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Ligand Xanthosine

Basic Ligand Information

Molecular Structure

Pathway Source

Pathways

BRENDA

purine metabolism

KEGG

ABC transporters, Biosynthesis of alkaloids derived from histidine and purine, Biosynthesis of secondary metabolites, Caffeine metabolism, Purine metabolism

MetaCyc

adenosine nucleotides degradation I, caffeine biosynthesis I, caffeine biosynthesis II (via paraxanthine), guanosine nucleotides degradation I, inosine 5'-phosphate degradation, purine ribonucleosides degradation, theobromine biosynthesis I, xanthine and xanthosine salvage more

Show all BRENDA pathways known for Xanthosine

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Roles as Enzyme Ligand

In Vivo Substrate in Enzyme-catalyzed Reactions (2 results)

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Show Natural Substrate (2 entries)

EC NUMBER

PROVEN IN VIVO REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

2.1.1.158

S-adenosyl-L-methionine + xanthosine = S-adenosyl-L-homocysteine + 7-methylxanthosine

721124, 668586, 670568, 670578, 667101, 670598, 667105, 670509, 669194, 670565, 667116, 670621, 655545

-

2.4.2.1

xanthosine + phosphate = xanthine + alpha-D-ribose 1-phosphate

759101, 760019

-

In Vivo Product in Enzyme-catalyzed Reactions (3 results)

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Show Natural Product (3 entries)

EC NUMBER

PROVEN IN VIVO REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

3.1.3.5

5'-XMP + H2O = xanthosine + phosphate

-

-

3.1.3.5

XMP + H2O = xanthosine + phosphate

-

-

3.1.3.5

2 entries

3.5.4.15

guanosine + H2O = xanthosine + NH3

209538, , 209536, 209537

7dca, 3D-view

Substrate in Enzyme-catalyzed Reactions (19 results)

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Show Substrate (19 entries)

EC NUMBER

REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

1.1.3.28

xanthosine + O2 = 9-riburonosylxanthine + H2O

287612

-

1.17.1.4

xanthosine + NAD+ + H2O = ? + NADH

644616

-

2.1.1.158

S-adenosyl-L-methionine + xanthosine = S-adenosyl-L-homocysteine + 7-methylxanthosine

655545, 721124, 670509, 667116, 670621, 670565, 668586, 669194, 670568, 670578, 757301, 667101, 670598, 667105

-

2.4.2.1

xanthosine + arsenate = xanthine + alpha-D-ribose 1-arsenate

489654, 489707

-

2.4.2.1

xanthosine + phosphate = alpha-D-ribose 1-phosphate + xanthine

489693, 489707, 489670, 489698, 489687, 489673, 489669, 662643

-

2.4.2.1

xanthosine + phosphate = xanthine + alpha-D-ribose 1-phosphate

759101, 760019

-

2.4.2.1

3 entries

2.7.1.73

ATP + xanthosine = ADP + XMP

641928

-

2.7.1.77

4-nitrophenyl phosphate + xanthosine = 4-nitrophenol + XMP

641995

-

2.7.1.77

diphosphate + xanthosine = phosphate + 5'-XMP

642002

-

3.1.3.5

5'-CMP + xanthosine = XMP + cytidine

665608

-

3.1.3.5

5'-GMP + xanthosine = XMP + guanosine

665608

-

3.1.3.5

5'-IMP + xanthosine = XMP + inosine

665608

-

3.1.3.5

5'-UMP + xanthosine = XMP + uridine

665608

-

3.2.2.1

xanthosine + H2O = D-ribose + xanthine

716358, 326370, 714225, 137116, 326385, 732656

-

3.2.2.1

xanthosine + H2O = xanthine + D-ribose

654127, 667792, 654255

-

3.2.2.2

xanthosine + H2O = D-ribose + hypoxanthine

716542

-

3.2.2.2

xanthosine + H2O = xanthine + D-ribose

137050, 137052

-

2.7.1.77

2 entries

3.1.3.5

4 entries

3.2.2.1

2 entries

3.2.2.2

2 entries

3.2.2.3

xanthosine + H2O = D-ribose + xanthine

731361, 716542, 732656

-

3.2.2.8

xanthosine + H2O = xanthine + D-ribose

137117, 137116, 137115, 716542

-

Product in Enzyme-catalyzed Reactions (10 results)

