The Enzyme Database

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EC 1.14.11.3     
Accepted name: pyrimidine-deoxynucleoside 2′-dioxygenase
Reaction: 2′-deoxyuridine + 2-oxoglutarate + O2 = uridine + succinate + CO2
Other name(s): deoxyuridine 2′-dioxygenase; deoxyuridine 2′-hydroxylase; pyrimidine deoxyribonucleoside 2′-hydroxylase; thymidine 2′-dioxygenase; thymidine 2′-hydroxylase; thymidine 2-oxoglutarate dioxygenase; thymidine dioxygenase
Systematic name: 2′-deoxyuridine,2-oxoglutarate:oxygen oxidoreductase (2′-hydroxylating)
Comments: Requires Fe(II) and ascorbate. Also acts on thymidine. cf. EC 1.14.11.10, pyrimidine-deoxynucleoside 1′-dioxygenase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9076-89-5
References:
1.  Bankel, L., Lindstedt, G. and Lindstedt, S. Thymidine 2′-hydroxylation in Neurospora crassa. J. Biol. Chem. 247 (1972) 6128–6134. [PMID: 4265566]
2.  Stubbe, J. Identification of two α-ketoglutarate-dependent dioxygenases in extracts of Rhodotorula glutinis catalyzing deoxyuridine hydroxylation. J. Biol. Chem. 260 (1985) 9972–9975. [PMID: 4040518]
3.  Warn-Cramer, B.J., Macrander, L.A. and Abbott, M.T. Markedly different ascorbate dependencies of the sequential α-ketoglutarate dioxygenase reactions catalyzed by an essentially homogeneous thymine 7-hydroxylase from Rhodotorula glutinis. J. Biol. Chem. 258 (1983) 10551–10557. [PMID: 6684117]
[EC 1.14.11.3 created 1972, modified 1976, modified 1989, modified 2002]
 
 
EC 1.14.11.30     
Accepted name: hypoxia-inducible factor-asparagine dioxygenase
Reaction: hypoxia-inducible factor-L-asparagine + 2-oxoglutarate + O2 = hypoxia-inducible factor-(3S)-3-hydroxy-L-asparagine + succinate + CO2
Other name(s): HIF hydroxylase
Systematic name: hypoxia-inducible factor-L-asparagine, 2-oxoglutarate:oxygen oxidoreductase (4-hydroxylating)
Comments: Contains iron, and requires ascorbate. Catalyses hydroxylation of an asparagine in the C-terminal transcriptional activation domain of HIF-α, the α subunit of the transcriptional regulator HIF (hypoxia-inducible factor), which reduces its interaction with the transcriptional coactivator protein p300. The requirement of oxygen for the hydroxylation reaction enables animals to respond to hypoxia.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Mahon, P.C., Hirota, K. and Semenza, G.L. FIH-1: a novel protein that interacts with HIF-1α and VHL to mediate repression of HIF-1 transcriptional activity. Genes Dev. 15 (2001) 2675–2686. [DOI] [PMID: 11641274]
2.  Hewitson, K.S., McNeill, L.A., Riordan, M.V., Tian, Y.M., Bullock, A.N., Welford, R.W., Elkins, J.M., Oldham, N.J., Bhattacharya, S., Gleadle, J.M., Ratcliffe, P.J., Pugh, C.W. and Schofield, C.J. Hypoxia-inducible factor (HIF) asparagine hydroxylase is identical to factor inhibiting HIF (FIH) and is related to the cupin structural family. J. Biol. Chem. 277 (2002) 26351–26355. [DOI] [PMID: 12042299]
3.  Dann, C.E., 3rd, Bruick, R.K. and Deisenhofer, J. Structure of factor-inhibiting hypoxia-inducible factor 1: An asparaginyl hydroxylase involved in the hypoxic response pathway. Proc. Natl. Acad. Sci. USA 99 (2002) 15351–15356. [DOI] [PMID: 12432100]
4.  Lando, D., Peet, D.J., Whelan, D.A., Gorman, J.J. and Whitelaw, M.L. Asparagine hydroxylation of the HIF transactivation domain a hypoxic switch. Science 295 (2002) 858–861. [DOI] [PMID: 11823643]
5.  Koivunen, P., Hirsila, M., Gunzler, V., Kivirikko, K.I. and Myllyharju, J. Catalytic properties of the asparaginyl hydroxylase (FIH) in the oxygen sensing pathway are distinct from those of its prolyl 4-hydroxylases. J. Biol. Chem. 279 (2004) 9899–9904. [DOI] [PMID: 14701857]
6.  Elkins, J.M., Hewitson, K.S., McNeill, L.A., Seibel, J.F., Schlemminger, I., Pugh, C.W., Ratcliffe, P.J. and Schofield, C.J. Structure of factor-inhibiting hypoxia-inducible factor (HIF) reveals mechanism of oxidative modification of HIF-1 α. J. Biol. Chem. 278 (2003) 1802–1806. [DOI] [PMID: 12446723]
[EC 1.14.11.30 created 2010]
 
