The Enzyme Database

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EC 1.1.1.244     
Accepted name: methanol dehydrogenase
Reaction: methanol + NAD+ = formaldehyde + NADH + H+
Systematic name: methanol:NAD+ oxidoreductase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 74506-37-9
References:
1.  Arfman, N., Watling, E.M., Clement, W., van Oosterwijk, R.J., de Vries, G.E., Harder, W., Attwood, M.M. and Dijkhuizen, L. Methanol metabolism in thermotolerant methylotrophic Bacillus strains involving a novel catabolic NAD-dependent methanol dehydrogenase as a key enzyme. Arch. Microbiol. 152 (1989) 280–288. [PMID: 2673121]
[EC 1.1.1.244 created 1992]
 
 
EC 1.1.1.284     
Accepted name: S-(hydroxymethyl)glutathione dehydrogenase
Reaction: S-(hydroxymethyl)glutathione + NAD(P)+ = S-formylglutathione + NAD(P)H + H+
Other name(s): NAD-linked formaldehyde dehydrogenase (incorrect); formaldehyde dehydrogenase (incorrect); formic dehydrogenase (incorrect); class III alcohol dehydrogenase; ADH3; χ-ADH; FDH (incorrect); formaldehyde dehydrogenase (glutathione) (incorrect); GS-FDH (incorrect); glutathione-dependent formaldehyde dehydrogenase (incorrect); GD-FALDH; NAD- and glutathione-dependent formaldehyde dehydrogenase; NAD-dependent formaldehyde dehydrogenase (incorrect)
Systematic name: S-(hydroxymethyl)glutathione:NAD+ oxidoreductase
Comments: The substrate, S-(hydroxymethyl)glutathione, forms spontaneously from glutathione and formaldehyde; its rate of formation is increased in some bacteria by the presence of EC 4.4.1.22, S-(hydroxymethyl)glutathione synthase. This enzyme forms part of the pathway that detoxifies formaldehyde, since the product is hydrolysed by EC 3.1.2.12, S-formylglutathione hydrolase. The human enzyme belongs to the family of zinc-dependent alcohol dehydrogenases. Also specifically reduces S-nitrosylglutathione.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, UM-BBD
References:
1.  Jakoby, W.B. Aldehyde dehydrogenases. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Ed.), The Enzymes, 2nd edn, vol. 7, Academic Press, New York, 1963, pp. 203–221.
2.  Rose, Z.B. and Racker, E. Formaldehyde dehydrogenase. Methods Enzymol. 9 (1966) 357–360.
3.  Liu, L., Hausladen, A., Zeng, M., Que, L., Heitman, J. and Stamler, J.S. A metabolic enzyme for S-nitrosothiol conserved from bacteria to humans. Nature 410 (2001) 490–494. [DOI] [PMID: 11260719]
4.  Sanghani, P.C., Stone, C.L., Ray, B.D., Pindel, E.V., Hurley, T.D. and Bosron, W.F. Kinetic mechanism of human glutathione-dependent formaldehyde dehydrogenase. Biochemistry 39 (2000) 10720–10729. [DOI] [PMID: 10978156]
5.  van Ophem, P.W. and Duine, J.A. NAD- and co-substrate (GSH or factor)-dependent formaldehyde dehydrogenases from methylotrophic microorganisms act as a class III alcohol dehydrogenase. FEMS Microbiol. Lett. 116 (1994) 87–94.
6.  Ras, J., van Ophem, P.W., Reijnders, W.N., Van Spanning, R.J., Duine, J.A., Stouthamer, A.H. and Harms, N. Isolation, sequencing, and mutagenesis of the gene encoding NAD- and glutathione-dependent formaldehyde dehydrogenase (GD-FALDH) from Paracoccus denitrificans, in which GD-FALDH is essential for methylotrophic growth. J. Bacteriol. 177 (1995) 247–251. [DOI] [PMID: 7798140]
7.  Barber, R.D., Rott, M.A. and Donohue, T.J. Characterization of a glutathione-dependent formaldehyde dehydrogenase from Rhodobacter sphaeroides. J. Bacteriol. 178 (1996) 1386–1393. [DOI] [PMID: 8631716]
[EC 1.1.1.284 created 2005 (EC 1.2.1.1 created 1961, modified 1982, modified 2002, part transferred 2005 to EC 1.1.1.284)]
 
 
EC 1.1.1.306     
Accepted name: S-(hydroxymethyl)mycothiol dehydrogenase
Reaction: S-(hydroxymethyl)mycothiol + NAD+ = S-formylmycothiol + NADH + H+
Glossary: mycothiol = 1-O-[2-(N2-acetyl-L-cysteinamido)-2-deoxy-α-D-glucopyranosyl]-1D-myo-inositol
Other name(s): NAD/factor-dependent formaldehyde dehydrogenase; mycothiol-dependent formaldehyde dehydrogenase
Systematic name: S-(hydroxymethyl)mycothiol:NAD+ oxidoreductase
Comments: S-hydroxymethylmycothiol is believed to form spontaneously from formaldehyde and mycothiol. This enzyme oxidizes the product of this spontaneous reaction to S-formylmycothiol, in a reaction that is analogous to EC 1.1.1.284, S-(hydroxymethyl)glutathione dehydrogenase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 192140-85-5
References:
1.  Misset-Smits, M., Van Ophem, P.W., Sakuda, S. and Duine, J.A. Mycothiol, 1-O-(2′-[N-acetyl-L-cysteinyl]amido-2′-deoxy-α-D-glucopyranosyl)-D-myo-inositol, is the factor of NAD/factor-dependent formaldehyde dehydrogenase. FEBS Lett. 409 (1997) 221–222. [DOI] [PMID: 9202149]
2.  Norin, A., Van Ophem, P.W., Piersma, S.R., Person, B., Duine, J.A. and Jornvall, H. Mycothiol-dependent formaldehyde dehydrogenase, a prokaryotic medium-chain dehydrogenase/reductase, phylogenetically links different eukaryotic alcohol dehydrogenase's - primary structure, conformational modelling and functional correlations. Eur. J. Biochem. 248 (1997) 282–289. [DOI] [PMID: 9346279]
3.  Vogt, R.N., Steenkamp, D.J., Zheng, R. and Blanchard, J.S. The metabolism of nitrosothiols in the Mycobacteria: identification and characterization of S-nitrosomycothiol reductase. Biochem. J. 374 (2003) 657–666. [DOI] [PMID: 12809551]
4.  Rawat, M. and Av-Gay, Y. Mycothiol-dependent proteins in actinomycetes. FEMS Microbiol. Rev. 31 (2007) 278–292. [DOI] [PMID: 17286835]
[EC 1.1.1.306 created 2010 as EC 1.2.1.66, transferred 2010 to EC 1.1.1.306]
 
 
EC 1.1.1.343     
Accepted name: phosphogluconate dehydrogenase (NAD+-dependent, decarboxylating)
Reaction: 6-phospho-D-gluconate + NAD+ = D-ribulose 5-phosphate + CO2 + NADH + H+
For diagram of the pentose phosphate pathway (early stages), click here
Other name(s): 6-PGDH (ambiguous); gntZ (gene name); GNDl
Systematic name: 6-phospho-D-gluconate:NAD+ 2-oxidoreductase (decarboxylating)
Comments: Highly specific for NAD+. The enzyme catalyses both the oxidation and decarboxylation of 6-phospho-D-gluconate. In the bacterium Methylobacillus flagellatus the enzyme participates in a formaldehyde oxidation pathway [4]. cf. EC 1.1.1.44, phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating).
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9073-95-4
References:
1.  Kiriuchin, M. Y., Kletsova, L. V., Chistoserdov, A. Y. and Tsygankov, Y. D. Properties of glucose 6-phosphate and 6-phosphogluconate dehydrogenases of the obligate methylotroph Methylobacillus flagellatum KT. FEMS Microbiol. Lett. 52 (1988) 199–204.
2.  Ohara, H., Russell, R.A., Uchida, K. and Kondo, H. Purification and characterization of NAD-specific 6-phosphogluconate dehydrogenase from Leuconostoc lactis SHO-54. J. Biosci. Bioeng. 98 (2004) 126–128. [DOI] [PMID: 16233677]
3.  Zamboni, N., Fischer, E., Laudert, D., Aymerich, S., Hohmann, H.P. and Sauer, U. The Bacillus subtilis yqjI gene encodes the NADP+-dependent 6-P-gluconate dehydrogenase in the pentose phosphate pathway. J. Bacteriol. 186 (2004) 4528–4534. [DOI] [PMID: 15231785]
4.  Chistoserdova, L., Gomelsky, L., Vorholt, J.A., Gomelsky, M., Tsygankov, Y.D. and Lidstrom, M.E. Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph. Microbiology 146 (2000) 233–238. [DOI] [PMID: 10658669]
[EC 1.1.1.343 created 2013]
 