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Show Product (10 entries)

EC NUMBER

REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

1.1.1.205

inosine + NAD+ + H2O = xanthosine + NADH

-

-

2.4.2.5

inosine + xanthine = hypoxanthine + xanthosine

-

-

2.4.2.6

thymidine + xanthine = 9-deoxyribosylxanthine + 7-deoxyribosylxanthine

638042

-

2.4.2.6

deoxycytidine + xanthine = cytosine + xanthosine

-

-

2.4.2.6

thymidine + xanthine = thymine + xanthosine

-

-

3.1.3.5

5'-XMP + H2O = xanthosine + phosphate

95035, , 95045, 95031, 95025

-

3.1.3.5

XMP + H2O = xanthosine + phosphate

-

-

2.4.2.6

3 entries

3.1.3.5

2 entries

3.5.4.15

guanosine + H2O = xanthosine + NH3

209538, , 209536, 209537

7dca, 3D-view

3.5.4.3

guanosine + H2O = xanthosine + NH3

-

-

3.5.4.4

guanosine + H2O = xanthosine + NH3

-

-

Inhibitor in Enzyme-catalyzed Reactions (7 results)

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Show Inhibitors (7 entries)

EC NUMBER

COMMENTARY

LITERATURE

ENZYME 3D STRUCTURE

2.4.2.1

poor inhibitor of phosphorolysis of guanosine

489707

-

2.7.1.20

weak inhibition

641096

-

3.2.2.1

competitive inhibitor of inosine hydrolysis

326370

-

3.2.2.1

moderate

137116

-

3.2.2.1

2 entries

3.5.4.3

-

209585

-

4.1.1.23

potent inhibitor

715860

-

6.3.4.2

-

674909

-

3D Structure of Enzyme-Ligand-Complex (PDB) (2 results)

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Show 3D Structure of Enzyme-Ligand-Complex (PDB) (2 entries)

EC NUMBER

ENZYME 3D STRUCTURE

3.2.2.22

6lov, 3D-view

3.5.4.15

7dca, 3D-view

Enzyme Kinetic Parameters

k_cat Value (Turnover Number) (20 results)

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Show Turnover Number (20 entries)

EC NUMBER

TURNOVER NUMBER [1/S]

TURNOVER NUMBER MAXIMUM [1/S]

COMMENTARY

LITERATURE

2.4.2.1

4

-

-

489678

2.4.2.1

16.8

-

recombinant wild-type enzyme, pH 7.0, 25°C

760019

2.4.2.1

23.3

-

recombinant mutant N256D, pH 7.0, 25°C

760019

3.2.2.1

0.029

-

-

654127

3.2.2.1

0.19

-

pH 7.5, 30°C, mutant Y241A

732656

3.2.2.1

0.43

-

pH 7.5, 30°C, mutant Y255A

732656

3.2.2.1

0.58

-

pH 7.5, 30°C, mutant Y244A

732656

3.2.2.1

1.1

-

pH 7.5, 30°C, mutant Y249A

732656

3.2.2.1

1.3

-

pH 7.5, 30°C, mutant H245A

732656

3.2.2.1

2.5

-

pH 7.5, 30°C, mutant D252A

732656

3.2.2.1

6.2

-

at pH 7.0 and 35°C

714225

3.2.2.1

6.2

-

pH 7.5, 30°C, recombinant enzyme

732656

3.2.2.1

7

-

pH 7.5, 30°C, wild-type enzyme

732656

3.2.2.1

7.2

-

pH 7.5, 30°C, mutant E247A

732656

3.2.2.1

8.4

-

pH 7.5, 30°C, mutant D250A

732656

3.2.2.1

26.3

-

pH 6.0, 37°C

667792

3.2.2.1

62

-

pH 7.2, 37°C

667792

3.2.2.3

1.3

-

pH 7.5, 30°C, recombinant enzyme

732656

3.2.2.3

4.6

-

pH 7.5, 30°C, recombinant enzyme

732656

3.2.2.3

6.3

-

pH 7.2, 32°C, recombinant His-tagged enzyme

731361

2.4.2.1

3 entries

3.2.2.1

14 entries

3.2.2.3

3 entries

K_M Value (37 results)

