The Enzyme Database

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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]
 
 
EC 1.14.13.251     
Accepted name: glycine betaine monooxygenase
Reaction: glycine betaine + NADH + H+ + O2 = N,N-dimethylglycine + formaldehyde + NAD+ + H2O
Other name(s): glycine betaine dioxygenase (incorrect); bmoAB (gene names); gbcAB (gene names)
Systematic name: glycine betaine,NADH:oxygen oxidoreductase (demethylating)
Comments: The enzyme, characterized from the bacteria Pseudomonas aeruginosa and Chromohalobacter salexigens, is involved in a degradation pathway of glycine betaine. It is composed of two subunits - a ferredoxin reductase component that contains FAD, and a terminal oxygenase component that contains a [2Fe-2S] Rieske-type iron-sulfur cluster and a nonheme iron centre.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Wargo, M.J., Szwergold, B.S. and Hogan, D.A. Identification of two gene clusters and a transcriptional regulator required for Pseudomonas aeruginosa glycine betaine catabolism. J. Bacteriol. 190 (2008) 2690–2699. [DOI] [PMID: 17951379]
2.  Li, S., Yu, X. and Beattie, G.A. Glycine betaine catabolism contributes to Pseudomonas syringae tolerance to hyperosmotic stress by relieving betaine-mediated suppression of compatible solute synthesis. J. Bacteriol. 195 (2013) 2415–2423. [DOI] [PMID: 23524610]
3.  Shao, Y.H., Guo, L.Z., Zhang, Y.Q., Yu, H., Zhao, B.S., Pang, H.Q. and Lu, W.D. Glycine betaine monooxygenase, an unusual Rieske-type oxygenase system, catalyzes the oxidative N-demethylation of glycine betaine in Chromohalobacter salexigens DSM 3043. Appl. Environ. Microbiol. 84 (2018) . [DOI] [PMID: 29703733]
[EC 1.14.13.251 created 2022]
 
 
EC 1.14.14.34     
Accepted name: methanesulfonate monooxygenase (FMNH2)
Reaction: methanesulfonate + FMNH2 + O2 = formaldehyde + FMN + sulfite + H2O
Glossary: methanesulfonate = CH3-SO3-
formaldehyde = H-CHO
Other name(s): msuD (gene name); ssuD (gene name)
Systematic name: methanesulfonate,FMNH2:oxygen oxidoreductase
Comments: The enzyme, characterized from Pseudomonas strains, allows the organisms to utilize methanesulfonate as their sulfur source. It acts in combination with a dedicated NADH-dependent FMN reductase (EC 1.5.1.42), which provides it with reduced FMN. cf. EC 1.14.13.111, methanesulfonate monooxygenase (NADH).
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Kertesz, M.A., Schmidt-Larbig, K. and Wuest, T. A novel reduced flavin mononucleotide-dependent methanesulfonate sulfonatase encoded by the sulfur-regulated msu operon of Pseudomonas aeruginosa. J. Bacteriol. 181 (1999) 1464–1473. [PMID: 10049377]
2.  Endoh, T., Kasuga, K., Horinouchi, M., Yoshida, T., Habe, H., Nojiri, H. and Omori, T. Characterization and identification of genes essential for dimethyl sulfide utilization in Pseudomonas putida strain DS1. Appl. Microbiol. Biotechnol. 62 (2003) 83–91. [DOI] [PMID: 12835925]
[EC 1.14.14.34 created 2016]
 
 
EC 1.14.14.35     
Accepted name: dimethylsulfone monooxygenase
Reaction: dimethyl sulfone + FMNH2 + O2 = methanesulfinate + formaldehyde + FMN + H2O
Other name(s): sfnG (gene name)
Systematic name: dimethyl sulfone,FMNH2:oxygen oxidoreductase
Comments: The enzyme, characterized from Pseudomonas spp., is involved in a dimethyl sulfide degradation pathway. It is dependent on NAD(P)H-dependent FMN reductase (EC 1.5.1.38, EC 1.5.1.39, or EC 1.5.1.42), which provides it with reduced FMN. The product, methanesulfinate, is oxidized spontaneously to methanesulfonate in the presence of dioxygen and FMNH2.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Endoh, T., Habe, H., Nojiri, H., Yamane, H. and Omori, T. The σ54-dependent transcriptional activator SfnR regulates the expression of the Pseudomonas putida sfnFG operon responsible for dimethyl sulphone utilization. Mol. Microbiol. 55 (2005) 897–911. [DOI] [PMID: 15661012]
2.  Wicht, D.K. The reduced flavin-dependent monooxygenase SfnG converts dimethylsulfone to methanesulfinate. Arch. Biochem. Biophys. 604 (2016) 159–166. [DOI] [PMID: 27392454]
[EC 1.14.14.35 created 2016]
 
 
EC 1.14.15.38     
Accepted name: N,N-dimethyl phenylurea N-demethylase
Reaction: an N,N-dimethyl-N′-phenylurea compound + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2 = an N-methyl-N′-phenylurea compound + formaldehyde + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
Other name(s): pdmAB (gene names)
Systematic name: N,N-dimethyl-N′-phenylurea compound,NAD(P)H:oxygen oxidoreductase (formaldehyde-forming)
Comments: The enzyme, found in members of the Sphingobium genus, initiates the degradation of N,N-dimethyl-phenylurea herbicides by mono-N-demethylation. 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 enzyme associates with additional proteins (a reductase and a [3Fe-4S] type ferredoxin) that are involved in the transfer of electrons from NAD(P)H to the active site.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Gu, T., Zhou, C., Sorensen, S.R., Zhang, J., He, J., Yu, P., Yan, X. and Li, S. The novel bacterial N-demethylase PdmAB is responsible for the initial step of N,N-dimethyl-substituted phenylurea herbicide degradation. Appl. Environ. Microbiol. 79 (2013) 7846–7856. [PMID: 24123738]
[EC 1.14.15.38 created 2020]
 