 
EC 1.1.2.7     
Accepted name: methanol dehydrogenase (cytochrome c)
Reaction: a primary alcohol + 2 ferricytochrome cL = an aldehyde + 2 ferrocytochrome cL + 2 H+
Other name(s): methanol dehydrogenase; MDH (ambiguous)
Systematic name: methanol:cytochrome c oxidoreductase
Comments: A periplasmic quinoprotein alcohol dehydrogenase that only occurs in methylotrophic bacteria. It uses the novel specific cytochrome cL as acceptor. Acts on a wide range of primary alcohols, including ethanol, duodecanol, chloroethanol, cinnamyl alcohol, and also formaldehyde. Activity is stimulated by ammonia or methylamine. It is usually assayed with phenazine methosulfate. Like all other quinoprotein alcohol dehydrogenases it has an 8-bladed ’propeller’ structure, a calcium ion bound to the PQQ in the active site and an unusual disulfide ring structure in close proximity to the PQQ. It differs from EC 1.1.2.8, alcohol dehydrogenase (cytochrome c), in having a high affinity for methanol and in having a second essential small subunit (no known function).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, UM-BBD, CAS registry number: 37205-43-9
References:
1.  Anthony, C. and Zatman, L.J. The microbial oxidation of methanol. 2. The methanol-oxidizing enzyme of Pseudomonas sp. M 27. Biochem. J. 92 (1964) 614–621. [PMID: 4378696]
2.  Anthony, C. and Zatman, L.J. The microbial oxidation of methanol. The prosthetic group of the alcohol dehydrogenase of Pseudomonas sp. M27: a new oxidoreductase prosthetic group. Biochem. J. 104 (1967) 960–969. [PMID: 6049934]
3.  Duine, J.A., Frank, J. and Verweil, P.E.J. Structure and activity of the prosthetic group of methanol dehydrogenase. Eur. J. Biochem. 108 (1980) 187–192. [DOI] [PMID: 6250827]
4.  Salisbury, S.A., Forrest, H.S., Cruse, W.B.T. and Kennard, O. A novel coenzyme from bacterial primary alcohol dehydrogenases. Nature (Lond.) 280 (1979) 843–844. [PMID: 471057]
5.  Cox, J.M., Day, D.J. and Anthony, C. The interaction of methanol dehydrogenase and its electron acceptor, cytochrome cL in methylotrophic bacteria. Biochim. Biophys. Acta 1119 (1992) 97–106. [DOI] [PMID: 1311606]
6.  Blake, C.C., Ghosh, M., Harlos, K., Avezoux, A. and Anthony, C. The active site of methanol dehydrogenase contains a disulphide bridge between adjacent cysteine residues. Nat. Struct. Biol. 1 (1994) 102–105. [PMID: 7656012]
7.  Xia, Z.X., He, Y.N., Dai, W.W., White, S.A., Boyd, G.D. and Mathews, F.S. Detailed active site configuration of a new crystal form of methanol dehydrogenase from Methylophilus W3A1 at 1.9 Å resolution. Biochemistry 38 (1999) 1214–1220. [DOI] [PMID: 9930981]
8.  Afolabi, P.R., Mohammed, F., Amaratunga, K., Majekodunmi, O., Dales, S.L., Gill, R., Thompson, D., Cooper, J.B., Wood, S.P., Goodwin, P.M. and Anthony, C. Site-directed mutagenesis and X-ray crystallography of the PQQ-containing quinoprotein methanol dehydrogenase and its electron acceptor, cytochrome cL. Biochemistry 40 (2001) 9799–9809. [DOI] [PMID: 11502173]
9.  Anthony, C. and Williams, P. The structure and mechanism of methanol dehydrogenase. Biochim. Biophys. Acta 1647 (2003) 18–23. [DOI] [PMID: 12686102]
10.  Williams, P.A., Coates, L., Mohammed, F., Gill, R., Erskine, P.T., Coker, A., Wood, S.P., Anthony, C. and Cooper, J.B. The atomic resolution structure of methanol dehydrogenase from Methylobacterium extorquens. Acta Crystallogr. D Biol. Crystallogr. 61 (2005) 75–79. [DOI] [PMID: 15608378]
[EC 1.1.2.7 created 1972 as EC 1.1.99.8, modified 1982, part transferred 2010 to EC 1.1.2.7]
 
 
EC 1.1.2.10     
Accepted name: lanthanide-dependent methanol dehydrogenase
Reaction: methanol + 2 oxidized cytochrome cL = formaldehyde + 2 reduced cytochrome cL
Other name(s): XoxF; XoxF-MDH; Ce-MDH; La3+-dependent MDH; Ce3+-induced methanol dehydrogenase; cerium dependent MDH
Systematic name: methanol:cytochrome cL oxidoreductase
Comments: Isolated from the bacterium Methylacidiphilum fumariolicum and many Methylobacterium species. Requires La3+, Ce3+, Pr3+ or Nd3+. The higher lanthanides show decreasing activity with Sm3+, Eu3+ and Gd3+. The lanthanide is coordinated by the enzyme and pyrroloquinoline quinone. Shows little activity with Ca2+, the required cofactor of EC 1.1.2.7, methanol dehydrogenase (cytochrome c).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hibi, Y., Asai, K., Arafuka, H., Hamajima, M., Iwama, T. and Kawai, K. Molecular structure of La3+-induced methanol dehydrogenase-like protein in Methylobacterium radiotolerans. J. Biosci. Bioeng. 111 (2011) 547–549. [PMID: 21256798]
2.  Nakagawa, T., Mitsui, R., Tani, A., Sasa, K., Tashiro, S., Iwama, T., Hayakawa, T. and Kawai, K. A catalytic role of XoxF1 as La3+-dependent methanol dehydrogenase in Methylobacterium extorquens strain AM1. PLoS One 7:e50480 (2012). [PMID: 23209751]
3.  Pol, A., Barends, T.R., Dietl, A., Khadem, A.F., Eygensteyn, J., Jetten, M.S. and Op den Camp, H.J. Rare earth metals are essential for methanotrophic life in volcanic mudpots. Environ. Microbiol. 16 (2014) 255–264. [PMID: 24034209]
4.  Bogart, J.A., Lewis, A.J. and Schelter, E.J. DFT study of the active site of the XoxF-type natural, cerium-dependent methanol dehydrogenase enzyme. Chemistry Eur. J. 21 (2015) 1743–1748. [PMID: 25421364]
5.  Prejano, M., Marino, T. and Russo, N. How can methanol dehydrogenase from Methylacidiphilum fumariolicum work with the alien Ce(III) ion in the active center? A theoretical study. Chemistry 23 (2017) 8652–8657. [PMID: 28488399]
6.  Masuda, S., Suzuki, Y., Fujitani, Y., Mitsui, R., Nakagawa, T., Shintani, M. and Tani, A. Lanthanide-dependent regulation of methylotrophy in Methylobacterium aquaticum strain 22A. mSphere 3 (2018) e00462. [PMID: 29404411]
[EC 1.1.2.10 created 2019]
 
 
EC 1.1.5.5     
Accepted name: alcohol dehydrogenase (quinone)
Reaction: ethanol + ubiquinone = acetaldehyde + ubiquinol
Other name(s): type III ADH; membrane associated quinohaemoprotein alcohol dehydrogenase
Systematic name: alcohol:quinone oxidoreductase
Comments: Only described in acetic acid bacteria where it is involved in acetic acid production. Associated with membrane. Electron acceptor is membrane ubiquinone. A model structure suggests that, like all other quinoprotein alcohol dehydrogenases, the catalytic subunit has an 8-bladed ‘propeller’ structure, a calcium ion bound to the PQQ in the active site and an unusual disulfide ring structure in close proximity to the PQQ; the catalytic subunit also has a heme c in the C-terminal domain. The enzyme has two additional subunits, one of which contains three molecules of heme c. It does not require amines for activation. It has a restricted substrate specificity, oxidizing a few primary alcohols (C2 to C6), but not methanol, secondary alcohols and some aldehydes. It is assayed with phenazine methosulfate or with ferricyanide.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Gomez-Manzo, S., Contreras-Zentella, M., Gonzalez-Valdez, A., Sosa-Torres, M., Arreguin-Espinoza, R. and Escamilla-Marvan, E. The PQQ-alcohol dehydrogenase of Gluconacetobacter diazotrophicus. Int. J. Food Microbiol. 125 (2008) 71–78. [DOI] [PMID: 18321602]
2.  Shinagawa, E., Toyama, H., Matsushita, K., Tuitemwong, P., Theeragool, G. and Adachi, O. A novel type of formaldehyde-oxidizing enzyme from the membrane of Acetobacter sp. SKU 14. Biosci. Biotechnol. Biochem. 70 (2006) 850–857. [DOI] [PMID: 16636451]
3.  Chinnawirotpisan, P., Theeragool, G., Limtong, S., Toyama, H., Adachi, O.O. and Matsushita, K. Quinoprotein alcohol dehydrogenase is involved in catabolic acetate production, while NAD-dependent alcohol dehydrogenase in ethanol assimilation in Acetobacter pasteurianus SKU1108. J. Biosci. Bioeng. 96 (2003) 564–571. [DOI] [PMID: 16233574]
4.  Frebortova, J., Matsushita, K., Arata, H. and Adachi, O. Intramolecular electron transport in quinoprotein alcohol dehydrogenase of Acetobacter methanolicus: a redox-titration stud. Biochim. Biophys. Acta 1363 (1998) 24–34. [DOI] [PMID: 9526036]
5.  Matsushita, K., Kobayashi, Y., Mizuguchi, M., Toyama, H., Adachi, O., Sakamoto, K. and Miyoshi, H. A tightly bound quinone functions in the ubiquinone reaction sites of quinoprotein alcohol dehydrogenase of an acetic acid bacterium, Gluconobacter suboxydans. Biosci. Biotechnol. Biochem. 72 (2008) 2723–2731. [DOI] [PMID: 18838797]
6.  Matsushita, K., Yakushi, T., Toyama, H., Shinagawa, E. and Adachi, O. Function of multiple heme c moieties in intramolecular electron transport and ubiquinone reduction in the quinohemoprotein alcohol dehydrogenase-cytochrome c complex of Gluconobacter suboxydans. J. Biol. Chem. 271 (1996) 4850–4857. [DOI] [PMID: 8617755]
7.  Matsushita, K., Takaki, Y., Shinagawa, E., Ameyama, M. and Adachi, O. Ethanol oxidase respiratory chain of acetic acid bacteria. Reactivity with ubiquinone of pyrroloquinoline quinone-dependent alcohol dehydrogenases purified from Acetobacter aceti and Gluconobacter suboxydans. Biosci. Biotechnol. Biochem. 56 (1992) 304–310.
8.  Matsushita, K., Toyama, H. and Adachi, O. Respiratory chains and bioenergetics of acetic acid bacteria. Adv. Microb. Physiol. 36 (1994) 247–301. [PMID: 7942316]
9.  Cozier, G.E., Giles, I.G. and Anthony, C. The structure of the quinoprotein alcohol dehydrogenase of Acetobacter aceti modelled on that of methanol dehydrogenase from Methylobacterium extorquens. Biochem. J. 308 (1995) 375–379. [PMID: 7772016]
[EC 1.1.5.5 created 2009, modified 2010]
 
