The Enzyme Database

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EC 1.1.4.1      
Transferred entry: vitamin-K-epoxide reductase (warfarin-sensitive). Now EC 1.17.4.4, vitamin-K-epoxide reductase (warfarin-sensitive)
[EC 1.1.4.1 created 1989, deleted 2014]
 
 
EC 1.1.4.2      
Transferred entry: vitamin-K-epoxide reductase (warfarin-insensitive). Now EC 1.17.4.5, vitamin-K-epoxide reductase (warfarin-insensitive)
[EC 1.1.4.2 created 1989, deleted 2014]
 
 
EC 1.8.3.7     
Accepted name: formylglycine-generating enzyme
Reaction: a [sulfatase]-L-cysteine + O2 + 2 a thiol = a [sulfatase]-3-oxo-L-alanine + hydrogen sulfide + a disulfide + H2O
Glossary: 3-oxo-L-alanine = formylglycine = Cα-formylglycine = FGly
Other name(s): sulfatase-modifying factor 1; Cα-formylglycine-generating enzyme 1; SUMF1 (gene name)
Systematic name: [sulfatase]-L-cysteine:oxygen oxidoreductase (3-oxo-L-alanine-forming)
Comments: Requires a copper cofactor and Ca2+. The enzyme, which is found in both prokaryotes and eukaryotes, catalyses a modification of a conserved L-cysteine residue in the active site of sulfatases, generating a unique 3-oxo-L-alanine residue that is essential for sulfatase activity. The exact nature of the thiol involved is still not clear - dithiothreitol and cysteamine are the most efficiently used thiols in vitro. Glutathione alo acts in vitro, but it is not known whether it is used in vivo.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Dierks, T., Schmidt, B. and von Figura, K. Conversion of cysteine to formylglycine: a protein modification in the endoplasmic reticulum. Proc. Natl. Acad. Sci. USA 94 (1997) 11963–11968. [DOI] [PMID: 9342345]
2.  Dierks, T., Miech, C., Hummerjohann, J., Schmidt, B., Kertesz, M.A. and von Figura, K. Posttranslational formation of formylglycine in prokaryotic sulfatases by modification of either cysteine or serine. J. Biol. Chem. 273 (1998) 25560–25564. [DOI] [PMID: 9748219]
3.  Preusser-Kunze, A., Mariappan, M., Schmidt, B., Gande, S.L., Mutenda, K., Wenzel, D., von Figura, K. and Dierks, T. Molecular characterization of the human Cα-formylglycine-generating enzyme. J. Biol. Chem. 280 (2005) 14900–14910. [DOI] [PMID: 15657036]
4.  Roeser, D., Preusser-Kunze, A., Schmidt, B., Gasow, K., Wittmann, J.G., Dierks, T., von Figura, K. and Rudolph, M.G. A general binding mechanism for all human sulfatases by the formylglycine-generating enzyme. Proc. Natl. Acad. Sci. USA 103 (2006) 81–86. [DOI] [PMID: 16368756]
5.  Carlson, B.L., Ballister, E.R., Skordalakes, E., King, D.S., Breidenbach, M.A., Gilmore, S.A., Berger, J.M. and Bertozzi, C.R. Function and structure of a prokaryotic formylglycine-generating enzyme. J. Biol. Chem. 283 (2008) 20117–20125. [DOI] [PMID: 18390551]
6.  Holder, P.G., Jones, L.C., Drake, P.M., Barfield, R.M., Banas, S., de Hart, G.W., Baker, J. and Rabuka, D. Reconstitution of formylglycine-generating enzyme with copper(II) for aldehyde tag conversion. J. Biol. Chem. 290 (2015) 15730–15745. [DOI] [PMID: 25931126]
7.  Knop, M., Engi, P., Lemnaru, R. and Seebeck, F.P. In vitro reconstitution of formylglycine-generating enzymes requires copper(I). ChemBioChem 16 (2015) 2147–2150. [DOI] [PMID: 26403223]
8.  Knop, M., Dang, T.Q., Jeschke, G. and Seebeck, F.P. Copper is a cofactor of the formylglycine-generating enzyme. ChemBioChem 18 (2017) 161–165. [DOI] [PMID: 27862795]
9.  Meury, M., Knop, M. and Seebeck, F.P. Structural basis for copper-oxygen mediated C-H bond activation by the formylglycine-generating enzyme. Angew. Chem. Int. Ed. Engl. (2017) . [DOI] [PMID: 28544744]
[EC 1.8.3.7 created 2014]
 