 
EC 1.14.99.15     
Accepted name: 4-methoxybenzoate monooxygenase (O-demethylating)
Reaction: 4-methoxybenzoate + reduced acceptor + O2 = 4-hydroxybenzoate + formaldehyde + acceptor + H2O
Other name(s): 4-methoxybenzoate 4-monooxygenase (O-demethylating); 4-methoxybenzoate O-demethylase; p-anisic O-demethylase; piperonylate-4-O-demethylase
Systematic name: 4-methoxybenzoate,hydrogen-donor:oxygen oxidoreductase (O-demethylating)
Comments: The bacterial enzyme consists of a ferredoxin-type protein and an iron-sulfur flavoprotein (FMN). Also acts on 4-ethoxybenzoate, N-methyl-4-aminobenzoate and toluate. The fungal enzyme acts best on veratrate.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37256-78-3
References:
1.  Bernhardt, F.-H., Nastainczyk, W. and Seydewitz, V. Kinetic studies on a 4-methoxybenzoate O-demethylase from Pseudomonas putida. Eur. J. Biochem. 72 (1977) 107–115. [DOI] [PMID: 188654]
2.  Paszcynski, A. and Trojanowski, J. An affinity-column procedure for the purification of veratrate O-demethylase from fungi. Microbios 18 (1977) 111–121. [PMID: 25369]
3.  Twilfer, H., Bernhardt, F.-H. and Gersonde, K. An electron-spin-resonance study on the redox-active centers of the 4-methoxybenzoate monooxygenase from Pseudomonas putida. Eur. J. Biochem. 119 (1981) 595–602. [DOI] [PMID: 6273164]
[EC 1.14.99.15 created 1972]
 
 
EC 1.14.99.48     
Accepted name: heme oxygenase (staphylobilin-producing)
Reaction: (1) protoheme + 5 reduced acceptor + 4 O2 = β-staphylobilin + Fe2+ + formaldehyde + 5 acceptor + 4 H2O
(2) protoheme + 5 reduced acceptor + 4 O2 = δ-staphylobilin + Fe2+ + formaldehyde + 5 acceptor + 4 H2O
For diagram of staphylobilin biosynthesis, click here
Glossary: β-staphylobilin = 10-oxo-β-bilirubin = 3,7-bis(2-carboxyethyl)-2,8,13,18-tetramethyl-12,17-divinylbiladiene-ac-1,10,19(21H,24H)-trione
δ-staphylobilin = 10-oxo-δ-bilirubin = 3,7-bis(2-carboxyethyl)-2,8,12,17-tetramethyl-13,18-divinylbiladiene-ac-1,10,19(21H,24H)-trione
Other name(s): haem oxygenase (ambiguous); heme oxygenase (decyclizing) (ambiguous); heme oxidase (ambiguous); haem oxidase (ambiguous); heme oxygenase (ambiguous); isdG (gene name); isdI (gene name)
Systematic name: protoheme,hydrogen-donor:oxygen oxidoreductase (δ/β-methene-oxidizing, hydroxylating)
Comments: This enzyme, which is found in some pathogenic bacteria, is involved in an iron acquisition system that catabolizes the host’s hemoglobin. The two enzymes from the bacterium Staphylococcus aureus, encoded by the isdG and isdI genes, produce 67.5 % and 56.2 % δ-staphylobilin, respectively.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Reniere, M.L., Ukpabi, G.N., Harry, S.R., Stec, D.F., Krull, R., Wright, D.W., Bachmann, B.O., Murphy, M.E. and Skaar, E.P. The IsdG-family of haem oxygenases degrades haem to a novel chromophore. Mol. Microbiol. 75 (2010) 1529–1538. [DOI] [PMID: 20180905]
2.  Matsui, T., Nambu, S., Ono, Y., Goulding, C.W., Tsumoto, K. and Ikeda-Saito, M. Heme degradation by Staphylococcus aureus IsdG and IsdI liberates formaldehyde rather than carbon monoxide. Biochemistry 52 (2013) 3025–3027. [DOI] [PMID: 23600533]
3.  Streit, B.R., Kant, R., Tokmina-Lukaszewska, M., Celis, A.I., Machovina, M.M., Skaar, E.P., Bothner, B. and DuBois, J.L. Time-resolved studies of IsdG protein identify molecular signposts along the non-canonical heme oxygenase pathway. J. Biol. Chem. 291 (2016) 862–871. [DOI] [PMID: 26534961]
[EC 1.14.99.48 created 2013]
 