 
EC 1.1.99.37     
Accepted name: methanol dehydrogenase (nicotinoprotein)
Reaction: methanol + acceptor = formaldehyde + reduced acceptor
Other name(s): NDMA-dependent methanol dehydrogenase; nicotinoprotein methanol dehydrogenase; methanol:N,N-dimethyl-4-nitrosoaniline oxidoreductase
Systematic name: methanol:acceptor oxidoreductase
Comments: Contains Zn2+ and Mg2+. Nicotinoprotein methanol dehydrogenases have a tightly bound NADP+/NADPH cofactor that does not dissociate during the catalytic process. Instead, the cofactor is regenerated by a second substrate or electron carrier. While the in vivo electron acceptor is not known, N,N-dimethyl-4-nitrosoaniline (NDMA), which is reduced to 4-(hydroxylamino)-N,N-dimethylaniline, can serve this function in vitro. The enzyme has been detected in several Gram-positive methylotrophic bacteria, including Amycolatopsis methanolica, Rhodococcus rhodochrous and Rhodococcus erythropolis [1-3]. These enzymes are decameric, and possess a 5-fold symmetry [4]. Some of the enzymes can also dismutate formaldehyde to methanol and formate [5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Vonck, J., Arfman, N., De Vries, G.E., Van Beeumen, J., Van Bruggen, E.F. and Dijkhuizen, L. Electron microscopic analysis and biochemical characterization of a novel methanol dehydrogenase from the thermotolerant Bacillus sp. C1. J. Biol. Chem. 266 (1991) 3949–3954. [PMID: 1995642]
2.  Van Ophem, P.W., Van Beeumen, J. and Duine, J.A. Nicotinoprotein [NAD(P)-containing] alcohol/aldehyde oxidoreductases. Purification and characterization of a novel type from Amycolatopsis methanolica. Eur. J. Biochem. 212 (1993) 819–826. [DOI] [PMID: 8385013]
3.  Bystrykh, L.V., Vonck, J., van Bruggen, E.F., van Beeumen, J., Samyn, B., Govorukhina, N.I., Arfman, N., Duine, J.A. and Dijkhuizen, L. Electron microscopic analysis and structural characterization of novel NADP(H)-containing methanol: N,N′-dimethyl-4-nitrosoaniline oxidoreductases from the gram-positive methylotrophic bacteria Amycolatopsis methanolica and Mycobacterium gastri MB19. J. Bacteriol. 175 (1993) 1814–1822. [DOI] [PMID: 8449887]
4.  Hektor, H.J., Kloosterman, H. and Dijkhuizen, L. Identification of a magnesium-dependent NAD(P)(H)-binding domain in the nicotinoprotein methanol dehydrogenase from Bacillus methanolicus. J. Biol. Chem. 277 (2002) 46966–46973. [DOI] [PMID: 12351635]
5.  Park, H., Lee, H., Ro, Y.T. and Kim, Y.M. Identification and functional characterization of a gene for the methanol : N,N′-dimethyl-4-nitrosoaniline oxidoreductase from Mycobacterium sp. strain JC1 (DSM 3803). Microbiology 156 (2010) 463–471. [DOI] [PMID: 19875438]
[EC 1.1.99.37 created 2010]
 
 
EC 1.2.1.1      
Deleted entry:  glutathione-dependent formaldehyde dehydrogenase. This enzyme was classified on the basis of an incorrect reaction. It has been replaced by two enzymes, EC 1.1.1.284, S-(hydroxymethyl)glutathione dehydrogenase and EC 4.4.1.22, S-(hydroxymethyl)glutathione synthase
[EC 1.2.1.1 created 1961, modified 1982, modified 2002, deleted 2005]
 
 
EC 1.2.1.46     
Accepted name: formaldehyde dehydrogenase
Reaction: formaldehyde + NAD+ + H2O = formate + NADH + 2 H+
Other name(s): NAD-linked formaldehyde dehydrogenase; NAD-dependent formaldehyde dehydrogenase
Systematic name: formaldehyde:NAD+ oxidoreductase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, UM-BBD, CAS registry number: 9028-84-6
References:
1.  Hohnloser, W., Osswald, B. and Lingens, F. Enzymological aspects of caffeine demethylation and formaldehyde oxidation by Pseudomonas putida C1. Hoppe-Seyler's Z. Physiol. Chem. 361 (1980) 1763–1766. [PMID: 7461603]
[EC 1.2.1.46 created 1982]
 
 
EC 1.2.1.66      
Transferred entry: mycothiol-dependent formaldehyde dehydrogenase. Now EC 1.1.1.306, S-(hydroxymethyl)mycothiol dehydrogenase
[EC 1.2.1.66 created 2000, deleted 2010]
 
 
EC 1.2.1.73     
Accepted name: sulfoacetaldehyde dehydrogenase
Reaction: 2-sulfoacetaldehyde + H2O + NAD+ = sulfoacetate + NADH + 2 H+
Glossary: 2-sulfoacetaldehyde = 2-oxoethanesulfonate
taurine = 2-aminoethanesulfonate
Other name(s): SafD
Systematic name: 2-sulfoacetaldehyde:NAD+ oxidoreductase
Comments: This reaction is part of a bacterial pathway that can utilize the amino group of taurine as a sole source of nitrogen for growth. At physiological concentrations, NAD+ cannot be replaced by NADP+. The enzyme is specific for sulfoacetaldehyde, as formaldehyde, acetaldehyde, betaine aldehyde, propanal, glyceraldehyde, phosphonoacetaldehyde, glyoxylate, glycolaldehyde and 2-oxobutyrate are not substrates.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Krejčík, Z., Denger, K., Weinitschke, S., Hollemeyer, K., Pačes, V., Cook, A.M. and Smits, T.H.M. Sulfoacetate released during the assimilation of taurine-nitrogen by Neptuniibacter caesariensis: purification of sulfoacetaldehyde dehydrogenase. Arch. Microbiol. 190 (2008) 159–168. [DOI] [PMID: 18506422]
[EC 1.2.1.73 created 2008]
 
 
EC 1.2.7.5     
Accepted name: aldehyde ferredoxin oxidoreductase
Reaction: an aldehyde + H2O + 2 oxidized ferredoxin = a carboxylate + 2 H+ + 2 reduced ferredoxin
Other name(s): AOR
Systematic name: aldehyde:ferredoxin oxidoreductase
Comments: This is an oxygen-sensitive enzyme that contains tungsten-molybdopterin and iron-sulfur clusters. Catalyses the oxidation of aldehydes (including crotonaldehyde, acetaldehyde, formaldehyde and glyceraldehyde) to their corresponding acids. However, it does not oxidize glyceraldehyde 3-phosphate [see EC 1.2.7.6, glyceraldehyde-3-phosphate dehydrogenase (ferredoxin)]. Can use ferredoxin or methylviologen but not NAD(P)+ as electron acceptor.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 138066-90-7
References:
1.  Mukund, S. and Adams, M.W.W. The novel tungsten-iron-sulfur protein of the hyperthermophilic archaebacterium, Pyrococcus furiosus, is an aldehyde ferredoxin oxidoreductase - evidence for its participation in a unique glycolytic pathway. J. Biol. Chem. 266 (1991) 14208–14216. [PMID: 1907273]
2.  Johnson, J.L., Rajagopalan, K.V., Mukund, S. and Adams, M.W.W. Identification of molybdopterin as the organic-component of the tungsten cofactor in four enzymes from hyperthermophilic archaea. J. Biol. Chem. 268 (1993) 4848–4852. [PMID: 8444863]
3.  Chan, M.K., Mukund, S., Kletzin, A., Adams, M.W.W. and Rees, D.C. Structure of a hyperthermophilic tungstopterin enzyme, aldehyde ferredoxin oxidoreductase. Science 267 (1995) 1463–1469. [DOI] [PMID: 7878465]
4.  Roy, R., Menon, A.L. and Adams, M.W.W. Aldehyde oxidoreductases from Pyrococcus furiosus. Methods Enzymol. 331 (2001) 132–144. [DOI] [PMID: 11265456]
[EC 1.2.7.5 created 2003]
 
 
EC 1.2.98.1     
Accepted name: formaldehyde dismutase
Reaction: 2 formaldehyde + H2O = formate + methanol
Other name(s): aldehyde dismutase; cannizzanase; nicotinoprotein aldehyde dismutase
Systematic name: formaldehyde:formaldehyde oxidoreductase
Comments: The enzyme contains a tightly but noncovalently bound NADP(H) cofactor, as well as Zn2+ and Mg2+. Enzyme-bound NADPH formed by oxidation of formaldehyde to formate is oxidized back to NADP+ by reaction with a second formaldehyde, yielding methanol. The enzyme from the bacterium Mycobacterium sp. DSM 3803 also catalyses the reactions of EC 1.1.99.36, alcohol dehydrogenase (nicotinoprotein) and EC 1.1.99.37, methanol dehydrogenase (nicotinoprotein) [3]. Formaldehyde and acetaldehyde can act as donors; formaldehyde, acetaldehyde and propanal can act as acceptors [1,2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 85204-94-0
References:
1.  Kato, N., Shirakawa, K., Kobayashi, H. and Sakazawa, C. The dismutation of aldehydes by a bacterial enzyme. Agric. Biol. Chem. 47 (1983) 39–46.
2.  Kato, N., Yamagami, T., Shimao, M. and Sakazawa, C. Formaldehyde dismutase, a novel NAD-binding oxidoreductase from Pseudomonas putida F61. Eur. J. Biochem. 156 (1986) 59–64. [DOI] [PMID: 3514215]
3.  Park, H., Lee, H., Ro, Y.T. and Kim, Y.M. Identification and functional characterization of a gene for the methanol : N,N′-dimethyl-4-nitrosoaniline oxidoreductase from Mycobacterium sp. strain JC1 (DSM 3803). Microbiology 156 (2010) 463–471. [DOI] [PMID: 19875438]
[EC 1.2.98.1 created 1986 as EC 1.2.99.4, modified 2012, transferred 2015 to EC 1.2.98.1]
 
 
EC 1.2.99.4      
Transferred entry: formaldehyde dismutase. Now EC 1.2.98.1, formaldehyde dismutase.
[EC 1.2.99.4 created 1986, modified 2012, deleted 2015]
 
 
EC 1.4.9.1     
Accepted name: methylamine dehydrogenase (amicyanin)
Reaction: methylamine + H2O + 2 amicyanin = formaldehyde + NH3 + 2 reduced amicyanin
Glossary: TTQ = tryptophan tryptophylquinone
amicyanin = an electron-transfer protein containing a type-1 copper site.
Other name(s): amine dehydrogenase; primary-amine dehydrogenase; amine: (acceptor) oxidoreductase (deaminating); primary-amine:(acceptor) oxidoreductase (deaminating)
Systematic name: methylamine:amicyanin oxidoreductase (deaminating)
Comments: Contains tryptophan tryptophylquinone (TTQ) cofactor. The enzyme oxidizes aliphatic monoamines and diamines, histamine and ethanolamine, but not secondary and tertiary amines, quaternary ammonium salts or aromatic amines.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, UM-BBD
References:
1.  De Beer, R., Duine, J.A., Frank, J., Jr. and Large, P.J. The prosthetic group of methylamine dehydrogenase from Pseudomonas AM1: evidence for a quinone structure. Biochim. Biophys. Acta 622 (1980) 370–374. [DOI] [PMID: 6246962]
2.  Eady, R.R. and Large, P.J. Purification and properties of an amine dehydrogenase from Pseudomonas AM1 and its role in growth on methylamine. Biochem. J. 106 (1968) 245–255. [PMID: 4388687]
3.  Eady, R.R. and Large, P.J. Microbial oxidation of amines. Spectral and kinetic properties of the primary amine dehydrogenase of Pseudomonas AM1. Biochem. J. 123 (1971) 757–771. [PMID: 5124384]
4.  Cavalieri, C., Biermann, N., Vlasie, M.D., Einsle, O., Merli, A., Ferrari, D., Rossi, G.L. and Ubbink, M. Structural comparison of crystal and solution states of the 138 kDa complex of methylamine dehydrogenase and amicyanin from Paracoccus versutus. Biochemistry 47 (2008) 6560–6570. [DOI] [PMID: 18512962]
5.  Meschi, F., Wiertz, F., Klauss, L., Cavalieri, C., Blok, A., Ludwig, B., Heering, H.A., Merli, A., Rossi, G.L. and Ubbink, M. Amicyanin transfers electrons from methylamine dehydrogenase to cytochrome c-551i via a ping-pong mechanism, not a ternary complex. J. Am. Chem. Soc. 132 (2010) 14537–14545. [DOI] [PMID: 20873742]
[EC 1.4.9.1 created 1978 as EC 1.4.99.3, modified 1986, transferred 2011 to EC 1.4.98.1, transferred 2011 to EC 1.4.9.1]
 