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Show KM Value (37 entries)

EC NUMBER

KM VALUE [MM]

KM VALUE MAXIMUM [MM]

COMMENTARY

LITERATURE

2.1.1.158

0.0737

-

-

668586

2.1.1.158

0.078

-

recombinant XMT1

670578

2.4.2.1

0.051

-

-

489693

2.4.2.1

0.072

-

pH 7.1, 25°C, wild-type enzyme

662643

2.4.2.1

0.095

-

-

489670

2.4.2.1

0.4

-

pH 5.7

489707

2.4.2.1

0.45

-

-

489678

2.4.2.1

0.536

-

recombinant mutant N256D, pH 7.0, 25°C

760019

2.4.2.1

0.555

-

recombinant wild-type enzyme, pH 7.0, 25°C

760019

2.4.2.1

0.58

-

pH 5.7

489707

2.4.2.1

1.1

-

pH 6.5

489707

2.4.2.1

1.6

-

pH 6.5

489707

3.2.2.1

0.0158

-

-

654255

3.2.2.1

0.116

-

pH 7.5, 30°C, wild-type enzyme

732656

3.2.2.1

0.14

-

pH 7.5, 30°C, mutant E247A

732656

3.2.2.1

0.171

-

pH 7.5, 30°C, mutant D250A

732656

3.2.2.1

0.206

-

pH 7.5, 30°C, mutant Y244A

732656

3.2.2.1

0.232

-

pH 7.5, 30°C, mutant D252A

732656

3.2.2.1

0.28

-

at pH 7.0 and 35°C

714225

3.2.2.1

0.356

-

pH 7.5, 30°C, mutant H245A

732656

3.2.2.1

0.367

-

pH 7.5, 30°C, mutant Y255A

732656

3.2.2.1

0.396

-

pH 7.5, 30°C, recombinant enzyme

732656

3.2.2.1

0.487

-

pH 7.5, 30°C, mutant Y241A

732656

3.2.2.1

0.596

-

pH 7.5, 30°C, mutant Y249A

732656

3.2.2.1

0.79

-

pH 6.0, 37°C

667792

3.2.2.1

0.8

-

-

326370

3.2.2.1

1.038

-

-

654127

3.2.2.1

5.9

-

pH 7.2, 37°C

667792

3.2.2.2

1.2

-

pH 7.1

137052

3.2.2.2

1.69

-

pH and temperature not specified in the publication

716542

3.2.2.3

0.109

-

pH 7.5, 30°C, recombinant enzyme

732656

3.2.2.3

0.178

-

pH 7.5, 30°C, recombinant enzyme

732656

3.2.2.3

0.454

-

pH 7.2, 32°C, recombinant His-tagged enzyme

731361

3.2.2.3

1.69

-

at 30°C, pH not specified in the publication

716542

3.2.2.8

1.11

-

-

137116

3.2.2.8

1.69

-

isoform NSH1, pH not specified in the publication, at 30°C

716542

3.2.2.8

6.5

-

-

137117

2.1.1.158

2 entries

2.4.2.1

10 entries

3.2.2.1

16 entries

3.2.2.2

2 entries

3.2.2.3

4 entries

3.2.2.8

3 entries

IC₅₀ Value (2 results)

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Show IC50 Value (2 entries)