 
EC 1.14.11.31     
Accepted name: thebaine 6-O-demethylase
Reaction: thebaine + 2-oxoglutarate + O2 = neopinone + formaldehyde + succinate + CO2
Other name(s): T6ODM
Systematic name: thebaine,2-oxoglutarate:oxygen oxidoreductase (6-O-demethylating)
Comments: Requires Fe2+. Catalyses a step in morphine biosynthesis. The product neopinione spontaneously rearranges to the more stable codeinone. The enzyme also catalyses the 6-O-demethylation of oripavine to morphinone, with lower efficiency.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hagel, J.M. and Facchini, P.J. Dioxygenases catalyze the O-demethylation steps of morphine biosynthesis in opium poppy. Nat. Chem. Biol. 6 (2010) 273–275. [DOI] [PMID: 20228795]
[EC 1.14.11.31 created 2010]
 
 
EC 1.14.11.32     
Accepted name: codeine 3-O-demethylase
Reaction: codeine + 2-oxoglutarate + O2 = morphine + formaldehyde + succinate + CO2
Other name(s): codeine O-demethylase; CODM
Systematic name: codeine,2-oxoglutarate:oxygen oxidoreductase (3-O-demethylating)
Comments: Requires Fe2+. Catalyses a step in morphine biosynthesis. The enzyme also catalyses the 3-O-demethylation of thebaine to oripavine, with lower efficiency.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hagel, J.M. and Facchini, P.J. Dioxygenases catalyze the O-demethylation steps of morphine biosynthesis in opium poppy. Nat. Chem. Biol. 6 (2010) 273–275. [DOI] [PMID: 20228795]
[EC 1.14.11.32 created 2010]
 
 
EC 1.14.11.33     
Accepted name: DNA oxidative demethylase
Reaction: DNA-base-CH3 + 2-oxoglutarate + O2 = DNA-base + formaldehyde + succinate + CO2
Other name(s): alkylated DNA repair protein; α-ketoglutarate-dependent dioxygenase ABH1; alkB (gene name)
Systematic name: methyl DNA-base, 2-oxoglutarate:oxygen oxidoreductase (formaldehyde-forming)
Comments: Contains iron; activity is slightly stimulated by ascorbate. Catalyses oxidative demethylation of the DNA base lesions N1-methyladenine, N3-methylcytosine, N1-methylguanine, and N3-methylthymine. It works better on single-stranded DNA (ssDNA) and is capable of repairing damaged bases in RNA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Falnes, P.O., Johansen, R.F. and Seeberg, E. AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli. Nature 419 (2002) 178–182. [DOI] [PMID: 12226668]
2.  Yi, C., Yang, C.G. and He, C. A non-heme iron-mediated chemical demethylation in DNA and RNA. Acc. Chem. Res. 42 (2009) 519–529. [DOI] [PMID: 19852088]
3.  Yi, C., Jia, G., Hou, G., Dai, Q., Zhang, W., Zheng, G., Jian, X., Yang, C.G., Cui, Q. and He, C. Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase. Nature 468 (2010) 330–333. [DOI] [PMID: 21068844]
[EC 1.14.11.33 created 2011]
 
 
EC 1.14.11.34      
Transferred entry: 2-oxoglutarate/L-arginine monooxygenase/decarboxylase (succinate-forming). Now EC 1.14.20.7, 2-oxoglutarate/L-arginine monooxygenase/decarboxylase (succinate-forming)
[EC 1.14.11.34 created 2011, deleted 2018]
 
