The Enzyme Database

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EC 1.1.1.205     
Accepted name: IMP dehydrogenase
Reaction: IMP + NAD+ + H2O = XMP + NADH + H+
For diagram of AMP and GMP biosynthesis, click here
Glossary: IMP = inosine 5′-phosphate
XMP = xanthosine 5′-phosphate
Other name(s): inosine-5′-phosphate dehydrogenase; inosinic acid dehydrogenase; inosinate dehydrogenase; inosine 5′-monophosphate dehydrogenase; inosine monophosphate dehydrogenase; IMP oxidoreductase; inosine monophosphate oxidoreductase
Systematic name: IMP:NAD+ oxidoreductase
Comments: The enzyme acts on the hydroxy group of the hydrated derivative of the substrate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9028-93-7
References:
1.  Magasanik, B., Moyed, H.S. and Gehring, L.B. Enzymes essential for the biosynthesis of nucleic acid guanine; inosine 5′-phosphate dehydrogenase of Aerobacter aerogenes. J. Biol. Chem. 226 (1957) 339–350. [PMID: 13428767]
2.  Turner, J.F. and King, J.E. Inosine 5-phosphate dehydrogenase of pea seeds. Biochem. J. 79 (1961) 147. [PMID: 13778733]
[EC 1.1.1.205 created 1961 as EC 1.2.1.14, transferred 1984 to EC 1.1.1.205]
 
 
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 2.4.2.22     
Accepted name: xanthine phosphoribosyltransferase
Reaction: XMP + diphosphate = 5-phospho-α-D-ribose 1-diphosphate + xanthine
Glossary: XMP = 9-(5-phospho-β-D-ribosyl)xanthine = xanthosine 5′-phosphate
Other name(s): Xan phosphoribosyltransferase; xanthosine 5′-phosphate pyrophosphorylase; xanthylate pyrophosphorylase; xanthylic pyrophosphorylase; XMP pyrophosphorylase; 5-phospho-α-D-ribose-1-diphosphate:xanthine phospho-D-ribosyltransferase; 9-(5-phospho-β-D-ribosyl)xanthine:diphosphate 5-phospho-α-D-ribosyltransferase
Systematic name: XMP:diphosphate 5-phospho-α-D-ribosyltransferase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9023-10-3
References:
1.  Krenitsky, T.A., Neil, S.M. and Miller, R.L. Guanine and xanthine phosphoribosyltransfer activities of Lactobacillus casei and Escherichia coli. Their relationship to hypoxanthine and adenine phosphoribosyltransfer activities. J. Biol. Chem. 245 (1970) 2605–2611. [PMID: 4910918]
[EC 2.4.2.22 created 1972]
 
 
EC 2.7.4.33     
Accepted name: AMP-polyphosphate phosphotransferase
Reaction: ADP + (phosphate)n = AMP + (phosphate)n+1
Other name(s): PA3455 (locus name); PPK2D; PAP
Systematic name: ADP:polyphosphate phosphotransferase
Comments: The enzyme, characterized from the bacteria Acinetobacter johnsonii and Pseudomonas aeruginosa, transfers a phosphate group from polyphosphates to nucleotide monophosphates. The highest activity is achieved with AMP, but the enzyme can also phosphorylate GMP, dAMP, dGMP, IMP, and XMP. The reverse reactions were not detected.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Bonting, C.F., Kortstee, G.J. and Zehnder, A.J. Properties of polyphosphate: AMP phosphotransferase of Acinetobacter strain 210A. J. Bacteriol. 173 (1991) 6484–6488. [PMID: 1655714]
2.  Shiba, T., Itoh, H., Kameda, A., Kobayashi, K., Kawazoe, Y. and Noguchi, T. Polyphosphate:AMP phosphotransferase as a polyphosphate-dependent nucleoside monophosphate kinase in Acinetobacter johnsonii 210A. J. Bacteriol. 187 (2005) 1859–1865. [PMID: 15716459]
3.  Nocek, B., Kochinyan, S., Proudfoot, M., Brown, G., Evdokimova, E., Osipiuk, J., Edwards, A.M., Savchenko, A., Joachimiak, A. and Yakunin, A.F. Polyphosphate-dependent synthesis of ATP and ADP by the family-2 polyphosphate kinases in bacteria. Proc. Natl. Acad. Sci. USA 105 (2008) 17730–17735. [PMID: 19001261]
[EC 2.7.4.33 created 2020]
 