 
EC 1.8.4.5      
Transferred entry: methionine-S-oxide reductase. Now EC 1.8.4.13, L-methionine (S)-S-oxide reductase and EC 1.8.4.14, L-methionine (R)-S-oxide reductase
[EC 1.8.4.5 created 1984, deleted 2006]
 
 
EC 1.8.4.6      
Transferred entry: protein-methionine-S-oxide reductase. Proved to be due to EC 1.8.4.11, peptide-methionine (S)-S-oxide reductase
[EC 1.8.4.6 created 1984, deleted 2006]
 
 
EC 1.8.4.9     
Accepted name: adenylyl-sulfate reductase (glutathione)
Reaction: AMP + sulfite + glutathione disulfide = adenylyl sulfate + 2 glutathione
Other name(s): 5′-adenylylsulfate reductase (also used for EC 1.8.99.2); AMP,sulfite:oxidized-glutathione oxidoreductase (adenosine-5′-phosphosulfate-forming); plant-type 5′-adenylylsulfate reductase
Systematic name: AMP,sulfite:glutathione-disulfide oxidoreductase (adenosine-5′-phosphosulfate-forming)
Comments: This enzyme differs from EC 1.8.99.2, adenylyl-sulfate reductase, in using glutathione as the reductant. Glutathione can be replaced by γ-glutamylcysteine or dithiothreitol, but not by thioredoxin, glutaredoxin or 2-sulfanylethan-1-ol (2-mercaptoethanol). The enzyme from the mouseear cress, Arabidopsis thaliana, contains a glutaredoxin-like domain. The enzyme is also found in other photosynthetic eukaryotes, e.g., the Madagascar periwinkle, Catharanthus roseus and the hollow green seaweed, Ulva intestinalis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 355840-27-6
References:
1.  Gutierrez-Marcos, J.F., Roberts, M.A., Campbell, E.I. and Wray, J.L. Three members of a novel small gene-family from Arabidopsis thaliana able to complement functionally an Escherichia coli mutant defective in PAPS reductase activity encode proteins with a thioredoxin-like domain and 'APS reductase' activity. Proc. Natl. Acad. Sci. USA 93 (1996) 13377–13382. [DOI] [PMID: 8917599]
2.  Setya, A., Murillo, M. and Leustek, T. Sulfate reduction in higher plants: Molecular evidence for a novel 5-adenylylphosphosulfate (APS) reductase. Proc. Natl. Acad. Sci. USA 93 (1996) 13383–13388. [DOI] [PMID: 8917600]
3.  Bick, J.A., Aslund, F., Cen, Y. and Leustek, T. Glutaredoxin function for the carboxyl-terminal domain of the plant-type 5′-adenylylsulfate reductase. Proc. Natl. Acad. Sci. USA 95 (1998) 8404–8409. [DOI] [PMID: 9653199]
[EC 1.8.4.9 created 2000, modified 2002]
 
 
EC 1.8.4.13     
Accepted name: L-methionine (S)-S-oxide reductase
Reaction: L-methionine + thioredoxin disulfide + H2O = L-methionine (S)-S-oxide + thioredoxin
For diagram of reaction, click here and for mechanism of reaction, click here
Other name(s): fSMsr; methyl sulfoxide reductase I and II; acetylmethionine sulfoxide reductase; methionine sulfoxide reductase; L-methionine:oxidized-thioredoxin S-oxidoreductase; methionine-S-oxide reductase; free-methionine (S)-S-oxide reductase
Systematic name: L-methionine:thioredoxin-disulfide S-oxidoreductase
Comments: Requires NADPH [2]. The reaction occurs in the opposite direction to that given above. Dithiothreitol can replace reduced thioredoxin. L-Methionine (R)-S-oxide is not a substrate [see EC 1.8.4.14, L-methionine (R)-S-oxide reductase].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Black, S., Harte, E.M., Hudson, B. and Wartofsky, L. A specific enzymatic reduction of L-(-)methionine sulfoxide and a related nonspecific reduction of diulfides. J. Biol. Chem. 235 (1960) 2910–2916.
2.  Ejiri, S.-I., Weissbach, H. and Brot, N. Reduction of methionine sulfoxide to methionine by Escherichia coli. J. Bacteriol. 139 (1979) 161–164. [PMID: 37234]
3.  Ejiri, S.-I., Weissbach, H. and Brot, N. The purification of methionine sulfoxide reductase from Escherichia coli. Anal. Biochem. 102 (1980) 393–398. [DOI] [PMID: 6999943]
4.  Weissbach, H., Resnick, L. and Brot, N. Methionine sulfoxide reductases: history and cellular role in protecting against oxidative damage. Biochim. Biophys. Acta 1703 (2005) 203–212. [DOI] [PMID: 15680228]
[EC 1.8.4.13 created 1984 as EC 1.8.4.5, part transferred 2006 to EC 1.8.4.13]
 