EC NUMBER

IC50 VALUE

IC50 VALUE MAXIMUM

COMMENTARY

LITERATURE

6.3.4.2

0.22

-

IC50 for inhibition of Gln-dependent CTP formation

674909

6.3.4.2

0.29

-

IC50 for inhibition of NH3-dependent CTP formation

674909

6.3.4.2

2 entries

References & Links

Literature References (59)

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Show Reference (59 entries)

BRENDA REFERENCE ID

PUBMED ID

TITLE

YEAR

AUTHORS

JOURNAL

VOLUME

PAGES

95025

2848805

High Km soluble 5'-nucleotidase from human placenta. Properties and allosteric regulation by IMP and ATP

1988

Spychala, J.; Madrid-Marina, V.; Fox, I.H.

J. Biol. Chem.

263

18759-18765

95031

-

Properties of 5'-nucleotidase from nodules of pigeonpea (Cajanus cajan)

1986

Singh, A.; Singh, R.

Phytochemistry

25

2267-2270

95035

3001058

Human placental cytoplasmic 5'-nucleotidase. Kinetic properties and inhibition

1986

Madrid-Marina, V.; Fox, I.H.

J. Biol. Chem.

261

444-452

95045

6260203

Purification and some properties of cytosol 5'-nucleotidase from rat liver

1981

Itoh, R.

Biochim. Biophys. Acta

657

402-410

137050

16662492

Purine catabolism in plants

1982

Guranowski, A.

Plant Physiol.

70

344-349

137052

31149

Inosine nucleosidase from Azotobacter vinelandii. Purification and properties

1978

Yoshino, M.; Tsukada, T.; Tsushima, K.

Arch. Microbiol.

119

59-64

137115

-

Purine salvage enzymes in man and Leishmania donovani

1980

Krenitsky, T.A.; Koszalka, G.W.; Tuttle, J.V.; Adamczyk, D.L.; Elion, G.B.; Marr, J.J.

Adv. Exp. Med. Biol.

122

51-56

137116

468819

Nucleosidases from Leishmania donovani. Pyrimidine ribonucleosidase, purine ribonucleosidase, and a novel purine 2-deoxyribonucleosidase

1979

Koszalka, G.W.; Krenitsky, T.A.

J. Biol. Chem.

254

8185-8193

137117

12325375

Purification and properties of nucleoside hydrolase from Pseudomonas fluorescens

1967

Terada, M.; Tatibana, M.; Hayaishi, O.

J. Biol. Chem.

242

5578-5585

209536

-

Purine, purine nucleoside, and purine nucleotide aminohydrolases

1971

Zielke, C.L.; Suelter, C.H.

Enzyme

4

47-78

209537

-

Studies on the guanosine degrading system in bacterial cell. Part III. Purification and properties of guanosine deaminase

1969

Ishida, Y.; Shirafuji, H.; Kida, M.; Yoneda, M.

Agric. Biol. Chem.

33

384-390

209538

10348987

Adenosine deaminase and guanosine deaminase activities in sera of patients with viral hepatitis

1999

Kalkan, A.; Bulut, V.; Erel, O.; Avci, S.; Bingol, N.K.

Mem. Inst. Oswaldo Cruz

94

383-386

209585

-

Purification and characterization of guanine aminohydrolase from human liver

1985

Kimm, S.W.; Park, J.B.; Lee, I.S.

Korean J. Biochem.

17

139-148

287612

-

Properties of a new enzyme, nucleoside oxidase, from Pseudomonas maltophilia LB-86

1989

Isono, Y.; Sudo, T.; Hoshino, M.

Agric. Biol. Chem.

53

1671-1677

326370

-

Purification and properties of purine nucleosidase from N2-fixing nodules of cowpea (Vigna unguiculata)

1989

Atkins, C.A.; Shelp, B.J.; Storer, P.J.

J. Plant Physiol.

134

447-452

326385

5726308

Purine ribonucleosidase g from Aspergillus foetidus

1968

Reese, E.T.; Maguire, A.H.

J. Bacteriol.

96

1696-1699

489654

-

Purine nucleoside phosphorylase

1972

Parks, R.E.; Agarwal, R.P.

