes an enzyme for the hydration and cleavage of a hydroxycinnamic acid SCoA thioester. J. Biol. Chem. 273 (1998) 4163–4170. [PMID: 9461612]
4.  Overhage, J., Priefert, H. and Steinbuchel, A. Biochemical and genetic analyses of ferulic acid catabolism in Pseudomonas sp. Strain HR199. Appl. Environ. Microbiol. 65 (1999) 4837–4847. [PMID: 10543794]
5.  Bennett, J.P., Bertin, L., Moulton, B., Fairlamb, I.J., Brzozowski, A.M., Walton, N.J. and Grogan, G. A ternary complex of hydroxycinnamoyl-CoA hydratase-lyase (HCHL) with acetyl-CoA and vanillin gives insights into substrate specificity and mechanism. Biochem. J. 414 (2008) 281–289. [PMID: 18479250]
6.  Hirakawa, H., Schaefer, A.L., Greenberg, E.P. and Harwood, C.S. Anaerobic p-coumarate degradation by Rhodopseudomonas palustris and identification of CouR, a MarR repressor protein that binds p-coumaroyl coenzyme A. J. Bacteriol. 194 (2012) 1960–1967. [PMID: 22328668]
7.  Yang, W., Tang, H., Ni, J., Wu, Q., Hua, D., Tao, F. and Xu, P. Characterization of two Streptomyces enzymes that convert ferulic acid to vanillin. PLoS One 8:e67339 (2013). [PMID: 23840666]
[EC 4.1.2.61 created 2020 (EC 4.1.2.41 created 2000, incorporated 2020, EC 4.2.1.101 created 2000, incorporated 2020)]
 
 
*EC 4.2.1.96 – public review until 16 March 2020 [Last modified: 2020-02-19 09:43:57]
Accepted name: 4a-hydroxytetrahydrobiopterin dehydratase
Reaction: 4a-hydroxytetrahydrobiopterin = 6,7-dihydrobiopterin + H2O
For diagram of biopterin biosynthesis, click here
Glossary: 4a-hydroxytetrahydrobiopterin = 6-[(1R,2S)-1,2-dihydroxypropyl]-5,6,7,8-tetrahydro-4a-hydroxypterin
6,7-dihydrobiopterin = 6-[(1R,2S)-1,2-dihydroxypropyl]-6,7-dihydropterin
Other name(s): 4α-hydroxy-tetrahydropterin dehydratase; 4a-carbinolamine dehydratase; pterin-4α-carbinolamine dehydratase; 4a-hydroxytetrahydrobiopterin hydro-lyase
Systematic name: 4a-hydroxytetrahydrobiopterin hydro-lyase (6,7-dihydrobiopterin-forming)
Comments: In concert with EC 1.5.1.34, 6,7-dihydropteridine reductase, the enzyme recycles 4a-hydroxytetrahydrobiopterin back to tetrahydrobiopterin, a cosubstrate for several enzymes, including aromatic amino acid hydroxylases. The enzyme is bifunctional, and also acts as a dimerization cofactor of hepatocyte nuclear factor-1α (HNF-1).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 87683-70-3
References:
1.  Citron, B.A., Davis, M.D., Milstien, S., Gutierrez, J., Mendel, D.B., Crabtree, G.R. and Kaufman, S. Identity of 4a-carbinolamine dehydratase, a component of the phenylalanine hydroxylation system, and DCoH, a transregulator of homeodomain proteins. Proc. Natl. Acad. Sci. USA 89 (1992) 11891–11894. [PMID: 1465414]
2.  Hauer, C.R., Rebrin, I., Thöny, B., Neuheiser, F., Curtius, H.C., Hunziker, P., Blau, N., Ghisla, S., Heizmann, C.W. Phenylalanine hydroxylase-stimulating protein: pterin-4α-carbinolamine dehydratase from rat and human liver. J. Biol. Chem. 268 (1993) 4828–4831. [PMID: 8444860]
3.  Thony, B., Neuheiser, F., Blau, N. and Heizmann, C.W. Characterization of the human PCBD gene encoding the bifunctional protein pterin-4 α-carbinolamine dehydratase/dimerization cofactor for the transcription factor HNF-1 α. Biochem. Biophys. Res. Commun. 210 (1995) 966–973. [PMID: 7763270]
4.  Endrizzi, J.A., Cronk, J.D., Wang, W., Crabtree, G.R. and Alber, T. Crystal structure of DCoH, a bifunctional, protein-binding transcriptional coactivator. Science 268 (1995) 556–559. [PMID: 7725101]
5.  Cronk, J.D., Endrizzi, J.A. and Alber, T. High-resolution structures of the bifunctional enzyme and transcriptional coactivator DCoH and its complex with a product analogue. Protein Sci. 5 (1996) 1963–1972. [PMID: 8897596]
[EC 4.2.1.96 created 1999, modified 2020]
 