 
EC 1.4.98.1      
Transferred entry: amine dehydrogenase. Now EC 1.4.9.1, methylamine dehydrogenase (amicyanin)
[EC 1.4.98.1 created 1978 as EC 1.4.99.3, modified 1986, transferred 2011 to EC 1.4.98.1, deleted 2011]
 
 
EC 1.5.3.1     
Accepted name: sarcosine oxidase
Reaction: sarcosine + H2O + O2 = glycine + formaldehyde + H2O2
Systematic name: sarcosine:oxygen oxidoreductase (demethylating)
Comments: A flavoprotein (FAD). The flavin is both covalently and non-covalently bound in a molar ratio of 1:1.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9029-22-5
References:
1.  Hayashi, S., Nakamura, S. and Suzuki, M. Corynebacterium sarcosine oxidase: a unique enzyme having covalently-bound and noncovalently-bound flavins. Biochem. Biophys. Res. Commun. 96 (1980) 924–930. [DOI] [PMID: 6158947]
2.  Mori, N., Sano, M., Tani, Y. and Yamada, H. Purification and propertie of sarcosine oxidase from Cylindrocarpon didymum M-1. Agric. Biol. Chem. 44 (1980) 1391–1397.
3.  Suzuki, M. Purification and some properties of sarcosine oxidase from Corynebacterium sp. U-96. J. Biochem. (Tokyo) 89 (1981) 599–607. [PMID: 7240129]
[EC 1.5.3.1 created 1961]
 
 
EC 1.5.3.2     
Accepted name: N-methyl-L-amino-acid oxidase
Reaction: an N-methyl-L-amino acid + H2O + O2 = an L-amino acid + formaldehyde + H2O2
Other name(s): N-methylamino acid oxidase; demethylase
Systematic name: N-methyl-L-amino-acid:oxygen oxidoreductase (demethylating)
Comments: A flavoprotein.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9029-23-6
References:
1.  Moritani, M. Demethylase. IV. Kinetics and reaction mechanism. Hukuoka Acta Med. 43 (1952) 651–658.
2.  Moritani, M. Demethylase. V. Specificity and its relation to amino acid oxidase. Hukuoka Acta Med. 43 (1952) 731–735.
3.  Moritani, M., Tung, T.-C., Fujii, S., Mito, H., Izumika, N., Kenmochi, K. and Hirohata, R. Specificity of rabbit kidney demethylase. J. Biol. Chem. 209 (1954) 485–492. [PMID: 13192101]
[EC 1.5.3.2 created 1961]
 
 
EC 1.5.3.4     
Accepted name: N6-methyl-lysine oxidase
Reaction: N6-methyl-L-lysine + H2O + O2 = L-lysine + formaldehyde + H2O2
Other name(s): ε-alkyl-L-lysine:oxygen oxidoreductase ; N6-methyllysine oxidase; ε-N-methyllysine demethylase; ε-alkyllysinase; 6-N-methyl-L-lysine:oxygen oxidoreductase (demethylating)
Systematic name: N6-methyl-L-lysine:oxygen oxidoreductase (demethylating)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37256-28-3
References:
1.  Kim, S., Benoiton, L. and Paik, W.K. α-Alkyllysinase. Purification and properties of the enzyme. J. Biol. Chem. 239 (1964) 3790–3796. [PMID: 14257609]
[EC 1.5.3.4 created 1972]
 
 
EC 1.5.3.10     
Accepted name: dimethylglycine oxidase
Reaction: N,N-dimethylglycine + H2O + O2 = sarcosine + formaldehyde + H2O2
Systematic name: N,N-dimethylglycine:oxygen oxidoreductase (demethylating)
Comments: A flavoprotein (FAD). Does not oxidize sarcosine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37256-30-7
References:
1.  Mori, N., Kawakami, B., Tani, Y. and Yamada, H. Purification and properties of dimethylglycine oxidase from Cylindrocarpon didymum M-1. Agric. Biol. Chem. 44 (1980) 1383–1389.
[EC 1.5.3.10 created 1992]
 
 
EC 1.5.3.19     
Accepted name: 4-methylaminobutanoate oxidase (formaldehyde-forming)
Reaction: 4-methylaminobutanoate + O2 + H2O = 4-aminobutanoate + formaldehyde + H2O2
For diagram of nicotine catabolism by arthrobacter, click here
Other name(s): mabO (gene name)
Systematic name: 4-methylaminobutanoate:oxygen oxidoreductase (formaldehyde-forming)
Comments: A flavoprotein (FAD). In the enzyme from the soil bacterium Arthrobacter nicotinovorans the cofactor is covalently bound. Participates in the nicotine degradation pathway of this organism.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, UM-BBD
References:
1.  Chiribau, C.B., Sandu, C., Fraaije, M., Schiltz, E. and Brandsch, R. A novel γ-N-methylaminobutyrate demethylating oxidase involved in catabolism of the tobacco alkaloid nicotine by Arthrobacter nicotinovorans pAO1. Eur. J. Biochem. 271 (2004) 4677–4684. [DOI] [PMID: 15606755]
[EC 1.5.3.19 created 2012]
 
 
EC 1.5.8.1     
Accepted name: dimethylamine dehydrogenase
Reaction: dimethylamine + H2O + electron-transfer flavoprotein = methylamine + formaldehyde + reduced electron-transfer flavoprotein
Systematic name: dimethylamine:electron-transfer flavoprotein oxidoreductase
Comments: Contains FAD and a [4Fe-4S] cluster.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, UM-BBD, CAS registry number: 68247-64-3
References:
1.  Yang, C.C., Packman, L.C. and Scrutton, N.S. The primary structure of Hyphomicrobium X dimethylamine dehydrogenase. Relationship to trimethylamine dehydrogenase and implications for substrate recognition. Eur. J. Biochem. 232 (1995) 264–271. [DOI] [PMID: 7556160]
[EC 1.5.8.1 created 1999 as EC 1.5.99.10, transferred 2002 to EC 1.5.8.1]
 
 
EC 1.5.8.2     
Accepted name: trimethylamine dehydrogenase
Reaction: trimethylamine + H2O + electron-transfer flavoprotein = dimethylamine + formaldehyde + reduced electron-transfer flavoprotein
Systematic name: trimethylamine:electron-transfer flavoprotein oxidoreductase (demethylating)
Comments: A number of alkyl-substituted derivatives of trimethylamine can also act as electron donors; phenazine methosulfate and 2,6-dichloroindophenol can act as electron acceptors. Contains FAD and a [4Fe-4S] cluster.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, UM-BBD, CAS registry number: 39307-09-0
References:
1.  Colby, J. and Zatman, L.J. The purification and properties of a bacterial trimethylamine dehydrogenase. Biochem. J. 121 (1971) 9P–10P. [PMID: 5116569]
2.  Steenkamp, D.J. and Singer, T.P. Participation of the iron-sulphur cluster and of the covalently bound coenzyme of trimethylamine dehydrogenase in catalysis. Biochem. J. 169 (1978) 361–369. [PMID: 204297]
3.  Huang, L.X., Rohlfs, R.J. and Hille, R. The reaction of trimethylamine dehydrogenase with electron transferring flavoprotein. J. Biol. Chem. 270 (1995) 23958–23965. [DOI] [PMID: 7592591]
4.  Jones, M., Talfournier, F., Bobrov, A., Grossmann, J.G., Vekshin, N., Sutcliffe, M.J. and Scrutton, N.S. Electron transfer and conformational change in complexes of trimethylamine dehydrogenase and electron transferring flavoprotein. J. Biol. Chem. 277 (2002) 8457–8465. [DOI] [PMID: 11756429]
5.  Scrutton, N.S. and Sutcliffe, M.J. Trimethylamine dehydrogenase and electron transferring flavoprotein. Subcell. Biochem. 35 (2000) 145–181. [PMID: 11192721]
[EC 1.5.8.2 created 1976 as EC 1.5.99.7, transferred 2002 to EC 1.5.8.2]
 
 
EC 1.5.8.3     
Accepted name: sarcosine dehydrogenase
Reaction: sarcosine + H2O + electron-transfer flavoprotein = glycine + formaldehyde + reduced electron-transfer flavoprotein
Other name(s): sarcosine N-demethylase; monomethylglycine dehydrogenase; sarcosine:(acceptor) oxidoreductase (demethylating)
Systematic name: sarcosine:electron-transfer flavoprotein oxidoreductase (demethylating)
Comments: A flavoprotein (FMN). Tetrahydrofolate is also a substrate, being converted to N5,N10-methylenetetrahydrofolate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37228-65-2, 93389-49-2
References:
1.  Hoskins, D.D. and MacKenzie, C.G. Solubilization and electron transfer flavoprotein requirement of mitochondrial sarcosine dehydrogenase and dimethylglycine dehydrogenase. J. Biol. Chem. 236 (1961) 177–183. [PMID: 13716069]
2.  Frisell, W.R. and MacKenzie, C.G. Separation and purification of sarcosine dehydrogenase and dimethylglycine dehydrogenase. J. Biol. Chem. 237 (1962) 94–98. [PMID: 13895406]
3.  Steenkamp, D.J. and Husain, M. The effect of tetrahydrofolate on the reduction of electron transfer flavoprotein by sarcosine and dimethylglycine dehydrogenases. Biochem. J. 203 (1982) 707–715. [PMID: 6180732]
[EC 1.5.8.3 created 1972 as EC 1.5.99.1, transferred 2012 to EC 1.5.8.3]
 