 
EC 1.14.99.57     
Accepted name: heme oxygenase (mycobilin-producing)
Reaction: (1) protoheme + 3 reduced acceptor + 3 O2 = mycobilin a + Fe2+ + 3 acceptor + 3 H2O
(2) protoheme + 3 reduced acceptor + 3 O2 = mycobilin b + Fe2+ + 3 acceptor + 3 H2O
For diagram of mycobilin biosynthesis, click here
Glossary: mycobilin a = 8,12-bis(2-carboxyethyl)-19-formyl-3,7,13,18-tetramethyl-3,17-divinylbiladiene-ab-1,15(21H)-dione
mycobilin b = 8,12-bis(2-carboxyethyl)-19-formyl-2,7,13,17-tetramethyl-3,18-divinylbiladiene-ab-1,15(21H)-dione
Other name(s): mhuD (gene name)
Systematic name: protoheme,donor:oxygen oxidoreductase (mycobilin-producing)
Comments: The enzyme, characterized from the bacterium Mycobacterium tuberculosis, is involved in heme degradation and iron utilization. The enzyme binds two stacked protoheme molecules per monomer. Unlike the canonical heme oxygenases, the enzyme does not release carbon monoxide or formaldehyde. Instead, it forms unique products, named mycobilins, that retain the α-meso-carbon at the ring cleavage site as an aldehyde group. EC 1.6.2.4, NADPH-hemoprotein reductase, can act as electron donor in vitro.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Chim, N., Iniguez, A., Nguyen, T.Q. and Goulding, C.W. Unusual diheme conformation of the heme-degrading protein from Mycobacterium tuberculosis. J. Mol. Biol. 395 (2010) 595–608. [DOI] [PMID: 19917297]
2.  Nambu, S., Matsui, T., Goulding, C.W., Takahashi, S. and Ikeda-Saito, M. A new way to degrade heme: the Mycobacterium tuberculosis enzyme MhuD catalyzes heme degradation without generating CO. J. Biol. Chem. 288 (2013) 10101–10109. [DOI] [PMID: 23420845]
3.  Graves, A.B., Morse, R.P., Chao, A., Iniguez, A., Goulding, C.W. and Liptak, M.D. Crystallographic and spectroscopic insights into heme degradation by Mycobacterium tuberculosis MhuD. Inorg. Chem. 53 (2014) 5931–5940. [DOI] [PMID: 24901029]
[EC 1.14.99.57 created 2017]
 
 
EC 1.14.99.66     
Accepted name: [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase
Reaction: a [histone H3]-N6,N6-dimethyl-L-lysine4 + 2 acceptor + 2 H2O = a [histone H3]-L-lysine4 + 2 formaldehyde + 2 reduced acceptor (overall reaction)
(1a) a [histone H3]-N6,N6-dimethyl-L-lysine4 + acceptor + H2O = a [histone H3]-N6-methyl-L-lysine4 + formaldehyde + reduced acceptor
(1b) a [histone H3]-N6-methyl-L-lysine4 + acceptor + H2O = a [histone H3]-L-lysine4 + formaldehyde + reduced acceptor
Other name(s): KDM1 (gene name); LSD1 (gene name); lysine-specific histone demethylase 1
Systematic name: [histone H3]-N6,N6-dimethyl-L-lysine4:acceptor oxidoreductase (demethylating)
Comments: The enzyme specifically removes methyl groups from mono- and dimethylated lysine4 of histone 3. During the reaction the substrate is oxidized by the FAD cofactor of the enzyme to generate the corresponding imine, which is subsequently hydrolysed in the form of formaldehyde.The enzyme is similar to flavin amine oxidases, and differs from all other known histone lysine demethylases, which are iron(II)- and 2-oxoglutarate-dependent dioxygenases. The physiological electron acceptor is not known with certainty. In vitro the enzyme can use oxygen, which is reduced to hydrogen peroxide, but generation of hydrogen peroxide in the chromatin environment is unlikely as it will result in oxidative damage of DNA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Forneris, F., Binda, C., Vanoni, M.A., Mattevi, A. and Battaglioli, E. Histone demethylation catalysed by LSD1 is a flavin-dependent oxidative process. FEBS Lett. 579 (2005) 2203–2207. [PMID: 15811342]
2.  Forneris, F., Battaglioli, E., Mattevi, A. and Binda, C. New roles of flavoproteins in molecular cell biology: histone demethylase LSD1 and chromatin. FEBS J. 276 (2009) 4304–4312. [PMID: 19624733]
[EC 1.14.99.66 created 2019]
 
 
EC 2.1.1.54     
Accepted name: deoxycytidylate C-methyltransferase
Reaction: 5,10-methylenetetrahydrofolate + dCMP = dihydrofolate + deoxy-5-methylcytidylate
Other name(s): deoxycytidylate methyltransferase; dCMP methyltransferase
Systematic name: 5,10-methylenetetrahydrofolate:dCMP C-methyltransferase
Comments: dCMP is methylated by formaldehyde in the presence of tetrahydrofolate. CMP, dCTP and CTP can act as acceptors, but more slowly.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 61970-01-2
References:
1.  Kuo, T.-T. and Tu, J. Enzymatic synthesis of deoxy-5-methyl-cytidylic acid replacing deoxycytidylic acid in Xanthomonas oryzae phage Xp12DNA. Nature 263 (1976) 615. [PMID: 980110]
[EC 2.1.1.54 created 1978]
 