 
EC 4.2.1.101 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Transferred entry: trans-feruloyl-CoA hydratase. Now included with EC 4.1.2.61, feruloyl-CoA hydratase/lyase
[EC 4.2.1.101 created 2000, deleted 2020]
 
 
EC 4.2.2.27 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: pectin monosaccharide-lyase
Reaction: (1,4-α-D-galacturonosyl methyl ester)n = (1,4-α-D-galacturonosyl methyl ester)n-1 + 4-deoxy-6-O-methyl-L-threo-hex-4-enopyranuronate
Other name(s): exo-pectin lyase; PLIII
Systematic name: poly(1,4-α-D-galacturonosyl methyl ester) non-reducing-end-monosaccharide-lyase
Comments: The enzyme, isolated from the fungus Aspergillus giganteus, acts on the non-reducing end of methyl-esterified polygalacturonan, releasing either 4-deoxy--L-threo-hex-4-enopyranuronate or 4-deoxy-6-O-methyl-L-threo-hex-4-enopyranuronate. The enzyme is stimulated by divalent cations, with Co2+ having the strongest effect. It is able to act on substrates as short as a disaccharide, and was active on substrates with degrees of methyl esterification ranging between 34% and 90%.
References:
1.  Pedrolli, D.B. and Carmona, E.C. Purification and characterization of a unique pectin lyase from Aspergillus giganteus able to release unsaturated monogalacturonate during pectin degradation. Enzyme Res. 2014:353915 (2014). [PMID: 25610636]
[EC 4.2.2.27 created 2020]
 
 
*EC 4.3.3.7 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: 4-hydroxy-tetrahydrodipicolinate synthase
Reaction: pyruvate + L-aspartate-4-semialdehyde = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O
For diagram of lysine biosynthesis (early stages), click here
Glossary: (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate
Other name(s): dihydrodipicolinate synthase (incorrect); dihydropicolinate synthetase (incorrect); dihydrodipicolinic acid synthase (incorrect); L-aspartate-4-semialdehyde hydro-lyase (adding pyruvate and cyclizing); dapA (gene name).
Systematic name: L-aspartate-4-semialdehyde hydro-lyase [adding pyruvate and cyclizing; (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate-forming]
Comments: The reaction can be divided into three consecutive steps: Schiff base formation with pyruvate, the addition of L-aspartate-semialdehyde, and finally transimination leading to cyclization with simultaneous dissociation of the product. The product of the enzyme was initially thought to be (S)-2,3-dihydrodipicolinate [1,2], and the enzyme was classified accordingly as EC 4.2.1.52, dihydrodipicolinate synthase. Later studies of the enzyme from the bacterium Escherichia coli have suggested that the actual product of the enzyme is (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate [3], and thus the enzyme has been reclassified as 4-hydroxy-tetrahydrodipicolinate synthase. However, the identity of the product is still controversial, as more recently it has been suggested that it may be (S)-2,3-dihydrodipicolinate after all [5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Yugari, Y. and Gilvarg, C. The condensation step in diaminopimelate synthesis. J. Biol. Chem. 240 (1965) 4710–4716. [PMID: 5321309]
2.  Blickling, S., Renner, C., Laber, B., Pohlenz, H.D., Holak, T.A. and Huber, R. Reaction mechanism of Escherichia coli dihydrodipicolinate synthase investigated by X-ray crystallography and NMR spectroscopy. Biochemistry 36 (1997) 24–33. [DOI] [PMID: 8993314]
3.  Devenish, S.R., Blunt, J.W. and Gerrard, J.A. NMR studies uncover alternate substrates for dihydrodipicolinate synthase and suggest that dihydrodipicolinate reductase is also a dehydratase. J. Med. Chem. 53 (2010) 4808–4812. [DOI] [PMID: 20503968]
4.  Soares da Costa, T.P., Muscroft-Taylor, A.C., Dobson, R.C., Devenish, S.R., Jameson, G.B. and Gerrard, J.A. How essential is the ’essential’ active-site lysine in dihydrodipicolinate synthase. Biochimie 92 (2010) 837–845. [DOI] [PMID: 20353808]
5.  Karsten, W.E., Nimmo, S.A., Liu, J. and Chooback, L. Identification of 2,3-dihydrodipicolinate as the product of the dihydrodipicolinate synthase reaction from Escherichia coli. Arch. Biochem. Biophys. 653 (2018) 50–62. [PMID: 29944868]
[EC 4.3.3.7 created 1972 as EC 4.2.1.52, transferred 2012 to EC 4.3.3.7, modified 2020]
 