 
EC 1.10.99.3      
Transferred entry: violaxanthin de-epoxidase. Now classified as EC 1.23.5.1, violaxanthin de-epoxidase.
[EC 1.10.99.3 created 2005, deleted 2014]
 
 
EC 1.17.4.5     
Accepted name: vitamin-K-epoxide reductase (warfarin-insensitive)
Reaction: 3-hydroxy-2-methyl-3-phytyl-2,3-dihydro-1,4-naphthoquinone + oxidized dithiothreitol = 2,3-epoxy-2-methyl-3-phytyl-2,3-dihydro-1,4-naphthoquinone + 1,4-dithiothreitol
Glossary: 2,3-epoxy-2-methyl-3-phytyl-2,3-dihydro-1,4-naphthoquinone = vitamin K 2,3-epoxide
Systematic name: 3-hydroxy-2-methyl-3-phytyl-2,3-dihydronaphthoquinone:oxidized-dithiothreitol oxidoreductase
Comments: Vitamin K 2,3-epoxide is reduced to 3-hydroxy- (and 2-hydroxy-) vitamin K by 1,4-dithiothreitol, which is oxidized to a disulfide. Not inhibited by warfarin [cf. EC 1.17.4.4, vitamin-K-epoxide reductase (warfarin-sensitive)].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 97089-80-0
References:
1.  Mukharji, I. and Silverman, R.B. Purification of a vitamin K epoxide reductase that catalyzes conversion of vitamin K 2,3-epoxide to 3-hydroxy-2-methyl-3-phytyl-2,3-dihydronaphthoquinone. Proc. Natl. Acad. Sci. USA 82 (1985) 2713–2717. [DOI] [PMID: 3857611]
[EC 1.17.4.5 created 1989 as EC 1.1.4.2, transferred 2014 to EC 1.17.4.5]
 
 
EC 1.23.5.1     
Accepted name: violaxanthin de-epoxidase
Reaction: violaxanthin + 2 L-ascorbate = zeaxanthin + 2 L-dehydroascorbate + 2 H2O (overall reaction)
(1a) violaxanthin + L-ascorbate = antheraxanthin + L-dehydroascorbate + H2O
(1b) antheraxanthin + L-ascorbate = zeaxanthin + L-dehydroascorbate + H2O
For diagram of the xanthophyll cycle, click here
Glossary: violaxanthin = (3S,3′S,5R,5′R,6S,6′S)-5,6:5′,6′-diepoxy-5,5′,6,6′-tetrahydro-β,β-carotene-3,3′-diol
antheraxanthin = (3R,3′S,5′R,6′S)-5′,6′-epoxy-5′,6′-dihydro-β,β-carotene-3,3′-diol
zeaxanthin = (3R,3′R)-β,β-carotene-3,3′-diol
Other name(s): VDE
Systematic name: violaxanthin:ascorbate oxidoreductase
Comments: Along with EC 1.14.15.21, zeaxanthin epoxidase, this enzyme forms part of the xanthophyll (or violaxanthin) cycle for controlling the concentration of zeaxanthin in chloroplasts. It is activated by a low pH of the thylakoid lumen (produced by high light intensity). Zeaxanthin induces the dissipation of excitation energy in the chlorophyll of the light-harvesting protein complex of photosystem II. In higher plants the enzyme reacts with all-trans-diepoxides, such as violaxanthin, and all-trans-monoepoxides, but in the alga Mantoniella squamata, only the diepoxides are good substrates.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 57534-73-3
References:
1.  Yamamoto, H.Y. and Higashi, R.M. Violaxanthin de-epoxidase. Lipid composition and substrate specificity. Arch. Biochem. Biophys. 190 (1978) 514–522. [DOI] [PMID: 102251]
2.  Rockholm, D.C. and Yamamoto, H.Y. Violaxanthin de-epoxidase. Plant Physiol. 110 (1996) 697–703. [PMID: 8742341]
3.  Bugos, R.C., Hieber, A.D. and Yamamoto, H.Y. Xanthophyll cycle enzymes are members of the lipocalin family, the first identified from plants. J. Biol. Chem. 273 (1998) 15321–15324. [DOI] [PMID: 9624110]
4.  Kuwabara, T., Hasegawa, M., Kawano, M. and Takaichi, S. Characterization of violaxanthin de-epoxidase purified in the presence of Tween 20: effects of dithiothreitol and pepstatin A. Plant Cell Physiol. 40 (1999) 1119–1126. [PMID: 10635115]
5.  Latowski, D., Kruk, J., Burda, K., Skrzynecka-Jaskierm, M., Kostecka-Gugala, A. and Strzalka, K. Kinetics of violaxanthin de-epoxidation by violaxanthin de-epoxidase, a xanthophyll cycle enzyme, is regulated by membrane fluidity in model lipid bilayers. Eur. J. Biochem. 269 (2002) 4656–4665. [DOI] [PMID: 12230579]
6.  Goss, R. Substrate specificity of the violaxanthin de-epoxidase of the primitive green alga Mantoniella squamata (Prasinophyceae). Planta 217 (2003) 801–812. [DOI] [PMID: 12748855]
7.  Latowski, D., Akerlund, H.E. and Strzalka, K. Violaxanthin de-epoxidase, the xanthophyll cycle enzyme, requires lipid inverted hexagonal structures for its activity. Biochemistry 43 (2004) 4417–4420. [DOI] [PMID: 15078086]
[EC 1.23.5.1 created 2005 as EC 1.10.99.3, transfered 2015 to EC 1.23.5.1]
 