 
EC 1.5.8.4     
Accepted name: dimethylglycine dehydrogenase
Reaction: N,N-dimethylglycine + 5,6,7,8-tetrahydrofolate + electron-transfer flavoprotein = sarcosine + 5,10-methylenetetrahydrofolate + reduced electron-transfer flavoprotein
Glossary: sarcosine = N-methylglycine
Other name(s): N,N-dimethylglycine oxidase; N,N-dimethylglycine:(acceptor) oxidoreductase (demethylating); Me2GlyDH; N,N-dimethylglycine:electron-transfer flavoprotein oxidoreductase (demethylating)
Systematic name: N,N-dimethylglycine,5,6,7,8-tetrahydrofolate:electron-transferflavoprotein oxidoreductase (demethylating,5,10-methylenetetrahydrofolate-forming)
Comments: A flavoprotein, containing a histidyl(Nπ)-(8α)FAD linkage at position 91 in the human protein. An imine intermediate is channeled from the FAD binding site to the 5,6,7,8-tetrahydrofolate binding site through a 40 Å tunnel [5,8,9]. In the absence of 5,6,7,8-tetrahydrofolate the enzyme forms formaldehyde [5,9].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37256-30-7
References:
1.  Frisell, W.R. and MacKenzie, C.G. Separation and purification of sarcosine dehydrogenase and dimethylglycine dehydrogenase. J. Biol. Chem. 237 (1962) 94–98. [PMID: 13895406]
2.  Hoskins, D.D. and MacKenzie, C.G. Solubilization and electron transfer flavoprotein requirement of mitochondrial sarcosine dehydrogenase and dimethylglycine dehydrogenase. J. Biol. Chem. 236 (1961) 177–183. [PMID: 13716069]
3.  Wittwer, A.J. and Wagner, C. Identification of the folate-binding proteins of rat liver mitochondria as dimethylglycine dehydrogenase and sarcosine dehydrogenase. Purification and folate-binding characteristics. J. Biol. Chem. 256 (1981) 4102–4108. [PMID: 6163777]
4.  Wittwer, A.J. and Wagner, C. Identification of the folate-binding proteins of rat liver mitochondria as dimethylglycine dehydrogenase and sarcosine dehydrogenase. Flavoprotein nature and enzymatic properties of the purified proteins. J. Biol. Chem. 256 (1981) 4109–4115. [PMID: 6163778]
5.  Porter, D.H., Cook, R.J. and Wagner, C. Enzymatic properties of dimethylglycine dehydrogenase and sarcosine dehydrogenase from rat liver. Arch. Biochem. Biophys. 243 (1985) 396–407. [DOI] [PMID: 2417560]
6.  Brizio, C., Brandsch, R., Bufano, D., Pochini, L., Indiveri, C. and Barile, M. Over-expression in Escherichia coli, functional characterization and refolding of rat dimethylglycine dehydrogenase. Protein Expr. Purif. 37 (2004) 434–442. [DOI] [PMID: 15358367]
7.  Brizio, C., Brandsch, R., Douka, M., Wait, R. and Barile, M. The purified recombinant precursor of rat mitochondrial dimethylglycine dehydrogenase binds FAD via an autocatalytic reaction. Int. J. Biol. Macromol. 42 (2008) 455–462. [DOI] [PMID: 18423846]
8.  Luka, Z., Pakhomova, S., Loukachevitch, L.V., Newcomer, M.E. and Wagner, C. Folate in demethylation: the crystal structure of the rat dimethylglycine dehydrogenase complexed with tetrahydrofolate. Biochem. Biophys. Res. Commun. 449 (2014) 392–398. [DOI] [PMID: 24858690]
9.  Augustin, P., Hromic, A., Pavkov-Keller, T., Gruber, K. and Macheroux, P. Structure and biochemical properties of recombinant human dimethylglycine dehydrogenase and comparison to the disease-related H109R variant. FEBS J. 283 (2016) 3587–3603. [DOI] [PMID: 27486859]
[EC 1.5.8.4 created 1972 as EC 1.5.99.2, transferred 2012 to EC 1.5.8.4, modified 2017]
 
 
EC 1.5.99.1      
Transferred entry: sarcosine dehydrogenase. Now EC 1.5.8.3, sarcosine dehydrogenase
[EC 1.5.99.1 created 1972, deleted 2012]
 
 
EC 1.5.99.2      
Transferred entry: dimethylglycine dehydrogenase. Now EC 1.5.8.4, dimethylglycine dehydrogenase
[EC 1.5.99.2 created 1972, deleted 2012]
 
 
EC 1.5.99.5     
Accepted name: methylglutamate dehydrogenase
Reaction: N-methyl-L-glutamate + acceptor + H2O = L-glutamate + formaldehyde + reduced acceptor
Other name(s): N-methylglutamate dehydrogenase; N-methyl-L-glutamate:(acceptor) oxidoreductase (demethylating)
Systematic name: N-methyl-L-glutamate:acceptor oxidoreductase (demethylating)
Comments: A number of N-methyl-substituted amino acids can act as donor; 2,6-dichloroindophenol is the best acceptor.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37217-26-8
References:
1.  Hersh, L.B., Stark, M.J., Worthen, S. and Fiero, M.K. N-Methylglutamate dehydrogenase: kinetic studies on the solubilized enzyme. Arch. Biochem. Biophys. 150 (1972) 219–226. [DOI] [PMID: 5028076]
[EC 1.5.99.5 created 1976]
 
 
EC 1.8.3.4     
Accepted name: methanethiol oxidase
Reaction: methanethiol + O2 + H2O = formaldehyde + hydrogen sulfide + H2O2
For diagram of dimethyl sulfide catabolism, click here
Other name(s): methylmercaptan oxidase; methyl mercaptan oxidase; (MM)-oxidase; MT-oxidase
Systematic name: methanethiol:oxygen oxidoreductase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, UM-BBD, CAS registry number: 289686-00-6
References:
1.  Suylen, G.M.H., Large, P.J., van Dijken, J.P. and Kuenen, J.G. Methylmercaptan oxidase, a key enzyme in the metabolism of methylated sulphur compounds by Hyphomicrobium EG. J. Gen. Microbiol. 133 (1987) 2989–2997.
[EC 1.8.3.4 created 1990]
 
 
EC 1.14.11.27     
Accepted name: [histone H3]-dimethyl-L-lysine36 demethylase
Reaction: a [histone H3]-N6,N6-dimethyl-L-lysine36 + 2 2-oxoglutarate + 2 O2 = a [histone H3]-L-lysine36 + 2 succinate + 2 formaldehyde + 2 CO2 (overall reaction)
(1a) a [histone H3]-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2 = a [histone H3]-N6-methyl-L-lysine36 + succinate + formaldehyde + CO2
(1b) a [histone H3]-N6-methyl-L-lysine36 + 2-oxoglutarate + O2 = a [histone H3]-L-lysine36 + succinate + formaldehyde + CO2
Other name(s): KDM2A (gene name); KDM2B (gene name); JHDM1A (gene name); JHDM1B (gene name); JmjC domain-containing histone demethylase 1A; H3-K36-specific demethylase (ambiguous); histone-lysine (H3-K36) demethylase (ambiguous); histone demethylase (ambiguous); protein-6-N,6-N-dimethyl-L-lysine,2-oxoglutarate:oxygen oxidoreductase; protein-N6,N6-dimethyl-L-lysine,2-oxoglutarate:oxygen oxidoreductase; [histone-H3]-lysine-36 demethylase
Systematic name: [histone H3]-N6,N6-dimethyl-L-lysine36,2-oxoglutarate:oxygen oxidoreductase
Comments: Requires iron(II). Of the seven potential methylation sites in histones H3 (K4, K9, K27, K36, K79) and H4 (K20, R3) from HeLa cells, the enzyme is specific for Lys36. Lysine residues exist in three methylation states (mono-, di- and trimethylated). The enzyme preferentially demethylates the dimethyl form of Lys36 (K36me2), which is its natural substrate, to form the monomethylated and unmethylated forms of Lys36. It can also demethylate monomethylated (but not the trimethylated) Lys36. cf. EC 1.14.11.69, [histone H3]-trimethyl-L-lysine36 demethylase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Tsukada, Y., Fang, J., Erdjument-Bromage, H., Warren, M.E., Borchers, C.H., Tempst, P. and Zhang, Y. Histone demethylation by a family of JmjC domain-containing proteins. Nature 439 (2006) 811–816. [DOI] [PMID: 16362057]
[EC 1.14.11.27 created 2006, modified 2019]
 
 
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 1.14.11.51     
Accepted name: DNA N6-methyladenine demethylase
Reaction: N6-methyladenine in DNA + 2-oxoglutarate + O2 = adenine in DNA + formaldehyde + succinate + CO2
Other name(s): ALKBH1
Systematic name: DNA-N6-methyladenosine,2-oxoglutarate:oxygen oxidoreductase (formaldehyde-forming)
Comments: Contains iron(II). Catalyses oxidative demethylation of DNA N6-methyladenine, a prevalent modification in LINE-1 transposons, which are specifically enriched on the human X chromosome.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Wu, T.P., Wang, T., Seetin, M.G., Lai, Y., Zhu, S., Lin, K., Liu, Y., Byrum, S.D., Mackintosh, S.G., Zhong, M., Tackett, A., Wang, G., Hon, L.S., Fang, G., Swenberg, J.A. and Xiao, A.Z. DNA methylation on N-adenine in mammalian embryonic stem cells. Nature 532 (2016) 329–333. [DOI] [PMID: 27027282]
[EC 1.14.11.51 created 2016]
 