 
EC 2.2.1.2     
Accepted name: transaldolase
Reaction: sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-erythrose 4-phosphate + D-fructose 6-phosphate
For diagram of reaction, click here, of mechanism, click here and for diagram of the later stages of the pentose-phosphate pathway, click here
Other name(s): dihydroxyacetonetransferase; dihydroxyacetone synthase (incorrect); formaldehyde transketolase (incorrect)
Systematic name: sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphate glyceronetransferase
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9014-46-4
References:
1.  Horecker, B.L. and Smyrniotis, P.Z. Purification and properties of yeast transaldolase. J. Biol. Chem. 212 (1955) 811–825. [PMID: 14353883]
2.  Racker, E. Transaldolase. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Ed.), The Enzymes, 2nd edn, vol. 5, Academic Press, New York, 1961, pp. 407–412.
3.  Tsolas, O. and Horecker, B.L. Transaldolase. In: Boyer, P.D. (Ed.), The Enzymes, 3rd edn, vol. 7, Academic Press, New York, 1972, pp. 259–280.
[EC 2.2.1.2 created 1961]
 
 
EC 2.2.1.3     
Accepted name: formaldehyde transketolase
Reaction: D-xylulose 5-phosphate + formaldehyde = D-glyceraldehyde 3-phosphate + glycerone
For diagram of reaction, click here
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): dihydroxyacetone synthase
Systematic name: D-xylulose-5-phosphate:formaldehyde glycolaldehydetransferase
Comments: A thiamine-diphosphate protein. Not identical with EC 2.2.1.1 transketolase. Also converts hydroxypyruvate and formaldehyde into glycerone and CO2.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 124566-23-0
References:
1.  Bystrykh, L.V., Sokolov, A.P. and Trotsenko, Yu.A. Separation of transketolase and dihydroxyacetone synthase from methylotrophic yeasts. Dokl. Akad. Nauk S.S.S.R. 258 (1981) 499–501. [PMID: 7249920]
2.  Kato, N., Higuchi, T., Sakazawa, C., Nishizawa, T., Tani, Y. and Yamada, H. Purification and properties of a transketolase responsible for formaldehyde fixation in a methanol-utilizing yeast, Candida boidinii (Kloeckera sp.) No. 2201. Biochim. Biophys. Acta 715 (1982) 143–150. [DOI] [PMID: 7074134]
3.  Waites, M.J. and Quayle, J.R. The interrelation between transketolase and dihydroxyacetone synthase activities in the methylotrophic yeast Candida boidinii. J. Gen. Microbiol. 124 (1981) 309–316. [DOI] [PMID: 6276498]
[EC 2.2.1.3 created 1984]
 
 
EC 2.7.1.165     
Accepted name: glycerate 2-kinase
Reaction: ATP + D-glycerate = ADP + 2-phospho-D-glycerate
For diagram of the Entner-Doudoroff pathway, click here
Other name(s): D-glycerate-2-kinase; glycerate kinase (2-phosphoglycerate forming); ATP:(R)-glycerate 2-phosphotransferase
Systematic name: ATP:D-glycerate 2-phosphotransferase
Comments: A key enzyme in the nonphosphorylative Entner-Doudoroff pathway in archaea [1,2]. In the bacterium Hyphomicrobium methylovorum GM2 the enzyme is involved in formaldehyde assimilation I (serine pathway) [5]. In Escherichia coli the enzyme is involved in D-glucarate/D-galactarate degradation [6]. The enzyme requires a divalent metal ion [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Liu, B., Wu, L., Liu, T., Hong, Y., Shen, Y. and Ni, J. A MOFRL family glycerate kinase from the thermophilic crenarchaeon, Sulfolobus tokodaii, with unique enzymatic properties. Biotechnol. Lett. 31 (2009) 1937–1941. [DOI] [PMID: 19690808]
2.  Reher, M., Bott, M. and Schonheit, P. Characterization of glycerate kinase (2-phosphoglycerate forming), a key enzyme of the nonphosphorylative Entner-Doudoroff pathway, from the thermoacidophilic euryarchaeon Picrophilus torridus. FEMS Microbiol. Lett. 259 (2006) 113–119. [DOI] [PMID: 16684110]
3.  Liu, B., Hong, Y., Wu, L., Li, Z., Ni, J., Sheng, D. and Shen, Y. A unique highly thermostable 2-phosphoglycerate forming glycerate kinase from the hyperthermophilic archaeon Pyrococcus horikoshii: gene cloning, expression and characterization. Extremophiles 11 (2007) 733–739. [DOI] [PMID: 17563835]
4.  Noh, M., Jung, J.H. and Lee, S.B. Purification and characterization of glycerate kinase from the thermoacidophilic archaeon Thermoplasma acidophilum: an enzyme belonging to the second glycerate kinase family. Biotechnol. Bioprocess Eng. 11 (2006) 344–350.
5.  Yoshida, T., Fukuta, K., Mitsunaga, T., Yamada, H. and Izumi, Y. Purification and characterization of glycerate kinase from a serine-producing methylotroph, Hyphomicrobium methylovorum GM2. Eur. J. Biochem. 210 (1992) 849–854. [DOI] [PMID: 1336459]
6.  Hubbard, B.K., Koch, M., Palmer, D.R., Babbitt, P.C. and Gerlt, J.A. Evolution of enzymatic activities in the enolase superfamily: characterization of the (D)-glucarate/galactarate catabolic pathway in Escherichia coli. Biochemistry 37 (1998) 14369–14375. [DOI] [PMID: 9772162]
[EC 2.7.1.165 created 2010]
 