 
EC 3.6.1.66     
Accepted name: XTP/dITP diphosphatase
Reaction: (1) XTP + H2O = XMP + diphosphate
(2) dITP + H2O = dIMP + diphosphate
(3) ITP + H2O = IMP + diphosphate
Other name(s): hypoxanthine/xanthine dNTP pyrophosphatase; rdgB (gene name)
Systematic name: XTP/dITP diphosphohydrolase (diphosphate-forming)
Comments: The enzymes from the bacterium Escherichia coli and the archaea Methanococcus jannaschii and Archaeoglobus fulgidus are highly specific for XTP, dITP and ITP. The activity is dependent on divalent cations, Mg2+ is preferred.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hwang, K.Y., Chung, J.H., Kim, S.H., Han, Y.S. and Cho, Y. Structure-based identification of a novel NTPase from Methanococcus jannaschii. Nat. Struct. Biol. 6 (1999) 691–696. [DOI] [PMID: 10404228]
2.  Chung, J.H., Back, J.H., Park, Y.I. and Han, Y.S. Biochemical characterization of a novel hypoxanthine/xanthine dNTP pyrophosphatase from Methanococcus jannaschii. Nucleic Acids Res. 29 (2001) 3099–3107. [DOI] [PMID: 11452035]
3.  Chung, J.H., Park, H.Y., Lee, J.H. and Jang, Y. Identification of the dITP- and XTP-hydrolyzing protein from Escherichia coli. J. Biochem. Mol. Biol. 35 (2002) 403–408. [PMID: 12297000]
4.  Savchenko, A., Proudfoot, M., Skarina, T., Singer, A., Litvinova, O., Sanishvili, R., Brown, G., Chirgadze, N. and Yakunin, A.F. Molecular basis of the antimutagenic activity of the house-cleaning inosine triphosphate pyrophosphatase RdgB from Escherichia coli. J. Mol. Biol. 374 (2007) 1091–1103. [DOI] [PMID: 17976651]
[EC 3.6.1.66 created 2013]
 
 
EC 6.3.4.1      
Transferred entry: GMP synthase. Now included in EC 6.3.5.2, GMP synthase (glutamine-hydrolysing)
[EC 6.3.4.1 created 1961, deleted 2013]
 
 
EC 6.3.5.2     
Accepted name: GMP synthase (glutamine-hydrolysing)
Reaction: ATP + XMP + L-glutamine + H2O = AMP + diphosphate + GMP + L-glutamate (overall reaction)
(1a) L-glutamine + H2O = L-glutamate + NH3
(1b) ATP + XMP + NH3 = AMP + diphosphate + GMP
For diagram of AMP and GMP biosynthesis, click here
Glossary: XMP = xanthosine 5′-phosphate
Other name(s): GMP synthetase (glutamine-hydrolysing); guanylate synthetase (glutamine-hydrolyzing); guanosine monophosphate synthetase (glutamine-hydrolyzing); xanthosine 5′-phosphate amidotransferase; guanosine 5′-monophosphate synthetase
Systematic name: xanthosine-5′-phosphate:L-glutamine amido-ligase (AMP-forming)
Comments: Involved in the de novo biosynthesis of guanosine nucleotides. An N-terminal glutaminase domain binds L-glutamine and generates ammonia, which is transferred by a substrate-protective tunnel to the ATP-pyrophosphatase domain. The enzyme can catalyse the second reaction alone in the presence of ammonia.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37318-71-1
References:
1.  Lagerkvist, U. Biosynthesis of guanosine 5′-phosphate. II. Amination of xanthosine 5′-phosphate by purified enzyme from pigeon liver. J. Biol. Chem. 233 (1958) 143–149. [PMID: 13563458]
2.  Abrams, R. and Bentley, M. Biosynthesis of nucleic acid purines. III. Guanosine 5′-phosphate formation from xanthosine 5′-phosphate and L-glutamine. Arch. Biochem. Biophys. 79 (1959) 91–110.
3.  Zalkin, H., Argos, P., Narayana, S.V., Tiedeman, A.A. and Smith, J.M. Identification of a trpG-related glutamine amide transfer domain in Escherichia coli GMP synthetase. J. Biol. Chem. 260 (1985) 3350–3354. [PMID: 2982857]
4.  Abbott, J.L., Newell, J.M., Lightcap, C.M., Olanich, M.E., Loughlin, D.T., Weller, M.A., Lam, G., Pollack, S. and Patton, W.A. The effects of removing the GAT domain from E. coli GMP synthetase. Protein J. 25 (2006) 483–491. [DOI] [PMID: 17103135]
[EC 6.3.5.2 created 1961, modified 2013]
 
 


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