 
EC 1.14.11.35     
Accepted name: 1-deoxypentalenic acid 11β-hydroxylase
Reaction: 1-deoxypentalenate + 2-oxoglutarate + O2 = 1-deoxy-11β-hydroxypentalenate + succinate + CO2
For diagram of pentalenolactone biosynthesis, click here
Glossary: 1-deoxypentalenate = (1R,3aR,5aS,8aR)-1,7,7-trimethyl-1,2,3,3a,5a,6,7,8-octahydrocyclopenta[c]pentalene-4-carboxylate
1-deoxy-11β-hydroxypentalenate = (1S,2R,3aR,5aS,8aR)-2-hydroxy-1,7,7-trimethyl-1,2,3,3a,5a,6,7,8-octahydrocyclopenta[c]pentalene-4-carboxylate
Other name(s): ptlH (gene name); sav2991 (gene name); pntH (gene name)
Systematic name: 1-deoxypentalenic acid,2-oxoglutarate:oxygen oxidoreductase
Comments: The enzyme requires Fe(II) and ascorbate. Isolated from the bacterium Streptomyces avermitilis. Part of the pathway for pentalenolactone biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  You, Z., Omura, S., Ikeda, H. and Cane, D.E. Pentalenolactone biosynthesis. Molecular cloning and assignment of biochemical function to PtlH, a non-heme iron dioxygenase of Streptomyces avermitilis. J. Am. Chem. Soc. 128 (2006) 6566–6567. [DOI] [PMID: 16704250]
2.  You, Z., Omura, S., Ikeda, H., Cane, D.E. and Jogl, G. Crystal structure of the non-heme iron dioxygenase PtlH in pentalenolactone biosynthesis. J. Biol. Chem. 282 (2007) 36552–36560. [DOI] [PMID: 17942405]
[EC 1.14.11.35 created 2012]
 
 
EC 1.14.11.36     
Accepted name: pentalenolactone F synthase
Reaction: pentalenolactone D + 2 2-oxoglutarate + 2 O2 = pentalenolactone F + 2 succinate + 2 CO2 + H2O (overall reaction)
(1a) pentalenolactone D + 2-oxoglutarate + O2 = pentalenolactone E + succinate + CO2 + H2O
(1b) pentalenolactone E + 2-oxoglutarate + O2 = pentalenolactone F + succinate + CO2
For diagram of pentalenolactone biosynthesis, click here
Glossary: pentalenolactone D = (1S,4aR,6aS,9aR)-1,8,8-trimethyl-2-oxo-1,2,4,4a,6a,7,8,9-octahydropentaleno[1,6a-c]pyran-5-carboxylate
pentalenolactone E = (4aR,6aS,9aR)-8,8-dimethyl-1-methylene-2-oxo-1,2,4,4a,6a,7,8,9-octahydropentaleno[1,6a-c]pyran-5-carboxylate
pentalenolactone F = (1′R,4′aR,6′aS,9′aR)-8′,8′-dimethyl-2′-oxo-4′,4′a,6′a,8′,9′-hexahydrospiro[oxirane-2,1′-pentaleno[1,6a-c]pyran]-5′-carboxylic acid
Other name(s): penD (gene name); pntD (gene name); ptlD (gene name)
Systematic name: pentalenolactone-D,2-oxoglutarate:oxygen oxidoreductase
Comments: Requires Fe(II) and ascorbate. Isolated from the bacteria Streptomyces exfoliatus, Streptomyces arenae and Streptomyces avermitilis. Part of the pentalenolactone biosynthesis pathway.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Seo, M.J., Zhu, D., Endo, S., Ikeda, H. and Cane, D.E. Genome mining in Streptomyces. Elucidation of the role of Baeyer-Villiger monooxygenases and non-heme iron-dependent dehydrogenase/oxygenases in the final steps of the biosynthesis of pentalenolactone and neopentalenolactone. Biochemistry 50 (2011) 1739–1754. [DOI] [PMID: 21250661]
[EC 1.14.11.36 created 2012]
 