 
EC 3.1.2.12     
Accepted name: S-formylglutathione hydrolase
Reaction: S-formylglutathione + H2O = glutathione + formate
Systematic name: S-formylglutathione hydrolase
Comments: Also hydrolyses S-acetylglutathione, but more slowly.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 83380-83-0
References:
1.  Uotila, L. Preparation and assay of glutathione thiol esters. Survey of human liver glutathione thiol esterases. Biochemistry 12 (1973) 3938–3943. [PMID: 4200890]
2.  Uotila, L. and Koivusalo, M. Purification and properties of S-formylglutathione hydrolase from human liver. J. Biol. Chem. 249 (1974) 7664–7672. [PMID: 4436331]
3.  Harms, N., Ras, J., Reijnders, W.N., van Spanning, R.J. and Stouthamer, A.H. S-Formylglutathione hydrolase of Paracoccus denitrificans is homologous to human esterase D: a universal pathway for formaldehyde detoxification? J. Bacteriol. 178 (1996) 6296–6299. [DOI] [PMID: 8892832]
[EC 3.1.2.12 created 1978]
 
 
EC 3.3.2.14     
Accepted name: 2,4-dinitroanisole O-demethylase
Reaction: 2,4-dinitroanisole + H2O = methanol + 2,4-dinitrophenol
Glossary: 2,4-dinitroanisole = 1-methoxy-2,4-dinitrobenzene
Other name(s): 2,4-dinitroanisole ether hydrolase; dnhA (gene name); dnhB (gene name); DNAN demethylase
Systematic name: 2,4-dinitroanisole methanol hydrolase
Comments: The enzyme, characterized from the bacterium Nocardioides sp. JS1661, is involved in the degradation of 2,4-dinitroanisole. Unlike other known O-demethylases, such as EC 1.14.99.15, 4-methoxybenzoate monooxygenase (O-demethylating), or EC 1.14.11.32, codeine 3-O-demethylase, it does not require oxygen or electron donors, and produces methanol rather than formaldehyde.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Fida, T.T., Palamuru, S., Pandey, G. and Spain, J.C. Aerobic biodegradation of 2,4-dinitroanisole by Nocardioides sp. strain JS1661. Appl. Environ. Microbiol. 80 (2014) 7725–7731. [DOI] [PMID: 25281383]
[EC 3.3.2.14 created 2015]
 
 
EC 3.5.3.21     
Accepted name: methylenediurea deaminase
Reaction: methylenediurea + 2 H2O = N-(hydroxymethyl)urea + 2 NH3 + CO2 (overall reaction)
(1a) methylenediurea + H2O = N-(carboxyaminomethyl)urea + NH3
(1b) N-(carboxyaminomethyl)urea = N-(aminomethyl)urea + CO2 (spontaneous)
(1c) N-(aminomethyl)urea + H2O = N-(hydroxymethyl)urea + NH3 (spontaneous)
Other name(s): methylenediurease
Systematic name: methylenediurea aminohydrolase
Comments: Methylenediurea is hydrolysed and decarboxylated to give an aminated methylurea, which then spontaneously hydrolyses to hydroxymethylurea. The enzyme from Ochrobactrum anthropi also hydrolyses dimethylenetriurea and trimethylenetetraurea as well as ureidoglycolate, which is hydrolysed to urea and glyoxylate, and allantoate, which is hydrolysed to ureidoglycolate, ammonia and carbon dioxide.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 205830-62-2
References:
1.  Jahns, T., Schepp, R., Kaltwasser, H. Purification and characterisation of an enzyme from a strain of Ochrobactrum anthroπ that degrades condensation products of urea and formaldehyde (ureaform). Can. J. Microbiol. 43 (1997) 1111–1117.
[EC 3.5.3.21 created 1999]
 
 
EC 3.8.1.1      
Deleted entry: alkylhalidase. Covered by EC 3.8.1.5, haloalkane dehalogenase.
[EC 3.8.1.1 created 1961, deleted 2020]
 
 
EC 4.1.2.2     
Accepted name: ketotetrose-phosphate aldolase
Reaction: erythrulose 1-phosphate = glycerone phosphate + formaldehyde
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): phosphoketotetrose aldolase; erythrulose-1-phosphate synthetase; erythrose-1-phosphate synthase; erythrulose-1-phosphate formaldehyde-lyase
Systematic name: erythrulose-1-phosphate formaldehyde-lyase (glycerone-phosphate-forming)
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number: 9024-45-7
References:
1.  Charalampous, F.C. and Mueller, G.C. Synthesis of erythrulose phosphate by a soluble enzyme from rat tissue. J. Biol. Chem. 201 (1953) 161–173. [PMID: 13044785]
[EC 4.1.2.2 created 1961]
 
 
EC 4.1.2.12     
Accepted name: 2-dehydropantoate aldolase
Reaction: 2-dehydropantoate = 3-methyl-2-oxobutanoate + formaldehyde
Glossary: pantoate = 2,4-dihydroxy-3,3-dimethylbutanoate
Other name(s): ketopantoaldolase; 2-dehydropantoate formaldehyde-lyase
Systematic name: 2-dehydropantoate formaldehyde-lyase (3-methyl-2-oxobutanoate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9024-51-5
References:
1.  McIntosh, E.N., Purko, M. and Wood, W.A. Ketopantoate formation by a hydroxymethylation enzyme from Escherichia coli. J. Biol. Chem. 228 (1957) 499–510. [PMID: 13475336]
[EC 4.1.2.12 created 1965, modified 2002]
 