 
EC 2.3.1.96      
Deleted entry: glycoprotein N-palmitoyltransferase
[EC 2.3.1.96 created 1989, deleted 2018]
 
 
EC 2.4.1.229     
Accepted name: [Skp1-protein]-hydroxyproline N-acetylglucosaminyltransferase
Reaction: UDP-N-acetyl-α-D-glucosamine + [Skp1-protein]-trans-4-hydroxy-L-proline = UDP + [Skp1-protein]-O-(N-acetyl-α-D-glucosaminyl)-trans-4-hydroxy-L-proline
Other name(s): Skp1-HyPro GlcNAc-transferase; UDP-N-acetylglucosamine (GlcNAc):hydroxyproline polypeptide GlcNAc-transferase; UDP-GlcNAc:Skp1-hydroxyproline GlcNAc-transferase; UDP-GlcNAc:hydroxyproline polypeptide GlcNAc-transferase; UDP-N-acetyl-D-glucosamine:[Skp1-protein]-hydroxyproline N-acetyl-D-glucosaminyl-transferase
Systematic name: UDP-N-acetyl-α-D-glucosamine:[Skp1-protein]-trans-4-hydroxy-L-proline N-acetyl-α-D-glucosaminyl-transferase
Comments: Skp1 is a cytoplasmic and nuclear protein required for the ubiquitination of cell cycle regulatory proteins and transcriptional factors. In Dictyostelium Skp1 is modified by the linear pentasaccharide Galα1-6Galα1-L-Fucα1-2Galβ1-3GlcNAc, which is attached to a hydroxyproline residue at position 143. This enzyme catalyses the first step in the building up of the pentasaccharide by attaching an N-acetylglucosaminyl group to the hydroxyproline residue. It requires dithiothreitol and a divalent cation for activity.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 256531-81-4
References:
1.  van der Wel, H., Morris, H.R., Panico, M., Paxton, T., Dell, A., Kaplan, L. and West, C.M. Molecular cloning and expression of a UDP-N-acetylglucosamine (GlcNAc):hydroxyproline polypeptide GlcNAc-transferase that modifies Skp1 in the cytoplasm of Dictyostelium. J. Biol. Chem. 277 (2002) 46328–46337. [DOI] [PMID: 12244115]
2.  Teng-umnuay, P., van der Wel, H. and West, C.M. Identification of a UDP-GlcNAc:Skp1-hydroxyproline GlcNAc-transferase in the cytoplasm of Dictyostelium. J. Biol. Chem. 274 (1999) 36392–36402. [DOI] [PMID: 10593934]
3.  West, C.M., van der Wel, H. and Gaucher, E.A. Complex glycosylation of Skp1 in Dictyostelium: implications for the modification of other eukaryotic cytoplasmic and nuclear proteins. Glycobiology 12 (2002) 17. [DOI] [PMID: 11886837]
[EC 2.4.1.229 created 2003, modified 2013]
 