 
EC 4.6.1.24 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: ribonuclease T1
Reaction: [RNA] containing guanosine + H2O = an [RNA fragment]-3′-guanosine-3′-phosphate + a 5′-hydroxy-ribonucleotide-3′-[RNA fragment] (overall reaction)
(1a) [RNA] containing guanosine = [RNA fragment]-3′-guanosine-2′,3′-cyclophosphate + a 5′-hydroxy-ribonucleotide-3′-[RNA fragment]
(1b) [RNA fragment]-3′-guanosine-2′,3′-cyclophosphate + H2O = [RNA fragment]-3′-guanosine-3′-phosphate
Other name(s): barnase; bacterial ribonuclease Sa; guanyloribonuclease; Aspergillus oryzae ribonuclease; RNase N1; RNase N2; ribonuclease N3; ribonuclease U1; ribonuclease F1; ribonuclease Ch; ribonuclease PP1; ribonuclease SA; RNase F1; ribonuclease C2; binase; RNase Sa; guanyl-specific RNase; RNase G; RNase T1; ribonuclease guaninenucleotido-2′-transferase (cyclizing); ribonuclease N1
Systematic name: [RNA]-guanosine 5′-hydroxy-ribonucleotide-3′-[RNA fragment]-lyase (cyclicizing; [RNA fragment]-3′-guanosine-2′,3′-cyclophosphate-forming and hydrolysing)
Comments: A family of related enzymes found in some fungi and bacteria. The enzyme is specific for cleavage at the 3′-phosphate group of guanosine in single stranded RNA, and catalyses a two-stage endonucleolytic cleavage. The first reaction produces 5′-hydroxy-phosphooligonucletides and 3′-phosphooligonucleotides ending in Gp with 2′,3′-cyclic phosphodiester, which are released from the enzyme. The enzyme then hydrolyses these cyclic compounds in a second reaction that takes place only when all the susceptible 3′,5′-phosphodiester bonds have been cyclised. The second reaction is a reversal of the first reaction using the hydroxyl group of water instead of the 5′-hydroxyl group of ribose. The overall process is that of a phosphorus-oxygen lyase followed by hydrolysis to form the 3′-nucleotides.
References:
1.  Takahashi, K. The structure and function of ribonuclease T1. I. Chromatographic purification and properties of ribonuclease T1. J. Biochem. (Tokyo) 49 (1961) 1–8.
2.  Kasai, K., Uchida, T., Egami, F., Yoshida, K. and Nomoto, M. Purification and crystallization of ribonuclease N1 from Neurospora crassa. J. Biochem. (Tokyo) 66 (1969) 389–396. [PMID: 5348588]
3.  Loverix, S., Laus, G., Martins, J.C., Wyns, L. and Steyaert, J. Reconsidering the energetics of ribonuclease catalysed RNA hydrolysis. Eur. J. Biochem. 257 (1998) 286–290. [PMID: 9799130]
[EC 4.6.1.24 created 1961 as EC 3.1.4.8, transferred 1965 to EC 2.7.7.26, reinstated 1972 as EC 3.1.4.8, transferred 1978 to EC 3.1.27.3, transferred 2020 to EC 4.6.1.24]
 