 
EC 1.14.11.53     
Accepted name: mRNA N6-methyladenine demethylase
Reaction: N6-methyladenine in mRNA + 2-oxoglutarate + O2 = adenine in mRNA + formaldehyde + succinate + CO2
Other name(s): ALKBH5; FTO
Systematic name: mRNA-N6-methyladenosine,2-oxoglutarate:oxygen oxidoreductase (formaldehyde-forming)
Comments: Contains iron(II). Catalyses oxidative demethylation of mRNA N6-methyladenine. The FTO enzyme from human can also demethylate N3-methylthymine from single stranded DNA and N3-methyluridine from single stranded RNA [1,2] with low activity [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Jia, G., Yang, C.G., Yang, S., Jian, X., Yi, C., Zhou, Z. and He, C. Oxidative demethylation of 3-methylthymine and 3-methyluracil in single-stranded DNA and RNA by mouse and human FTO. FEBS Lett. 582 (2008) 3313–3319. [DOI] [PMID: 18775698]
2.  Han, Z., Niu, T., Chang, J., Lei, X., Zhao, M., Wang, Q., Cheng, W., Wang, J., Feng, Y. and Chai, J. Crystal structure of the FTO protein reveals basis for its substrate specificity. Nature 464 (2010) 1205–1209. [DOI] [PMID: 20376003]
3.  Jia, G., Fu, Y., Zhao, X., Dai, Q., Zheng, G., Yang, Y., Yi, C., Lindahl, T., Pan, T., Yang, Y.G. and He, C. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat. Chem. Biol. 7 (2011) 885–887. [DOI] [PMID: 22002720]
4.  Zheng, G., Dahl, J.A., Niu, Y., Fedorcsak, P., Huang, C.M., Li, C.J., Vagbo, C.B., Shi, Y., Wang, W.L., Song, S.H., Lu, Z., Bosmans, R.P., Dai, Q., Hao, Y.J., Yang, X., Zhao, W.M., Tong, W.M., Wang, X.J., Bogdan, F., Furu, K., Fu, Y., Jia, G., Zhao, X., Liu, J., Krokan, H.E., Klungland, A., Yang, Y.G. and He, C. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol. Cell 49 (2013) 18–29. [DOI] [PMID: 23177736]
5.  Feng, C., Liu, Y., Wang, G., Deng, Z., Zhang, Q., Wu, W., Tong, Y., Cheng, C. and Chen, Z. Crystal structures of the human RNA demethylase Alkbh5 reveal basis for substrate recognition. J. Biol. Chem. 289 (2014) 11571–11583. [DOI] [PMID: 24616105]
6.  Xu, C., Liu, K., Tempel, W., Demetriades, M., Aik, W., Schofield, C.J. and Min, J. Structures of human ALKBH5 demethylase reveal a unique binding mode for specific single-stranded N6-methyladenosine RNA demethylation. J. Biol. Chem. 289 (2014) 17299–17311. [DOI] [PMID: 24778178]
7.  Aik, W., Scotti, J.S., Choi, H., Gong, L., Demetriades, M., Schofield, C.J. and McDonough, M.A. Structure of human RNA N6-methyladenine demethylase ALKBH5 provides insights into its mechanisms of nucleic acid recognition and demethylation. Nucleic Acids Res. 42 (2014) 4741–4754. [DOI] [PMID: 24489119]
[EC 1.14.11.53 created 2016]
 
 
EC 1.14.11.54     
Accepted name: mRNA N1-methyladenine demethylase
Reaction: N1-methyladenine in mRNA + 2-oxoglutarate + O2 = adenine in mRNA + formaldehyde + succinate + CO2
Other name(s): ALKBH3
Systematic name: mRNA-N1-methyladenine,2-oxoglutarate:oxygen oxidoreductase (formaldehyde-forming)
Comments: Contains iron(II). Catalyses oxidative demethylation of mRNA N1-methyladenine. The enzyme is also involved in alkylation repair in DNA [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Sundheim, O., Vågbø, C.B., Bjørås, M., Sousa, M.M., Talstad, V., Aas, P.A., Drabløs, F., Krokan, H.E., Tainer, J.A. and Slupphaug, G. Human ABH3 structure and key residues for oxidative demethylation to reverse DNA/RNA damage. EMBO J. 25 (2006) 3389–3397. [DOI] [PMID: 16858410]
2.  Dango, S., Mosammaparast, N., Sowa, M.E., Xiong, L.J., Wu, F., Park, K., Rubin, M., Gygi, S., Harper, J.W. and Shi, Y. DNA unwinding by ASCC3 helicase is coupled to ALKBH3-dependent DNA alkylation repair and cancer cell proliferation. Mol. Cell 44 (2011) 373–384. [DOI] [PMID: 22055184]
3.  Li, X., Xiong, X., Wang, K., Wang, L., Shu, X., Ma, S. and Yi, C. Transcriptome-wide mapping reveals reversible and dynamic N-methyladenosine methylome. Nat. Chem. Biol. (2016) . [DOI] [PMID: 26863410]
[EC 1.14.11.54 created 2016]
 
 
EC 1.14.11.65     
Accepted name: [histone H3]-dimethyl-L-lysine9 demethylase
Reaction: a [histone H3]-N6,N6-dimethyl-L-lysine9 + 2 2-oxoglutarate + 2 O2 = a [histone H3]-L-lysine9 + 2 succinate + 2 formaldehyde + 2 CO2 (overall reaction)
(1a) a [histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2 = a [histone H3]-N6-methyl-L-lysine9 + succinate + formaldehyde + CO2
(1b) a [histone H3]-N6-methyl-L-lysine9 + 2-oxoglutarate + O2 = a [histone H3]-L-lysine9 + succinate + formaldehyde + CO2
Other name(s): KDM3A (gene name); KDM3B (gene name); JMJD1A (gene name); JMJD1B (gene name); JHDM2A (gene name); JHDM2B (gene name); KDM7B (gene name); PHF8 (gene name); HR (gene name)
Systematic name: [histone H3]-N6,N6-dimethyl-L-lysine9,2-oxoglutarate:oxygen oxidoreductase
Comments: Requires iron(II). This entry describes a group of enzymes that demethylate N-methylated Lys-9 residues in the tail of the histone protein H3 (H3K9). This lysine residue can exist in three methylation states (mono-, di- and trimethylated), but this group of enzymes only act on the the di- and mono-methylated forms. The enzymes are dioxygenases and act by hydroxylating the methyl group, forming an unstable hemiaminal that leaves as formaldehyde. cf. EC 1.14.11.66, [histone H3]-trimethyl-L-lysine9 demethylase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Yamane, K., Toumazou, C., Tsukada, Y., Erdjument-Bromage, H., Tempst, P., Wong, J. and Zhang, Y. JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor. Cell 125 (2006) 483–495. [PMID: 16603237]
2.  Loh, Y.H., Zhang, W., Chen, X., George, J. and Ng, H.H. Jmjd1a and Jmjd2c histone H3 Lys 9 demethylases regulate self-renewal in embryonic stem cells. Genes Dev. 21 (2007) 2545–2557. [PMID: 17938240]
3.  Feng, W., Yonezawa, M., Ye, J., Jenuwein, T. and Grummt, I. PHF8 activates transcription of rRNA genes through H3K4me3 binding and H3K9me1/2 demethylation. Nat. Struct. Mol. Biol. 17 (2010) 445–450. [PMID: 20208542]
4.  Kuroki, S., Matoba, S., Akiyoshi, M., Matsumura, Y., Miyachi, H., Mise, N., Abe, K., Ogura, A., Wilhelm, D., Koopman, P., Nozaki, M., Kanai, Y., Shinkai, Y. and Tachibana, M. Epigenetic regulation of mouse sex determination by the histone demethylase Jmjd1a. Science 341 (2013) 1106–1109. [PMID: 24009392]
5.  Liu, L., Kim, H., Casta, A., Kobayashi, Y., Shapiro, L.S. and Christiano, A.M. Hairless is a histone H3K9 demethylase. FASEB J. 28 (2014) 1534–1542. [PMID: 24334705]
[EC 1.14.11.65 created 2019]
 
 
EC 1.14.11.66     
Accepted name: [histone H3]-trimethyl-L-lysine9 demethylase
Reaction: a [histone H3]-N6,N6,N6-trimethyl-L-lysine9 + 2 2-oxoglutarate + 2 O2 = a [histone H3]-N6-methyl-L-lysine9 + 2 succinate + 2 formaldehyde + 2 CO2 (overall reaction)
(1a) a [histone H3]-N6,N6,N6-trimethyl-L-lysine9 + 2-oxoglutarate + O2 = a [histone H3]-N6,N6-dimethyl-L-lysine9 + succinate + formaldehyde + CO2
(1b) a [histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2 = a [histone H3]-N6-methyl-L-lysine9 + succinate + formaldehyde + CO2
Other name(s): KDM4A (gene name); KDM4B (gene name); KDM4C (gene name); KDM4D (gene name); JHDM3A (gene name); JMJD2 (gene name); JMJD2A (gene name); GASC1 (gene name)
Systematic name: [histone H3]-N6,N6,N6-trimethyl-L-lysine9,2-oxoglutarate:oxygen oxidoreductase
Comments: Requires iron(II). This entry describes a group of enzymes that demethylate N-methylated Lys-9 residues in the tail of the histone protein H3 (H3K9). This lysine residue can exist in three methylation states (mono-, di- and trimethylated), but this group of enzymes only act on the the tri- and di-methylated forms. The enzymes are dioxygenases and act by hydroxylating the methyl group, forming an unstable hemiaminal that leaves as formaldehyde. cf. EC 1.14.11.65, [histone H3]-dimethyl-L-lysine9 demethylase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Cloos, P.A., Christensen, J., Agger, K., Maiolica, A., Rappsilber, J., Antal, T., Hansen, K.H. and Helin, K. The putative oncogene GASC1 demethylates tri- and dimethylated lysine 9 on histone H3. Nature 442 (2006) 307–311. [PMID: 16732293]
2.  Fodor, B.D., Kubicek, S., Yonezawa, M., O'Sullivan, R.J., Sengupta, R., Perez-Burgos, L., Opravil, S., Mechtler, K., Schotta, G. and Jenuwein, T. Jmjd2b antagonizes H3K9 trimethylation at pericentric heterochromatin in mammalian cells. Genes Dev. 20 (2006) 1557–1562. [PMID: 16738407]
3.  Klose, R.J., Yamane, K., Bae, Y., Zhang, D., Erdjument-Bromage, H., Tempst, P., Wong, J. and Zhang, Y. The transcriptional repressor JHDM3A demethylates trimethyl histone H3 lysine 9 and lysine 36. Nature 442 (2006) 312–316. [PMID: 16732292]
4.  Whetstine, J.R., Nottke, A., Lan, F., Huarte, M., Smolikov, S., Chen, Z., Spooner, E., Li, E., Zhang, G., Colaiacovo, M. and Shi, Y. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 125 (2006) 467–481. [PMID: 16603238]
[EC 1.14.11.66 created 2019]
 