The Enzymes, 3rd Ed. (Boyer, P. D. , ed. )

7

483-514

489669

-

Properties of purine nucleoside phosphorylase from Enterobacter cloacae

1981

Machida, Y.; Nakanishi, T.

Agric. Biol. Chem.

45

1801-1807

489670

7211

Purification and characterization of a purine-nucleoside phosphorylase from bovine thyroid

1976

Moyer, T.P.; Fischer, A.G.

Arch. Biochem. Biophys.

174

622-629

489673

1368697

Purification and properties of purine nucleoside phosphorylase from Brevibacterium acetylicum ATCC 954

1991

Shirae, H.; Yokozeki, K.

Agric. Biol. Chem.

55

493-499

489678

1445943

Purine nucleoside phosphorylase from bovine lens: purification and properties

1992

Barsacchi, D.; Cappiello, M.; Tozzi, M.G.; Del Corso, A.; Peccatori, M.; Camici, M.; Ipata, P.L.; Mura, U.

Biochim. Biophys. Acta

1160

163-170

489687

1390

Monomeric purine nucleoside phosphorylase from rabbit liver. Purification and characterization

1976

Lewis, A.S.; Glantz, M.D.

J. Biol. Chem.

251

407-413

489693

3042752

Purification and properties of inosine-guanosine phosphorylase from Escherichia coli K-12

1988

Koszalka, G.W.; Vanhooke, J.; Short, S.A.; Hall, W.W.

J. Bacteriol.

170

3493-3498

489698

8782414

Purification and characterization of purine nucleoside phosphorylase and pyrimidine nucleoside phosphorylase from Bacillus stearothermophilus TH 6-2

1996

Hamamoto, T.; Noguchi, T.; Midorikawa, Y.

Biosci. Biotechnol. Biochem.

60

1179-1180

489707

12180982

Xanthosine and xanthine. Substrate properties with purine nucleoside phosphorylases, and relevance to other enzyme systems

2002

Stoychev, G.; Kierdaszuk, B.; Shugar, D.

Eur. J. Biochem.

269

4048-4057

638042

692395

Nucleoside deoxyribosyltransferase from Lactobacillus helveticus

1978

Cardinaud, R.

Methods Enzymol.

51

446-455

641096

6289826

Adenosine kinase from Trypanosoma cruzi

1982

Kidder, G.W.

Biochem. Biophys. Res. Commun.

107

381-388

641928

10879466

End-product regulation and kinetic mechanism of guanosine-inosine kinase from Escherichia coli

2000

Kawasaki, H.; Shimaoka, M.; Usuda, Y.; Utagawa, T.

Biosci. Biotechnol. Biochem.

64

972-979

641995

3013235

Nucleoside phosphotransferase from malt sprouts. I. Isolation, characterization and specificity of the enzyme

1986

Billich, A.; Stockhowe, U.; Witzel, H.

Biol. Chem. Hoppe-Seyler

367

267-278

642002

16232546

A novel selective nucleoside phosphorylating enzyme from Morganella morganii

1999

Asano, Y.; Mihara, Y.; Yamada, H.

J. Biosci. Bioeng.

87

732-738

644616

479130

Purification and properties of xanthine dehydrogenase from Streptomyces cyanogenus

1979

Ohe, T.; Watanabe, Y.

J. Biochem.

86

45-53

654127

12777783

Cloning, preliminary characterization and crystallization of nucleoside hydrolases from Caenorhabditis elegans and Campylobacter jejuni

2003

Versees, W.; van Holsbeke, E.; de Vos, S.; Decanniere, K.; Zegers, I.; Steyaert, J.

Acta Crystallogr. Sect. D

D59

1087-1089

654255

11282633

Purification, characterization, and gene cloning of purine nucleosidase from Ochrobactrum anthropi

2001

Ogawa, J.; Takeda, S.; Xie, S.X.; Hatanaka, H.; Ashikari, T.; Amachi, T.; Shimizu, S.

Appl. Environ. Microbiol.