 
EC 4.1.2.24     
Accepted name: dimethylaniline-N-oxide aldolase
Reaction: N,N-dimethylaniline N-oxide = N-methylaniline + formaldehyde
Other name(s): microsomal oxidase II; microsomal N-oxide dealkylase; N,N-dimethylaniline-N-oxide formaldehyde-lyase
Systematic name: N,N-dimethylaniline-N-oxide formaldehyde-lyase (N-methylaniline-forming)
Comments: Acts on various N,N-dialkylarylamides.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37290-58-7
References:
1.  Machinist, J.M., Orme-Johnson, W.H. and Ziegler, D.M. Microsomal oxidases. II. Properties of a pork liver microsomal N-oxide dealkylase. Biochemistry 5 (1966) 2939–2943. [PMID: 5961882]
[EC 4.1.2.24 created 1972]
 
 
EC 4.1.2.32     
Accepted name: trimethylamine-oxide aldolase
Reaction: trimethylamine N-oxide = dimethylamine + formaldehyde
Other name(s): trimethylamine N-oxide formaldehyde-lyase; trimethylamine N-oxide aldolase; trimethylamine N-oxide demethylase; trimethylamine-N-oxide formaldehyde-lyase
Systematic name: trimethylamine-N-oxide formaldehyde-lyase (dimethylamine-forming)
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, CAS registry number: 72561-08-1
References:
1.  Large, P.J. Non-oxidative demethylation of trimethyl N-oxide by Pseudomonas aminovorans. FEBS Lett. 18 (1971) 297–300. [DOI] [PMID: 11946146]
2.  Myers, P.A. and Zatman, L.J. The metabolism of trimethylamine N-oxide by Bacillus PM6. Biochem. J. 121 (1971) 10. [PMID: 5116524]
[EC 4.1.2.32 created 1978]
 
 
EC 4.1.2.43     
Accepted name: 3-hexulose-6-phosphate synthase
Reaction: D-arabino-hex-3-ulose 6-phosphate = D-ribulose 5-phosphate + formaldehyde
For diagram of reaction, click here
Other name(s): D-arabino-3-hexulose 6-phosphate formaldehyde-lyase; 3-hexulosephosphate synthase; 3-hexulose phosphate synthase; HPS
Systematic name: D-arabino-hex-3-ulose-6-phosphate formaldehyde-lyase (D-ribulose-5-phosphate-forming)
Comments: Requires Mg2+ or Mn2+ for maximal activity [1]. The enzyme is specific for D-ribulose 5-phosphate as substrate as ribose 5-phosphate, xylulose 5-phosphate, allulose 6-phosphate and fructose 6-phosphate cannot act as substrate. In addition to formaldehyde, the enzyme can also use glycolaldehyde and methylglyoxal [7]. This enzyme, along with EC 5.3.1.27, 6-phospho-3-hexuloisomerase, plays a key role in the ribulose-monophosphate cycle of formaldehyde fixation, which is present in many microorganisms that are capable of utilizing C1-compounds [1]. The hyperthermophilic and anaerobic archaeon Pyrococcus horikoshii OT3 constitutively produces a bifunctional enzyme that sequentially catalyses the reactions of this enzyme and EC 5.3.1.27, 6-phospho-3-hexuloisomerase [6]. This enzyme is a member of the orotidine 5′-monophosphate decarboxylase (OMPDC) suprafamily [5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Ferenci, T., Strøm, T. and Quayle, J.R. Purification and properties of 3-hexulose phosphate synthase and phospho-3-hexuloisomerase from Methylococcus capsulatus. Biochem. J. 144 (1974) 477–486. [PMID: 4219834]
2.  Kato, N., Ohashi, H., Tani, Y. and Ogata, K. 3-Hexulosephosphate synthase from Methylomonas aminofaciens 77a. Purification, properties and kinetics. Biochim. Biophys. Acta 523 (1978) 236–244. [DOI] [PMID: 564713]
3.  Yanase, H., Ikeyama, K., Mitsui, R., Ra, S., Kita, K., Sakai, Y. and Kato, N. Cloning and sequence analysis of the gene encoding 3-hexulose-6-phosphate synthase from the methylotrophic bacterium, Methylomonas aminofaciens 77a, and its expression in Escherichia coli. FEMS Microbiol. Lett. 135 (1996) 201–205. [PMID: 8595859]
4.  Yurimoto, H., Kato, N. and Sakai, Y. Assimilation, dissimilation, and detoxification of formaldehyde, a central metabolic intermediate of methylotrophic metabolism. Chem. Rec. 5 (2005) 367–375. [DOI] [PMID: 16278835]
5.  Kato, N., Yurimoto, H. and Thauer, R.K. The physiological role of the ribulose monophosphate pathway in bacteria and archaea. Biosci. Biotechnol. Biochem. 70 (2006) 10–21. [DOI] [PMID: 16428816]
6.  Orita, I., Yurimoto, H., Hirai, R., Kawarabayasi, Y., Sakai, Y. and Kato, N. The archaeon Pyrococcus horikoshii possesses a bifunctional enzyme for formaldehyde fixation via the ribulose monophosphate pathway. J. Bacteriol. 187 (2005) 3636–3642. [DOI] [PMID: 15901685]
7.  Kato, N., Miyamoto, N., Shimao, M. and Sakazawa, C. 3-Hexulose phosphate pynthase from a new facultative methylotroph, Mycobacterium gastri MB19. Agric. Biol. Chem. 52 (1988) 2659–2661.
[EC 4.1.2.43 created 2008]
 
