The Enzyme Database

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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 1.14.13.128     
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 1.14.13.178     
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 1.14.13.212     
Accepted name: 1,3,7-trimethyluric acid 5-monooxygenase
Reaction: 1,3,7-trimethylurate + NADH + H+ + O2 = 1,3,7-trimethyl-5-hydroxyisourate + NAD+ + H2O
Glossary: isourate = 1,3,5,7-tetrahydropurine-2,6,8-trione
Other name(s): tmuM (gene name)
Systematic name: 1,3,7-trimethylurate,NADH:oxygen oxidoreductase (1,3,7-trimethyl-5-hydroxyisourate-forming)
Comments: The enzyme, characterized from the bacterium Pseudomonas sp. CBB1, is part of the bacterial C-8 oxidation-based caffeine degradation pathway. The product decomposes spontaneously to a racemic mixture of 3,6,8-trimethylallantoin. The enzyme shows no acitivity with urate. cf. EC 1.14.13.113, FAD-dependent urate hydroxylase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Mohanty, S.K., Yu, C.L., Das, S., Louie, T.M., Gakhar, L. and Subramanian, M. Delineation of the caffeine C-8 oxidation pathway in Pseudomonas sp. strain CBB1 via characterization of a new trimethyluric acid monooxygenase and genes involved in trimethyluric acid metabolism. J. Bacteriol. 194 (2012) 3872–3882. [DOI] [PMID: 22609920]
2.  Summers, R.M., Mohanty, S.K., Gopishetty, S. and Subramanian, M. Genetic characterization of caffeine degradation by bacteria and its potential applications. Microb. Biotechnol. 8 (2015) 369–378. [DOI] [PMID: 25678373]
[EC 1.14.13.212 created 2016]
 
 
EC 1.17.5.2     
Accepted name: caffeine dehydrogenase
Reaction: caffeine + ubiquinone + H2O = 1,3,7-trimethylurate + ubiquinol
Glossary: caffeine = 1,3,7-trimethylxanthine
Systematic name: caffeine:ubiquinone oxidoreductase
Comments: This enzyme, characterized from the soil bacterium Pseudomonas sp. CBB1, catalyses the incorporation of an oxygen atom originating from a water molecule into position C-8 of caffeine. The enzyme utilizes short-tail ubiquinones as the preferred electron acceptor.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Yu, C.L., Kale, Y., Gopishetty, S., Louie, T.M. and Subramanian, M. A novel caffeine dehydrogenase in Pseudomonas sp. strain CBB1 oxidizes caffeine to trimethyluric acid. J. Bacteriol. 190 (2008) 772–776. [DOI] [PMID: 17981969]
[EC 1.17.5.2 created 2010]
 
 
EC 2.1.1.158     
Accepted name: 7-methylxanthosine synthase
Reaction: S-adenosyl-L-methionine + xanthosine = S-adenosyl-L-homocysteine + 7-methylxanthosine
For diagram of caffeine biosynthesis, click here
Other name(s): xanthosine methyltransferase; XMT; xanthosine:S-adenosyl-L-methionine methyltransferase; CtCS1; CmXRS1; CaXMT1; S-adenosyl-L-methionine:xanthosine 7-N-methyltransferase
Systematic name: S-adenosyl-L-methionine:xanthosine N7-methyltransferase
Comments: The enzyme is specific for xanthosine, as XMP and xanthine cannot act as substrates [2,4]. The enzyme does not have N1- or N3- methylation activity [2]. This is the first methylation step in the production of caffeine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Negishi, O., Ozawa, T. and Imagawa, H. The role of xanthosine in the biosynthesis of caffeine in coffee plants. Agric. Biol. Chem. 49 (1985) 2221–2222.
2.  Mizuno, K., Kato, M., Irino, F., Yoneyama, N., Fujimura, T. and Ashihara, H. The first committed step reaction of caffeine biosynthesis: 7-methylxanthosine synthase is closely homologous to caffeine synthases in coffee (Coffea arabica L.). FEBS Lett. 547 (2003) 56–60. [DOI] [PMID: 12860386]
3.  Uefuji, H., Ogita, S., Yamaguchi, Y., Koizumi, N. and Sano, H. Molecular cloning and functional characterization of three distinct N-methyltransferases involved in the caffeine biosynthetic pathway in coffee plants. Plant Physiol. 132 (2003) 372–380. [DOI] [PMID: 12746542]
4.  Yoneyama, N., Morimoto, H., Ye, C.X., Ashihara, H., Mizuno, K. and Kato, M. Substrate specificity of N-methyltransferase involved in purine alkaloids synthesis is dependent upon one amino acid residue of the enzyme. Mol. Genet. Genomics 275 (2006) 125–135. [DOI] [PMID: 16333668]
[EC 2.1.1.158 created 2007]
 
 
EC 2.1.1.159     
Accepted name: theobromine synthase
Reaction: S-adenosyl-L-methionine + 7-methylxanthine = S-adenosyl-L-homocysteine + 3,7-dimethylxanthine
For diagram of caffeine biosynthesis, click here
Glossary: theobromine = 3,7-dimethylxanthine
paraxanthine = 1,7-dimethylxanthine
Other name(s): monomethylxanthine methyltransferase; MXMT; CTS1; CTS2; S-adenosyl-L-methionine:7-methylxanthine 3-N-methyltransferase
Systematic name: S-adenosyl-L-methionine:7-methylxanthine N3-methyltransferase
Comments: This is the third enzyme in the caffeine-biosynthesis pathway. This enzyme can also catalyse the conversion of paraxanthine into caffeine, although the paraxanthine pathway is considered to be a minor pathway for caffeine biosynthesis [2,3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Ogawa, M., Herai, Y., Koizumi, N., Kusano, T. and Sano, H. 7-Methylxanthine methyltransferase of coffee plants. Gene isolation and enzymatic properties. J. Biol. Chem. 276 (2001) 8213–8218. [DOI] [PMID: 11108716]
2.  Uefuji, H., Ogita, S., Yamaguchi, Y., Koizumi, N. and Sano, H. Molecular cloning and functional characterization of three distinct N-methyltransferases involved in the caffeine biosynthetic pathway in coffee plants. Plant Physiol. 132 (2003) 372–380. [DOI] [PMID: 12746542]
3.  Yoneyama, N., Morimoto, H., Ye, C.X., Ashihara, H., Mizuno, K. and Kato, M. Substrate specificity of N-methyltransferase involved in purine alkaloids synthesis is dependent upon one amino acid residue of the enzyme. Mol. Genet. Genomics 275 (2006) 125–135. [DOI] [PMID: 16333668]
[EC 2.1.1.159 created 2007]
 