 
EC 4.6.1.25 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: bacteriophage T4 restriction endoribonuclease RegB
Reaction: a [pre-mRNA]-containing guanosine-adenosine + H2O = a 5′ hydroxy-guanosine-[pre-mRNA fragment] + a [pre-mRNA fragment]-3′-adenosine-3′-phosphate
(1a) a [pre-mRNA]-containing guanosine-adenosine + H2O = a 5′ hydroxy-guanosine-[pre-mRNA fragment] + a [pre-mRNA fragment]-adenosine-2′,3′-cyclophosphate
(1b) a [pre-mRNA fragment]- adenosine-2′,3′-cyclophosphate + H2O = a [pre-mRNAfragment]-3′-adenosine-3′-phosphate
Other name(s): RegB
Systematic name: [pre-mRNA]-guanosine-adenosine 5′-hydroxy-guanosine-ribonucleotide-3′-[RNA fragment]-lyase (cyclicizing; [RNA fragment]-3′- adenosine -2′,3′-cyclophosphate-forming and hydrolysing)
Comments: The enzyme from bacteriophage T4 cleaves early mRNAs between Ap and Gp at one specific specific GpGpApGp site, favouring their further transition to middle-phase mRNA. The activity is enhanced by Ribosomal S1 protein. The enzyme catalyses a two-stage endonucleolytic cleavage. The first reaction produces 5′-hydroxy-phosphooligonucletides and 3′-phosphooligonucleotides ending with 2′,3′-cyclic phosphodiester, which are released from the enzyme. The enzyme then hydrolyses these cyclic compounds in a second reaction that takes place only when all the susceptible 3′,5′-phosphodiester bonds have been cyclised. The second reaction is a reversal of the first reaction using the hydroxyl group of water instead of the 5′-hydroxyl group of ribose. The overall process is that of a phosphorus-oxygen lyase followed by hydrolysis to form the 3′-nucleotides.
References:
1.  Sanson, B., Hu, R.M., Troitskayadagger, E., Mathy, N. and Uzan, M. Endoribonuclease RegB from bacteriophage T4 is necessary for the degradation of early but not middle or late mRNAs. J. Mol. Biol. 297 (2000) 1063–1074. [PMID: 10764573]
2.  Saida, F., Uzan, M. and Bontems, F. The phage T4 restriction endoribonuclease RegB: a cyclizing enzyme that requires two histidines to be fully active. Nucleic Acids Res. 31 (2003) 2751–2758. [PMID: 12771201]
3.  Odaert, B., Saida, F., Aliprandi, P., Durand, S., Crechet, J.B., Guerois, R., Laalami, S., Uzan, M. and Bontems, F. Structural and functional studies of RegB, a new member of a family of sequence-specific ribonucleases involved in mRNA inactivation on the ribosome. J. Biol. Chem. 282 (2007) 2019–2028. [PMID: 17046813]
[EC 4.6.1.25 created 2020]
 
 
EC 6.2.1.62 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: 3,4-dihydroxybenzoate—[aryl-carrier protein] ligase
Reaction: ATP + 3,4-dihydroxybenzoate + holo-[aryl-carrier protein] = AMP + diphosphate + 3,4-dihydroxybenzoyl-[aryl-carrier protein] (overall reaction)
(1a) ATP + 3,4-dihydroxybenzoate = diphosphate + (3,4-dihydroxybenzoyl)adenylate
(1b) (3,4-dihydroxybenzoyl)adenylate + holo-[aryl-carrier protein] = AMP + 3,4-dihydroxybenzoyl-[aryl-carrier protein]
Other name(s): asbC (gene name)
Systematic name: 3,4-dihydroxybenzoate:[aryl-carrier protein] ligase (AMP-forming)
Comments: The adenylation domain of the enzyme catalyses the activation of 3,4-dihydroxybenzoate to (3,4-dihydroxybenzoyl)adenylate, followed by the transfer of the activated compound to the free thiol of a phosphopantetheine arm of an aryl-carrier protein domain. The aryl-carrier protein domain may be part of the same protein, or of a different protein. This activity is often found as part of a larger non-ribosomal peptide synthase.
References:
1.  Pfleger, B.F., Lee, J.Y., Somu, R.V., Aldrich, C.C., Hanna, P.C. and Sherman, D.H. Characterization and analysis of early enzymes for petrobactin biosynthesis in Bacillus anthracis. Biochemistry 46 (2007) 4147–4157. [PMID: 17346033]
[EC 6.2.1.62 created 2020]
 
 
EC 6.2.1.63 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: L-arginine—[L-arginyl-carrier protein] ligase
Reaction: ATP + L-arginine + holo-[L-arginyl-carrier protein] = AMP + diphosphate + L-arginyl-[L-arginyl-carrier protein] (overall reaction)
(1a) ATP + L-arginine = diphosphate + (L-arginyl)adenylate
(1b) (L-arginyl)adenylate + holo-[L-arginyl-carrier protein] = AMP + L-arginyl-[L-arginyl-carrier protein]
Other name(s): vabF (gene name)
Systematic name: L-arginine:[L-arginyl-carrier protein] ligase (AMP-forming)
Comments: The adenylation domain of the enzyme catalyses the activation of L-arginine to (L-arginyl)adenylate, followed by the transfer of the activated compound to the free thiol of a phosphopantetheine arm of a peptidyl-carrier protein domain. The peptidyl-carrier protein domain may be part of the same protein, or of a different protein. This activity is often found as part of a larger non-ribosomal peptide synthase.
References:
1.  Balado, M., Osorio, C.R. and Lemos, M.L. A gene cluster involved in the biosynthesis of vanchrobactin, a chromosome-encoded siderophore produced by Vibrio anguillarum. Microbiology 152 (2006) 3517–3528. [PMID: 17159203]
[EC 6.2.1.63 created 2020]
 