 
EC 1.14.11.37     
Accepted name: kanamycin B dioxygenase
Reaction: kanamycin B + 2-oxoglutarate + O2 = 2′-dehydrokanamycin A + succinate + NH3 + CO2
For diagram of kanamycin A biosynthesis, click here
Other name(s): kanJ (gene name)
Systematic name: kanamycin-B,2-oxoglutarate:oxygen oxidoreductase (deaminating, 2′-hydroxylating)
Comments: Requires Fe2+ and ascorbate. Found in the bacterium Streptomyces kanamyceticus where it is involved in the conversion of the aminoglycoside antibiotic kanamycin B to kanamycin A.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Sucipto, H., Kudo, F. and Eguchi, T. The last step of kanamycin biosynthesis: unique deamination reaction catalyzed by the α-ketoglutarate-dependent nonheme iron dioxygenase KanJ and the NADPH-dependent reductase KanK. Angew. Chem. Int. Ed. Engl. 51 (2012) 3428–3431. [DOI] [PMID: 22374809]
[EC 1.14.11.37 created 2013, modified 2013]
 
 
EC 1.14.11.38     
Accepted name: verruculogen synthase
Reaction: fumitremorgin B + 2-oxoglutarate + 2 O2 + reduced acceptor = verruculogen + succinate + CO2 + H2O + acceptor
For diagram of fumitremorgin alkaloid biosynthesis (part 2), click here
Glossary: fumitremorgin B = (5aR,6S,12S,14aS)-5a,6-dihydroxy-9-methoxy-11-(3-methylbut-2-en-1-yl)-12-(2-methylprop-1-en-1-yl)-1,2,3,5a,6,11,12,14a-octahydro-5H,14H-pyrrolo[1′′,2′′:4′,5′]pyrazino[1′,2′:1,6]pyrido[3,4-b]indole-5,14-dione
verruculogen = (5R,10S,10aR,14aS,15bS)-10,10a-dihydroxy-6-methoxy-2,2-dimethyl-5-(2-methylprop-1-en-1-yl)-1,10,10a,14,14a,15b-hexahydro-12H-3,4-dioxa-5a,11a,15a-triazacycloocta[1,2,3-lm]indeno[5,6-b]fluorene-11,15(2H,13H)-dione
Other name(s): fmtF (gene name); FmtOx1
Systematic name: fumitremorgin B,2-oxoglutarate:oxygen oxidoreductase (verruculogen-forming)
Comments: Requires Fe2+ and ascorbate. Found in the fungus Aspergillus fumigatus. Both atoms of a dioxygen molecule are incorporated into verruculogen [1,2]. Involved in the biosynthetic pathways of several indole alkaloids such as fumitremorgin A.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Steffan, N., Grundmann, A., Afiyatullov, S., Ruan, H. and Li, S.M. FtmOx1, a non-heme Fe(II) and α-ketoglutarate-dependent dioxygenase, catalyses the endoperoxide formation of verruculogen in Aspergillus fumigatus. Org. Biomol. Chem. 7 (2009) 4082–4087. [DOI] [PMID: 19763315]
2.  Kato, N., Suzuki, H., Takagi, H., Uramoto, M., Takahashi, S. and Osada, H. Gene disruption and biochemical characterization of verruculogen synthase of Aspergillus fumigatus. ChemBioChem. 12 (2011) 711–714. [DOI] [PMID: 21404415]
[EC 1.14.11.38 created 2013]
 
 
EC 1.14.11.39     
Accepted name: L-asparagine hydroxylase
Reaction: L-asparagine + 2-oxoglutarate + O2 = (2S,3S)-3-hydroxyasparagine + succinate + CO2
Other name(s): L-asparagine 3-hydroxylase; AsnO
Systematic name: L-asparagine,2-oxoglutarate:oxygen oxidoreductase (3-hydroxylating)
Comments: Requires Fe2+. The enzyme is only able to hydroxylate free L-asparagine. It is not active toward D-asparagine. The β-hydroxylated asparagine produced is incorporated at position 9 of the calcium-dependent antibiotic (CDA), an 11-residue non-ribosomally synthesized acidic lipopeptide lactone.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Strieker, M., Kopp, F., Mahlert, C., Essen, L.O. and Marahiel, M.A. Mechanistic and structural basis of stereospecific Cβ-hydroxylation in calcium-dependent antibiotic, a daptomycin-type lipopeptide. ACS Chem. Biol. 2 (2007) 187–196. [DOI] [PMID: 17373765]
[EC 1.14.11.39 created 2013]
 
 


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