 
EC 3.1.2.15      
Deleted entry: This activity is covered by EC 3.4.19.12, ubiquitinyl hydrolase 1
[EC 3.1.2.15 created 1986, deleted 2014]
 
 
EC 3.4.13.18     
Accepted name: cytosol nonspecific dipeptidase
Reaction: Hydrolysis of dipeptides, preferentially hydrophobic dipeptides including prolyl amino acids
Other name(s): N2-β-alanylarginine dipeptidase; glycyl-glycine dipeptidase; glycyl-leucine dipeptidase; iminodipeptidase; peptidase A; Pro-X dipeptidase; prolinase; prolyl dipeptidase; prolylglycine dipeptidase; iminodipeptidase; prolinase; L-prolylglycine dipeptidase; prolylglycine dipeptidase; diglycinase; Gly-Leu hydrolase; glycyl-L-leucine dipeptidase; glycyl-L-leucine hydrolase; glycyl-L-leucine peptidase; L-amino-acyl-L-amino-acid hydrolase; glycylleucine peptidase; glycylleucine hydrolase; glycylleucine dipeptide hydrolase; non-specific dipeptidase; human cytosolic non-specific dipeptidase; glycyl-L-leucine hydrolase; glycyl-glycine dipeptidase
Comments: A zinc enzyme with broad specificity, varying somewhat with source species. Activated and stabilized by dithiothreitol and Mn2+. Inhibited by bestatin and leucine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9025-31-4
References:
1.  Bauer, K. Cytosol non-specific dipeptidase. In: Barrett, A.J., Rawlings, N.D. and Woessner, J.F. (Ed.), Handbook of Proteolytic Enzymes, Academic Press, London, 1998, pp. 1520–1522.
[EC 3.4.13.18 created 1961 as EC 3.4.3.1 and EC 3.4.3.2, transferred 1972 to EC 3.4.13.1 and EC 3.4.13.2, transferred 1978 to EC 3.4.13.11, part transferred 1992 to EC 3.4.13.18, modified 2000 (EC 3.4.13.15 created 1989, incorporated 1992)]
 
 
EC 4.4.1.16     
Accepted name: selenocysteine lyase
Reaction: L-selenocysteine + reduced acceptor = selenide + L-alanine + acceptor
Glossary: dithiothreitol = 1,4-bis(sulfanyl)butane-2,3-diol
Other name(s): selenocysteine reductase; selenocysteine β-lyase
Systematic name: L-selenocysteine selenide-lyase (L-alanine-forming)
Comments: A pyridoxal-phosphate protein. Dithiothreitol or 2-sulfanylethan-1-ol (2-mercaptoethanol) can act as the reducing agent in the reaction. The enzyme from animals does not act on cysteine, serine or chloroalanine [1,3], while the enzyme from bacteria shows activity with cysteine (cf. EC 2.8.1.7, cysteine desulfurase) [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 82047-76-5
References:
1.  Esaki, N., Nakamura, T., Tanaka, H. and Soda, K. Selenocysteine lyase, a novel enzyme that specifically acts on selenocysteine. Mammalian distribution and purification and properties of pig liver enzyme. J. Biol. Chem. 257 (1982) 4386–4391. [PMID: 6461656]
2.  Mihara, H., Kurihara, T., Yoshimura, T., Soda, K. and Esaki, N. Cysteine sulfinate desulfinase, a NIFS-like protein of Escherichia coli with selenocysteine lyase and cysteine desulfurase activities. Gene cloning, purification, and characterization of a novel pyridoxal enzyme. J. Biol. Chem. 272 (1997) 22417–22424. [DOI] [PMID: 9278392]
3.  Omi, R., Kurokawa, S., Mihara, H., Hayashi, H., Goto, M., Miyahara, I., Kurihara, T., Hirotsu, K. and Esaki, N. Reaction mechanism and molecular basis for selenium/sulfur discrimination of selenocysteine lyase. J. Biol. Chem. 285 (2010) 12133–12139. [DOI] [PMID: 20164179]
[EC 4.4.1.16 created 1986]
 
 


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