 
*EC 7.1.1.7 – public review until 16 March 2020 [Last modified: 2020-02-17 04:39:16]
Accepted name: quinol oxidase (electrogenic, proton-motive force generating)
Reaction: 2 quinol + O2[side 2] + 4 H+[side 2] = 2 quinone + 2 H2O[side 2] + 4 H+[side 1] (overall reaction)
(1a) 2 quinol = 2 quinone + 4 H+[side 1] + 4 e-
(1b) O2[side 2] + 4 H+[side 2] + 4 e- = 2 H2O[side 2]
Other name(s): cydAB (gene names); appBC (gene names); cytochrome bd oxidase; cytochrome bd-I oxidase; cytochrome bd-II oxidase; ubiquinol:O2 oxidoreductase (electrogenic, non H+-transporting); ubiquinol oxidase (electrogenic, proton-motive force generating); ubiquinol oxidase (electrogenic, non H+-transporting)
Systematic name: quinol:oxygen oxidoreductase (electrogenic, non H+-transporting)
Comments: This terminal oxidase enzyme is unable to pump protons but generates a proton motive force by transmembrane charge separation resulting from utilizing protons and electrons originating from opposite sides of the membrane to generate water. The bioenergetic efficiency (the number of charges driven across the membrane per electron used to reduce oxygen to water) is 1. The bd-I oxidase from the bacterium Escherichia coli is the predominant respiratory oxygen reductase that functions under microaerophilic conditions in that organism. cf. EC 7.1.1.3, ubiquinol oxidase (H+-transporting).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Miller, M.J., Hermodson, M. and Gennis, R.B. The active form of the cytochrome d terminal oxidase complex of Escherichia coli is a heterodimer containing one copy of each of the two subunits. J. Biol. Chem. 263 (1988) 5235–5240. [PMID: 3281937]
2.  Puustinen, A., Finel, M., Haltia, T., Gennis, R.B. and Wikstrom, M. Properties of the two terminal oxidases of Escherichia coli. Biochemistry 30 (1991) 3936–3942. [PMID: 1850294]
3.  Belevich, I., Borisov, V.B., Zhang, J., Yang, K., Konstantinov, A.A., Gennis, R.B. and Verkhovsky, M.I. Time-resolved electrometric and optical studies on cytochrome bd suggest a mechanism of electron-proton coupling in the di-heme active site. Proc. Natl. Acad. Sci. USA 102 (2005) 3657–3662. [DOI] [PMID: 15728392]
4.  Lenn, T., Leake, M.C. and Mullineaux, C.W. Clustering and dynamics of cytochrome bd-I complexes in the Escherichia coli plasma membrane in vivo. Mol. Microbiol. 70 (2008) 1397–1407. [DOI] [PMID: 19019148]
5.  Shepherd, M., Sanguinetti, G., Cook, G.M. and Poole, R.K. Compensations for diminished terminal oxidase activity in Escherichia coli: cytochrome bd-II-mediated respiration and glutamate metabolism. J. Biol. Chem. 285 (2010) 18464–18472. [DOI] [PMID: 20392690]
6.  Borisov, V.B., Murali, R., Verkhovskaya, M.L., Bloch, D.A., Han, H., Gennis, R.B. and Verkhovsky, M.I. Aerobic respiratory chain of Escherichia coli is not allowed to work in fully uncoupled mode. Proc. Natl. Acad. Sci. USA 108 (2011) 17320–17324. [DOI] [PMID: 21987791]
7.  Borisov, V.B., Gennis, R.B., Hemp, J. and Verkhovsky, M.I. The cytochrome bd respiratory oxygen reductases. Biochim. Biophys. Acta 1807 (2011) 1398–1413. [PMID: 21756872]
[EC 7.1.1.7 created 2014 as EC 1.10.3.14, modified 2017, transferred 2018 to EC 7.1.1.7, modified 2020]
 
 


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