 
EC 1.14.11.67     
Accepted name: [histone H3]-trimethyl-L-lysine4 demethylase
Reaction: a [histone H3]-N6,N6,N6-trimethyl-L-lysine4 + 3 2-oxoglutarate + 3 O2 = a [histone H3]-L-lysine4 + 3 succinate + 3 formaldehyde + 3 CO2 (overall reaction)
(1a) a [histone H3]-N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2 = a [histone H3]-N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
(1b) a [histone H3]-N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2 = a [histone H3]-N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
(1c) a [histone H3]-N6-methyl-L-lysine4 + 2-oxoglutarate + O2 = a [histone H3]-L-lysine4 + succinate + formaldehyde + CO2
Other name(s): KDM5A (gene name); KDM5B (gene name); KDM5C (gene name); KDM5D (gene name); JARID1A (gene name)
Systematic name: [histone H3]-N6,N6,N6-trimethyl-L-lysine4,2-oxoglutarate:oxygen oxidoreductase
Comments: Requires iron(II). This entry describes a group of enzymes that demethylate N-methylated L-lysine residues at position 4 of histone H3 (H3K4). The enzymes are dioxygenases and act by hydroxylating the methyl group, forming an unstable hemiaminal that leaves as formaldehyde. They can act on tri-, di-, and mono-methylated forms.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Seward, D.J., Cubberley, G., Kim, S., Schonewald, M., Zhang, L., Tripet, B. and Bentley, D.L. Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC proteins. Nat. Struct. Mol. Biol. 14 (2007) 240–242. [PMID: 17310255]
2.  Klose, R.J., Yan, Q., Tothova, Z., Yamane, K., Erdjument-Bromage, H., Tempst, P., Gilliland, D.G., Zhang, Y. and Kaelin, W.G., Jr. The retinoblastoma binding protein RBP2 is an H3K4 demethylase. Cell 128 (2007) 889–900. [PMID: 17320163]
3.  Iwase, S., Lan, F., Bayliss, P., de la Torre-Ubieta, L., Huarte, M., Qi, H.H., Whetstine, J.R., Bonni, A., Roberts, T.M. and Shi, Y. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell 128 (2007) 1077–1088. [PMID: 17320160]
4.  Christensen, J., Agger, K., Cloos, P.A., Pasini, D., Rose, S., Sennels, L., Rappsilber, J., Hansen, K.H., Salcini, A.E. and Helin, K. RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3. Cell 128 (2007) 1063–1076. [PMID: 17320161]
[EC 1.14.11.67 created 2019]
 
 
EC 1.14.11.68     
Accepted name: [histone H3]-trimethyl-L-lysine27 demethylase
Reaction: a [histone H3]-N6,N6,N6-trimethyl-L-lysine27 + 2 2-oxoglutarate + 2 O2 = a [histone H3]-N6-methyl-L-lysine27 + 2 succinate + 2 formaldehyde + 2 CO2 (overall reaction)
(1a) a [histone H3]-N6,N6,N6-trimethyl-L-lysine27 + 2-oxoglutarate + O2 = a [histone H3]-N6,N6-dimethyl-L-lysine27 + succinate + formaldehyde + CO2
(1b) a [histone H3]-N6,N6-dimethyl-L-lysine27 + 2-oxoglutarate + O2 = a [histone H3]-N6-methyl-L-lysine27 + succinate + formaldehyde + CO2
Other name(s): KDM6A (gene name); KDM6C (gene name); UTX (gene name); UTY (gene name); JMJD3 (gene name)
Systematic name: [histone H3]-N6,N6,N6-trimethyl-L-lysine27,2-oxoglutarate:oxygen oxidoreductase
Comments: Requires iron(II). This entry describes a group of enzymes that demethylate N-methylated L-lysine residues at position 27 of histone H3 (H3K27). The enzymes are dioxygenases and act by hydroxylating the methyl group, forming an unstable hemiaminal that leaves as formaldehyde. They can act on tri- and di-methylated forms, but have no activity with the mono-methylated form.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  De Santa, F., Totaro, M.G., Prosperini, E., Notarbartolo, S., Testa, G. and Natoli, G. The histone H3 lysine-27 demethylase Jmjd3 links inflammation to inhibition of polycomb-mediated gene silencing. Cell 130 (2007) 1083–1094. [PMID: 17825402]
2.  Hong, S., Cho, Y.W., Yu, L.R., Yu, H., Veenstra, T.D. and Ge, K. Identification of JmjC domain-containing UTX and JMJD3 as histone H3 lysine 27 demethylases. Proc. Natl. Acad. Sci. USA 104 (2007) 18439–18444. [PMID: 18003914]
3.  Lan, F., Bayliss, P.E., Rinn, J.L., Whetstine, J.R., Wang, J.K., Chen, S., Iwase, S., Alpatov, R., Issaeva, I., Canaani, E., Roberts, T.M., Chang, H.Y. and Shi, Y. A histone H3 lysine 27 demethylase regulates animal posterior development. Nature 449 (2007) 689–694. [PMID: 17851529]
4.  Lee, M.G., Villa, R., Trojer, P., Norman, J., Yan, K.P., Reinberg, D., Di Croce, L. and Shiekhattar, R. Demethylation of H3K27 regulates polycomb recruitment and H2A ubiquitination. Science 318 (2007) 447–450. [PMID: 17761849]
5.  Xiang, Y., Zhu, Z., Han, G., Lin, H., Xu, L. and Chen, C.D. JMJD3 is a histone H3K27 demethylase. Cell Res. 17 (2007) 850–857. [PMID: 17923864]
[EC 1.14.11.68 created 2019]
 
 
EC 1.14.11.69     
Accepted name: [histone H3]-trimethyl-L-lysine36 demethylase
Reaction: a [histone H3]-N6,N6,N6-trimethyl-L-lysine36 + 2 2-oxoglutarate + 2 O2 = a [histone H3]-N6-methyl-L-lysine36 + 2 succinate + 2 formaldehyde + 2 CO2 (overall reaction)
(1a) a [histone H3]-N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2 = a [histone H3]-N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2
(1b) a [histone H3]-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2 = a [histone H3]-N6-methyl-L-lysine36 + succinate + formaldehyde + CO2
Other name(s): KDM4A (gene name); KDM4B (gene name); RPH1 (gene name); JHDM3A (gene name); JHDM3B (gene name); JMJD2A (gene name); JMJD2B (gene name)
Systematic name: [histone H3]-N6,N6,N6-trimethyl-L-lysine36,2-oxoglutarate:oxygen oxidoreductase
Comments: Requires iron(II). This entry describes a group of enzymes that demethylate N-methylated Lys36 residues in the tail of the histone protein H3 (H3K36). This lysine residue can exist in three methylation states (mono-, di- and trimethylated), but this group of enzymes only act on the the tri- and di-methylated forms. The enzymes are dioxygenases and act by hydroxylating the methyl group, forming an unstable hemiaminal that leaves as formaldehyde. Since trimethylation of H3K36 enhances transcription, this enzyme acts as a transcription repressor. The enzymes that possess this activity often also catalyse the activity of EC 1.14.11.66, [histone H3]-trimethyl-L-lysine9 demethylase. cf. EC 1.14.11.27, [histone H3]-dimethyl-L-lysine36 demethylase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Whetstine, J.R., Nottke, A., Lan, F., Huarte, M., Smolikov, S., Chen, Z., Spooner, E., Li, E., Zhang, G., Colaiacovo, M. and Shi, Y. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 125 (2006) 467–481. [PMID: 16603238]
2.  Klose, R.J., Yamane, K., Bae, Y., Zhang, D., Erdjument-Bromage, H., Tempst, P., Wong, J. and Zhang, Y. The transcriptional repressor JHDM3A demethylates trimethyl histone H3 lysine 9 and lysine 36. Nature 442 (2006) 312–316. [PMID: 16732292]
3.  Kim, T. and Buratowski, S. Two Saccharomyces cerevisiae JmjC domain proteins demethylate histone H3 Lys36 in transcribed regions to promote elongation. J. Biol. Chem. 282 (2007) 20827–20835. [PMID: 17525156]
4.  Couture, J.F., Collazo, E., Ortiz-Tello, P.A., Brunzelle, J.S. and Trievel, R.C. Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase. Nat. Struct. Mol. Biol. 14 (2007) 689–695. [PMID: 17589523]
5.  Lin, C.H., Li, B., Swanson, S., Zhang, Y., Florens, L., Washburn, M.P., Abmayr, S.M. and Workman, J.L. Heterochromatin protein 1a stimulates histone H3 lysine 36 demethylation by the Drosophila KDM4A demethylase. Mol. Cell 32 (2008) 696–706. [PMID: 19061644]
6.  Colmenares, S.U., Swenson, J.M., Langley, S.A., Kennedy, C., Costes, S.V. and Karpen, G.H. Drosophila histone demethylase KDM4A has enzymatic and non-enzymatic roles in controlling heterochromatin integrity. Dev Cell 42 (2017) 156–169.e5. [PMID: 28743002]
[EC 1.14.11.69 created 2019]
 
 
EC 1.14.13.82     
Accepted name: vanillate monooxygenase
Reaction: vanillate + O2 + NADH + H+ = 3,4-dihydroxybenzoate + NAD+ + H2O + formaldehyde
Glossary: vanillate = 4-hydroxy-3-methoxybenzoate
Other name(s): 4-hydroxy-3-methoxybenzoate demethylase; vanillate demethylase
Systematic name: vanillate:oxygen oxidoreductase (demethylating)
Comments: Forms part of the vanillin degradation pathway in Arthrobacter sp.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, UM-BBD, CAS registry number: 39307-11-4
References:
1.  Brunel, F. and Davison, J. Cloning and sequencing of Pseudomonas genes encoding vanillate demethylase. J. Bacteriol. 170 (1988) 4924–4930. [DOI] [PMID: 3170489]
2.  Priefert, H., Rabenhorst, J. and Steinbuchel, A. Molecular characterization of genes of Pseudomonas sp. strain HR199 involved in bioconversion of vanillin to protocatechuate. J. Bacteriol. 179 (1997) 2595–2607. [DOI] [PMID: 9098058]
[EC 1.14.13.82 created 2000 as EC 1.2.3.12, transferred 2003 to EC 1.14.13.82]
 
 
EC 1.14.13.111     
Accepted name: methanesulfonate monooxygenase (NADH)
Reaction: methanesulfonate + NADH + H+ + O2 = formaldehyde + NAD+ + sulfite + H2O
Glossary: methanesulfonate = CH3-SO3-
formaldehyde = H-CHO
Other name(s): mesylate monooxygenase; mesylate,reduced-FMN:oxygen oxidoreductase; MsmABC; methanesulfonic acid monooxygenase; MSA monooxygenase; MSAMO
Systematic name: methanesulfonate,NADH:oxygen oxidoreductase
Comments: A flavoprotein. Methanesulfonate is the simplest of the sulfonates and is a substrate for the growth of certain methylotrophic microorganisms. Compared with EC 1.14.14.5, alkanesulfonate monooxygenase, this enzyme has a restricted substrate range that includes only the short-chain aliphatic sulfonates (methanesulfonate to butanesulfonate) and excludes all larger molecules, such as arylsulfonates [1]. The enzyme from the bacterium Methylosulfonomonas methylovora is a multicomponent system comprising a hydroxylase, a reductase (MsmD) and a ferredoxin (MsmC). The hydroxylase has both large (MsmA) and small (MsmB) subunits, with each large subunit containing a Rieske-type [2Fe-2S] cluster. cf. EC 1.14.14.34, methanesulfonate monooxygenase (FMNH2).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, UM-BBD
References:
1.  de Marco, P., Moradas-Ferreira, P., Higgins, T.P., McDonald, I., Kenna, E.M. and Murrell, J.C. Molecular analysis of a novel methanesulfonic acid monooxygenase from the methylotroph Methylosulfonomonas methylovora. J. Bacteriol. 181 (1999) 2244–2251. [PMID: 10094704]
2.  Higgins, T.P., Davey, M., Trickett, J., Kelly, D.P. and Murrell, J.C. Metabolism of methanesulfonic acid involves a multicomponent monooxygenase enzyme. Microbiology 142 (1996) 251–260. [DOI] [PMID: 8932698]
[EC 1.14.13.111 created 2009 as EC 1.14.14.6, transferred 2010 to EC 1.14.13.111, modified 2016]
 