67

1783-1787

655545

11418110

A new caffeine biosynthetic pathway in tea leaves: utilisation of adenosine released from the S-adenosyl-L-methionine cycle

2001

Koshiishi, C.; Kato, A.; Yama, S.; Crozier, A.; Ashihara, H.

FEBS Lett.

499

50-54

662643

15808857

Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene

2005

Dandanell, G.; Szczepanowski, R.H.; Kierdaszuk, B.; Shugar, D.; Bochtler, M.

J. Mol. Biol.

348

113-125

665608

15699053

Evidence for the involvement of cytosolic 5'-nucleotidase (cN-II) in the synthesis of guanine nucleotides from xanthosine

2005

Barsotti, C.; Pesi, R.; Giannecchini, M.; Ipata, P.L.

J. Biol. Chem.

280

13465-13469

667101

17401201

Cloning, expression, crystallization and preliminary x-ray analysis of the XMT and DXMT N-methyltransferases from Coffea canephora (robusta)

2007

McCarthy, A.A.; Biget, L.; Lin, C.; Petiard, V.; Tanksley, S.D.; McCarthy, J.G.

Acta Crystallogr. Sect. F

F63

304-307

667105

-

Cloning and characterization of a cDNA encoding xanthosine-N7-methyltransferase from coffee (Coffea arabica)

1998

Moisyadi, S.; Neupane, K.R.; Stiles, J.I.

Acta Hortic.

461

367-377

667116

-

The role of xanthosine in the biosynthesis of caffeine in coffe plants

1985

Negishi, O.; Ozawa, T.; Imagawa, H.

Agric. Biol. Chem.

49

2221-2222

667792

15784179

Purification and characterization of RihC, a xanthosine-inosine-uridine-adenosine-preferring hydrolase from Salmonella enterica serovar Typhimurium

2005

Hansen, M.R.; Dandanell, G.

Biochim. Biophys. Acta

1723

55-62

668586

12860386

The first committed step reaction of caffeine biosynthesis: 7-methylxanthosine synthase is closely homologous to caffeine synthases in coffee (Coffea arabica L.)

2003

Mizuno, K.; Kato, M.; Irino, F.; Yoneyama, N.; Fujimura, T.; Ashihara, H.

FEBS Lett.

547

56-60

669194

11108716

7-Methylxanthine methyltransferase of coffee plants. Gene isolation and enzymatic properties

2001

Ogawa, M.; Herai, Y.; Koizumi, N.; Kusano, T.; Sano, H.

J. Biol. Chem.

276

8213-8218

670509

9237402

Separation of the N-7 methyltransferase, the key enzyme in caffeine biosynthesis

1997

Waldhauser, S.S.M.; Gillies, F.M.; Crozier, A.; Baumann, T.W.

Phytochemistry

45

1407-1414

670565

15604660

Application of RNAi to confirm theobromine as the major intermediate for caffeine biosynthesis in coffee plants with potential for construction of decaffeinated varieties

2004

Ogita, S.; Uefuji, H.; Morimoto, M.; Sano, H.

Plant Mol. Biol.

54

931-941

670568

16247553

Caffeine production in tobacco plants by simultaneous expression of three coffee N-methyltranferases and its potential as a pest repellant

2005

Uefuji, H.; Tatsumi, Y.; Morimoto, M.; Kaothien-Nakayama, P.; Ogita, S.; Sano, H.

Plant Mol. Biol.

59

221-227

670578

12746542

Molecular cloning and functional characterization of three distinct N-methyltransferases involved in the caffeine biosynthetic pathway in coffee plants

2003

Uefuji, H.; Ogita, S.; Yamaguchi, Y.; Koizumi, N.; Sano, H.

Plant Physiol.

132

372-380

670598

17434991

The structure of two N-methyltransferases from the caffeine biosynthetic pathway

2007

McCarthy, A.A.; McCarthy, J.G.

Plant Physiol.

144

879-889

670621

100109436

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Links to other databases for Xanthosine

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