 
EC 4.1.99.24     
Accepted name: L-tyrosine isonitrile synthase
Reaction: L-tyrosine + D-ribulose 5-phosphate = (2S)-3-(4-hydroxyphenyl)-2-isocyanopropanoate + hydroxyacetone + formaldehyde + phosphate + H2O
Glossary: (2S)-3-(4-hydroxyphenyl)-2-isocyanopropanoate = L-tyrosine isonitrile
paerucumarin = 6,7-dihydroxy-3-isocyanochromen-2-one
rhabduscin = N-[(2S,3S,4R,5S,6R)-4,5-dihydroxy-6-{4-[(E)-2-isocyanoethenyl]phenoxy}-2-methyloxan-3-yl]acetamide
Other name(s): pvcA (gene name)
Systematic name: L-tyrosine:D-ribulose-5-phosphate lyase (isonitrile-forming)
Comments: The enzymes from the bacteria Pseudomonas aeruginosa and Xenorhabdus nematophila are involved in the biosynthesis of paerucumarin and rhabduscin, respectively. According to the proposed mechanism, the enzyme forms an imine intermediate composed of linked L-tyrosine and D-ribulose 5-phosphate, followed by loss of the phosphate group and formation of a β-keto imine and keto-enol tautomerization. This is followed by a C-C bond cleavage, the release of hydroxyacetone, and a retro aldol type reaction that releases formaldehyde and forms the final product [3]. cf. EC 4.1.99.25, L-tryptophan isonitrile synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Clarke-Pearson, M.F. and Brady, S.F. Paerucumarin, a new metabolite produced by the pvc gene cluster from Pseudomonas aeruginosa. J. Bacteriol. 190 (2008) 6927–6930. [DOI] [PMID: 18689486]
2.  Drake, E.J. and Gulick, A.M. Three-dimensional structures of Pseudomonas aeruginosa PvcA and PvcB, two proteins involved in the synthesis of 2-isocyano-6,7-dihydroxycoumarin. J. Mol. Biol. 384 (2008) 193–205. [DOI] [PMID: 18824174]
3.  Chang, W.C., Sanyal, D., Huang, J.L., Ittiamornkul, K., Zhu, Q. and Liu, X. In vitro stepwise reconstitution of amino acid derived vinyl isocyanide biosynthesis: detection of an elusive intermediate. Org. Lett. 19 (2017) 1208–1211. [DOI] [PMID: 28212039]
[EC 4.1.99.24 created 2018]
 
 
EC 4.1.99.25     
Accepted name: L-tryptophan isonitrile synthase
Reaction: L-tryptophan + D-ribulose 5-phosphate = (2S)-3-(1H-indol-3-yl)-2-isocyanopropanoate + hydroxyacetone + formaldehyde + phosphate + H2O
For diagram of tryptophan isonitrile biosynthesis, click here
Glossary: (2S)-3-(1H-indol-3-yl)-2-isocyanopropanoate = L-tryptophan isonitrile
hydroxyacetone = 1-hydroxypropan-2-one
Other name(s): isnA (gene name); ambI1 (gene name); well1 (gene name)
Systematic name: L-tryptophan:D-ribulose-5-phosphate lyase (isonitrile-forming)
Comments: The enzymes from cyanobacteria that belong to the Nostocales order participate in the biosynthesis of hapalindole-type alkaloids. According to the proposed mechanism, the enzyme forms an imine intermediate composed of linked L-tryptophan and D-ribulose 5-phosphate, followed by loss of the phosphate group and formation of a β-keto imine and keto-enol tautomerization. This is followed by a C-C bond cleavage, the release of hydroxyacetone, and a retro aldol type reaction that releases formaldehyde and forms the final product [3]. cf. EC 4.1.99.24, L-tyrosine isonitrile synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Brady, S.F. and Clardy, J. Cloning and heterologous expression of isocyanide biosynthetic genes from environmental DNA. Angew. Chem. Int. Ed. Engl. 44 (2005) 7063–7065. [PMID: 16206308]
2.  Brady, S.F. and Clardy, J. Systematic investigation of the Escherichia coli metabolome for the biosynthetic origin of an isocyanide carbon atom. Angew. Chem. Int. Ed. Engl. 44 (2005) 7045–7048. [PMID: 16217820]
3.  Hillwig, M.L., Zhu, Q. and Liu, X. Biosynthesis of ambiguine indole alkaloids in cyanobacterium Fischerella ambigua. ACS Chem. Biol. 9 (2014) 372–377. [DOI] [PMID: 24180436]
4.  Chang, W.C., Sanyal, D., Huang, J.L., Ittiamornkul, K., Zhu, Q. and Liu, X. In vitro stepwise reconstitution of amino acid derived vinyl isocyanide biosynthesis: detection of an elusive intermediate. Org. Lett. 19 (2017) 1208–1211. [DOI] [PMID: 28212039]
[EC 4.1.99.25 created 2018]
 
 
EC 4.2.1.147     
Accepted name: 5,6,7,8-tetrahydromethanopterin hydro-lyase
Reaction: 5,6,7,8-tetrahydromethanopterin + formaldehyde = 5,10-methylenetetrahydromethanopterin + H2O
Other name(s): formaldehyde-activating enzyme
Systematic name: 5,6,7,8-tetrahydromethanopterin hydro-lyase (formaldehyde-adding, tetrahydromethanopterin-forming)
Comments: Found in methylotrophic bacteria and methanogenic archaea.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Vorholt, J.A., Marx, C.J., Lidstrom, M.E. and Thauer, R.K. Novel formaldehyde-activating enzyme in Methylobacterium extorquens AM1 required for growth on methanol. J. Bacteriol. 182 (2000) 6645–6650. [DOI] [PMID: 11073907]
2.  Acharya, P., Goenrich, M., Hagemeier, C.H., Demmer, U., Vorholt, J.A., Thauer, R.K. and Ermler, U. How an enzyme binds the C1 carrier tetrahydromethanopterin. Structure of the tetrahydromethanopterin-dependent formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1. J. Biol. Chem. 280 (2005) 13712–13719. [DOI] [PMID: 15632161]
[EC 4.2.1.147 created 2014]
 