 
EC 1.14.13.128     
Accepted name: 7-methylxanthine demethylase
Reaction: 7-methylxanthine + O2 + NAD(P)H + H+ = xanthine + NAD(P)+ + H2O + formaldehyde
Other name(s): ndmC (gene name)
Systematic name: 7-methylxanthine:oxygen oxidoreductase (demethylating)
Comments: A non-heme iron oxygenase. The enzyme from the bacterium Pseudomonas putida prefers NADH over NADPH. The enzyme is specific for 7-methylxanthine [2]. Forms part of the caffeine degradation pathway.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, UM-BBD
References:
1.  Summers, R.M., Louie, T.M., Yu, C.L. and Subramanian, M. Characterization of a broad-specificity non-haem iron N-demethylase from Pseudomonas putida CBB5 capable of utilizing several purine alkaloids as sole carbon and nitrogen source. Microbiology 157 (2011) 583–592. [DOI] [PMID: 20966097]
2.  Summers, R.M., Louie, T.M., Yu, C.L., Gakhar, L., Louie, K.C. and Subramanian, M. Novel, highly specific N-demethylases enable bacteria to live on caffeine and related purine alkaloids. J. Bacteriol. 194 (2012) 2041–2049. [DOI] [PMID: 22328667]
[EC 1.14.13.128 created 2011]
 
 
EC 1.14.13.131     
Accepted name: dissimilatory dimethyl sulfide monooxygenase
Reaction: dimethyl sulfide + O2 + NADH + H+ = methanethiol + formaldehyde + NAD+ + H2O
For diagram of dimethyl sulfide catabolism, click here
Other name(s): dmoAB (gene names); dimethyl sulfide C-monooxygenase; dimethylsulfide monooxygenase (ambiguous); dimethyl sulfide monooxygenase (ambiguous)
Systematic name: dimethyl sulfide,NADH:oxygen oxidoreductase
Comments: The enzyme participates exclusively in sulfur dissimilation. It has lower activity with diethyl sulfide and other short-chain alkyl methyl sulfides. Its activity is stimulated by combined addition of FMN, and, after depletion of cations, of Mg2+ and Fe2+. The enzymes from bacteria of the Hyphomicrobium genus are a two component system that includes an FMN-dependent reductase subunit and a monooxygenase subunit.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  De Bont, J.A.M., Van Dijken, J.P. and Harder, W. Dimethyl sulphoxide and dimethyl sulphide as a carbon, sulphur and energy source for growth of Hyphomicrobium S. J. Gen. Microbiol. 127 (1981) 315–323.
2.  Boden, R., Borodina, E., Wood, A.P., Kelly, D.P., Murrell, J.C. and Schafer, H. Purification and characterization of dimethylsulfide monooxygenase from Hyphomicrobium sulfonivorans. J. Bacteriol. 193 (2011) 1250–1258. [DOI] [PMID: 21216999]
[EC 1.14.13.131 created 2011]
 
 
EC 1.14.13.178     
Accepted name: methylxanthine N1-demethylase
Reaction: (1) caffeine + O2 + NAD(P)H + H+ = theobromine + NAD(P)+ + H2O + formaldehyde
(2) theophylline + O2 + NAD(P)H + H+ = 3-methylxanthine + NAD(P)+ + H2O + formaldehyde
(3) paraxanthine + O2 + NAD(P)H + H+ = 7-methylxanthine + NAD(P)+ + H2O + formaldehyde
Glossary: caffeine = 1,3,7-trimethylxanthine
theobromine = 3,7-dimethylxanthine
theophylline = 1,3-dimethylxanthine
paraxanthine = 1,7-dimethylxanthine
Other name(s): ndmA (gene name)
Systematic name: caffeine:oxygen oxidoreductase (N1-demethylating)
Comments: A non-heme iron oxygenase. The enzyme from the bacterium Pseudomonas putida shares an NAD(P)H-FMN reductase subunit with EC 1.14.13.179, methylxanthine N3-demethylase, and has a 5-fold higher activity with NADH than with NADPH [2]. Also demethylate 1-methylxantine with lower efficiency. Forms part of the degradation pathway of methylxanthines.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Summers, R.M., Louie, T.M., Yu, C.L. and Subramanian, M. Characterization of a broad-specificity non-haem iron N-demethylase from Pseudomonas putida CBB5 capable of utilizing several purine alkaloids as sole carbon and nitrogen source. Microbiology 157 (2011) 583–592. [DOI] [PMID: 20966097]
2.  Summers, R.M., Louie, T.M., Yu, C.L., Gakhar, L., Louie, K.C. and Subramanian, M. Novel, highly specific N-demethylases enable bacteria to live on caffeine and related purine alkaloids. J. Bacteriol. 194 (2012) 2041–2049. [DOI] [PMID: 22328667]
[EC 1.14.13.178 created 2013]
 
 
EC 1.14.13.179     
Accepted name: methylxanthine N3-demethylase
Reaction: (1) theobromine + O2 + NAD(P)H + H+ = 7-methylxanthine + NAD(P)+ + H2O + formaldehyde
(2) 3-methylxanthine + O2 + NAD(P)H + H+ = xanthine + NAD(P)+ + H2O + formaldehyde
Glossary: theobromine = 3,7-dimethylxanthine
Other name(s): ndmB (gene name)
Systematic name: theobromine:oxygen oxidoreductase (N3-demethylating)
Comments: A non-heme iron oxygenase. The enzyme from the bacterium Pseudomonas putida shares an NAD(P)H-FMN reductase subunit with EC 1.14.13.178, methylxanthine N1-demethylase, and has higher activity with NADH than with NADPH [1]. Also demethylates caffeine and theophylline with lower efficiency. Forms part of the degradation pathway of methylxanthines.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Summers, R.M., Louie, T.M., Yu, C.L. and Subramanian, M. Characterization of a broad-specificity non-haem iron N-demethylase from Pseudomonas putida CBB5 capable of utilizing several purine alkaloids as sole carbon and nitrogen source. Microbiology 157 (2011) 583–592. [DOI] [PMID: 20966097]
2.  Summers, R.M., Louie, T.M., Yu, C.L., Gakhar, L., Louie, K.C. and Subramanian, M. Novel, highly specific N-demethylases enable bacteria to live on caffeine and related purine alkaloids. J. Bacteriol. 194 (2012) 2041–2049. [DOI] [PMID: 22328667]
[EC 1.14.13.179 created 2013]
 
 
EC 1.14.13.238     
Accepted name: dimethylamine monooxygenase
Reaction: dimethylamine + NADPH + H+ + O2 = methylamine + formaldehyde + NADP+ + H2O
Other name(s): dmmABC (gene names)
Systematic name: dimethylamine,NADPH:oxygen oxidoreductase (formaldehyde-forming)
Comments: The enzyme, characterized from several bacterial species, is involved in a pathway for the degradation of methylated amines. It is composed of three subunits, one of which is a ferredoxin, and contains heme iron and an FMN cofactor.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Eady, R.R. and Large, P.J. Bacterial oxidation of dimethylamine, a new mono-oxygenase reaction. Biochem. J. 111 (1969) 37P–38P. [PMID: 4389011]
2.  Eady, R.R., Jarman, T.R. and Large, P.J. Microbial oxidation of amines. Partial purification of a mixed-function secondary-amine oxidase system from Pseudomonas aminovorans that contains an enzymically active cytochrome-P-420-type haemoprotein. Biochem. J. 125 (1971) 449–459. [PMID: 4401380]
3.  Alberta, J.A. and Dawson, J.H. Purification to homogeneity and initial physical characterization of secondary amine monooxygenase. J. Biol. Chem. 262 (1987) 11857–11863. [PMID: 3624236]
4.  Lidbury, I., Mausz, M.A., Scanlan, D.J. and Chen, Y. Identification of dimethylamine monooxygenase in marine bacteria reveals a metabolic bottleneck in the methylated amine degradation pathway. ISME J. 11 (2017) 1592–1601. [DOI] [PMID: 28304370]
[EC 1.14.13.238 created 2017]
 
 
EC 1.14.13.247     
Accepted name: stachydrine N-demethylase
Reaction: L-proline betaine + NAD(P)H + H+ + O2 = N-methyl-L-proline + formaldehyde + NAD(P)+ + H2O
Other name(s): L-proline betaine N-demethylase; stc2 (gene name)
Systematic name: L-proline betaine,NAD(P)H:oxygen oxidoreductase (formaldehyde-forming)
Comments: The enzyme, characterized from the bacterium Sinorhizobium meliloti 1021, consists of three different types of subunits. The catalytic unit contains a Rieske [2Fe-2S] iron-sulfur cluster, and catalyses the monooxygenation of a methyl group. The resulting N-methoxyl group is unstable and decomposes spontaneously to form formaldehyde. The other subunits are involved in the transfer of electrons from NAD(P)H to the catalytic subunit.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Daughtry, K.D., Xiao, Y., Stoner-Ma, D., Cho, E., Orville, A.M., Liu, P. and Allen, K.N. Quaternary ammonium oxidative demethylation: X-ray crystallographic, resonance Raman, and UV-visible spectroscopic analysis of a Rieske-type demethylase. J. Am. Chem. Soc. 134 (2012) 2823–2834. [PMID: 22224443]
2.  Kumar, R., Zhao, S., Vetting, M.W., Wood, B.M., Sakai, A., Cho, K., Solbiati, J., Almo, S.C., Sweedler, J.V., Jacobson, M.P., Gerlt, J.A. and Cronan, J.E. Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine. MBio 5 (2014) e00933. [DOI] [PMID: 24520058]
[EC 1.14.13.247 created 2017]
 
 


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