 
EC 2.1.1.160     
Accepted name: caffeine synthase
Reaction: (1) S-adenosyl-L-methionine + 3,7-dimethylxanthine = S-adenosyl-L-homocysteine + 1,3,7-trimethylxanthine
(2) S-adenosyl-L-methionine + 1,7-dimethylxanthine = S-adenosyl-L-homocysteine + 1,3,7-trimethylxanthine
(3) S-adenosyl-L-methionine + 7-methylxanthine = S-adenosyl-L-homocysteine + 3,7-dimethylxanthine
For diagram of caffeine biosynthesis, click here
Glossary: theobromine = 3,7-dimethylxanthine
paraxanthine = 1,7-dimethylxanthine
caffeine = 1,3,7-trimethylxanthine
Other name(s): dimethylxanthine methyltransferase; 3N-methyltransferase; DXMT; CCS1; S-adenosyl-L-methionine:3,7-dimethylxanthine 1-N-methyltransferase
Systematic name: S-adenosyl-L-methionine:3,7-dimethylxanthine N1-methyltransferase
Comments: Paraxanthine is the best substrate for this enzyme but the paraxanthine pathway is considered to be a minor pathway for caffeine biosynthesis [2,3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kato, M., Mizuno, K., Fujimura, T., Iwama, M., Irie, M., Crozier, A. and Ashihara, H. Purification and characterization of caffeine synthase from tea leaves. Plant Physiol. 120 (1999) 579–586. [PMID: 10364410]
2.  Mizuno, K., Okuda, A., Kato, M., Yoneyama, N., Tanaka, H., Ashihara, H. and Fujimura, T. Isolation of a new dual-functional caffeine synthase gene encoding an enzyme for the conversion of 7-methylxanthine to caffeine from coffee (Coffea arabica L.). FEBS Lett. 534 (2003) 75–81. [DOI] [PMID: 12527364]
3.  Uefuji, H., Ogita, S., Yamaguchi, Y., Koizumi, N. and Sano, H. Molecular cloning and functional characterization of three distinct N-methyltransferases involved in the caffeine biosynthetic pathway in coffee plants. Plant Physiol. 132 (2003) 372–380. [DOI] [PMID: 12746542]
4.  Kato, M., Mizuno, K., Crozier, A., Fujimura, T. and Ashihara, H. Caffeine synthase gene from tea leaves. Nature 406 (2000) 956–957. [DOI] [PMID: 10984041]
[EC 2.1.1.160 created 2007]
 
 
EC 3.1.3.5     
Accepted name: 5′-nucleotidase
Reaction: a 5′-ribonucleotide + H2O = a ribonucleoside + phosphate
For diagram of caffeine biosynthesis, click here
Other name(s): uridine 5′-nucleotidase; 5′-adenylic phosphatase; adenosine 5′-phosphatase; AMP phosphatase; adenosine monophosphatase; 5′-mononucleotidase; AMPase; UMPase; snake venom 5′-nucleotidase; thimidine monophosphate nucleotidase; 5′-AMPase; 5′-AMP nucleotidase; AMP phosphohydrolase; IMP 5′-nucleotidase
Systematic name: 5′-ribonucleotide phosphohydrolase
Comments: Wide specificity for 5′-nucleotides.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9027-73-0
References:
1.  Gulland, J.M. and Jackson, E.M. 5-Nucleotidase. Biochem. J. 32 (1938) 597–601. [PMID: 16746659]
2.  Heppel, L.A. and Hilmoe, R.J. Purification and properties of 5-nucleotidase. J. Biol. Chem. 188 (1951) 665–676. [PMID: 14824154]
3.  Segal, H.L. and Brenner, B.M. 5′-Nucleotidase of rat liver microsomes. J. Biol. Chem. 235 (1960) 471–474. [PMID: 14444527]
[EC 3.1.3.5 created 1961]
 
 
EC 3.2.2.25     
Accepted name: N-methyl nucleosidase
Reaction: 7-methylxanthosine + H2O = 7-methylxanthine + D-ribose
For diagram of caffeine biosynthesis, click here
Other name(s): 7-methylxanthosine nucleosidase; N-MeNase; N-methyl nucleoside hydrolase; methylpurine nucleosidase
Systematic name: 7-methylxanthosine ribohydrolase
Comments: The enzyme preferentially hydrolyses 3- and 7-methylpurine nucleosides, such as 3-methylxanthosine, 3-methyladenosine and 7-methylguanosine. Hydrolysis of 7-methylxanthosine to form 7-methylxanthine is the second step in the caffeine-biosynthesis pathway.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Negishi, O., Ozawa, T. and Imagawa, H. N-Methyl nucleosidase from tea leaves. Agric. Biol. Chem. 52 (1988) 169–175.
[EC 3.2.2.25 created 2007]
 
 


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