 
EC 4.4.1.22     
Accepted name: S-(hydroxymethyl)glutathione synthase
Reaction: S-(hydroxymethyl)glutathione = glutathione + formaldehyde
Other name(s): glutathione-dependent formaldehyde-activating enzyme; Gfa; S-(hydroxymethyl)glutathione formaldehyde-lyase
Systematic name: S-(hydroxymethyl)glutathione formaldehyde-lyase (glutathione-forming)
Comments: The enzyme from Paracoccus denitrificans accelerates the spontaneous reaction in which the adduct of formaldehyde and glutathione is formed, i.e. the substrate for EC 1.1.1.284, S-(hydroxymethyl)glutathione dehydrogenase, in the formaldehyde-detoxification pathway.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 425642-27-9
References:
1.  Goenrich, M., Bartoschek, S., Hagemeier, C.H., Griesinger, C. and Vorholt, J.A. A glutathione-dependent formaldehyde-activating enzyme (Gfa) from Paracoccus denitrificans detected and purified via two-dimensional proton exchange NMR spectroscopy. J. Biol. Chem. 277 (2002) 3069–3072. [DOI] [PMID: 11741920]
[EC 4.4.1.22 created 2005 (EC 1.2.1.1 created 1961, modified 1982, modified 2002, part transferred 2005 to EC 4.4.1.22)]
 
 
EC 4.5.1.3     
Accepted name: dichloromethane dehalogenase
Reaction: dichloromethane + H2O = formaldehyde + 2 chloride
Other name(s): dichloromethane chloride-lyase (chloride-hydrolysing)
Systematic name: dichloromethane chloride-lyase (adding H2O; chloride-hydrolysing; formaldehyde-forming)
Comments: Requires glutathione.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, CAS registry number: 97002-70-5
References:
1.  Kohler-Staub, D. and Leisinger, T. Dichloromethane dehalogenase of Hyphomicrobium sp. strain DM2. J. Bacteriol. 162 (1985) 676–681. [PMID: 3988708]
[EC 4.5.1.3 created 1989]
 
 
EC 5.3.1.27     
Accepted name: 6-phospho-3-hexuloisomerase
Reaction: D-arabino-hex-3-ulose 6-phosphate = D-fructose 6-phosphate
For diagram of reaction, click here
Other name(s): 3-hexulose-6-phosphate isomerase; phospho-3-hexuloisomerase; PHI; 6-phospho-3-hexulose isomerase; YckF
Systematic name: D-arabino-hex-3-ulose-6-phosphate isomerase
Comments: This enzyme, along with EC 4.1.2.43, 3-hexulose-6-phosphate synthase, plays a key role in the ribulose-monophosphate cycle of formaldehyde fixation, which is present in many microorganisms that are capable of utilizing C1-compounds [1]. The hyperthermophilic and anaerobic archaeon Pyrococcus horikoshii OT3 constitutively produces a bifunctional enzyme that sequentially catalyses the reactions of EC 4.1.2.43 (3-hexulose-6-phosphate synthase) and this enzyme [4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Ferenci, T., Strøm, T. and Quayle, J.R. Purification and properties of 3-hexulose phosphate synthase and phospho-3-hexuloisomerase from Methylococcus capsulatus. Biochem. J. 144 (1974) 477–486. [PMID: 4219834]
2.  Yurimoto, H., Kato, N. and Sakai, Y. Assimilation, dissimilation, and detoxification of formaldehyde, a central metabolic intermediate of methylotrophic metabolism. Chem. Rec. 5 (2005) 367–375. [DOI] [PMID: 16278835]
3.  Kato, N., Yurimoto, H. and Thauer, R.K. The physiological role of the ribulose monophosphate pathway in bacteria and archaea. Biosci. Biotechnol. Biochem. 70 (2006) 10–21. [DOI] [PMID: 16428816]
4.  Orita, I., Yurimoto, H., Hirai, R., Kawarabayasi, Y., Sakai, Y. and Kato, N. The archaeon Pyrococcus horikoshii possesses a bifunctional enzyme for formaldehyde fixation via the ribulose monophosphate pathway. J. Bacteriol. 187 (2005) 3636–3642. [DOI] [PMID: 15901685]
5.  Martinez-Cruz, L.A., Dreyer, M.K., Boisvert, D.C., Yokota, H., Martinez-Chantar, M.L., Kim, R. and Kim, S.H. Crystal structure of MJ1247 protein from M. jannaschii at 2.0 Å resolution infers a molecular function of 3-hexulose-6-phosphate isomerase. Structure 10 (2002) 195–204. [DOI] [PMID: 11839305]
6.  Taylor, E.J., Charnock, S.J., Colby, J., Davies, G.J. and Black, G.W. Cloning, purification and characterization of the 6-phospho-3-hexulose isomerase YckF from Bacillus subtilis. Acta Crystallogr. D Biol. Crystallogr. 57 (2001) 1138–1140. [PMID: 11468398]
[EC 5.3.1.27 created 2008]
 
 


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