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Ligand pyridoxamine

Basic Ligand Information

Molecular Structure

Show all BRENDA pathways known for pyridoxamine

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Roles as Enzyme Ligand

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

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Show Natural Substrate (3 entries)

EC NUMBER

PROVEN IN VIVO REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

2.6.1.30

pyridoxamine + pyruvate = pyridoxal + L-alanine

639958, 639957, 639959, 639960, 759524, 639956

2z9v, 3D-view

2.6.1.31

pyridoxamine + oxaloacetate = pyridoxal + L-aspartate

639961, 639962

-

2.7.1.35

ATP + pyridoxamine = ADP + pyridoxamine 5'-phosphate

758844, 759183, 759346

1rft, 3D-view

Substrate in Enzyme-catalyzed Reactions (11 results)

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Show Substrate (11 entries)

EC NUMBER

REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

1.1.99.9

pyridoxamine + acceptor = 4-aminomethyl-5-formyl-2-methylpyridin-3-ol + reduced acceptor

287851, 287852

-

2.4.1.160

UDPglucose + pyridoxamine = UDP + 5'-O-beta-D-glucosylpyridoxamine

488674

-

2.6.1.30

pyridoxamine + 2-oxobutyrate = ?

671864

2z9v, 3D-view

2.6.1.30

pyridoxamine + 2-oxobutyrate = pyridoxal + (S)-2-aminobutyrate

671864

2z9v, 3D-view

2.6.1.30

pyridoxamine + 2-oxoglutarate = pyridoxal + L-glutamate

722999

2z9v, 3D-view

2.6.1.30

pyridoxamine + pyruvate = pyridoxal + L-alanine

639958, 739366, 639957, 639959, 639960, 671864, 670891, 687694, 722999, 759524, 639956

2z9v, 3D-view

2.6.1.30

4 entries

2.6.1.31

pyridoxamine + oxaloacetate = pyridoxal + L-aspartate

639961, 639962

-

2.6.1.54

pyridoxamine + 2-oxoglutarate = pyridoxal + D-glutamate

637633

-

2.7.1.35

ATP + pyridoxamine = ADP + pyridoxamine 5'-phosphate

662007, 675407, 671140, 663303, 641406, 641424, 662200, 723449, 723219, 662440, 673580, 677029, 723578, 758844, 662402, 759183, 759346, 641417, 641418, 641429

1rft, 3D-view

2.7.1.35

pyridoxamine + ATP = pyridoxamine 5'-phosphate

706419

1rft, 3D-view

2.7.1.35

2 entries

2.7.1.49

ATP + pyridoxamine = ADP + pyridoxamine 5'-phosphate

641658

-

Product in Enzyme-catalyzed Reactions (3 results)

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Show Product (3 entries)

EC NUMBER

REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

2.6.1.30

pyridoxal + L-alanine = pyridoxamine + pyruvate

-

2z9v, 3D-view

3.1.3.2

pyridoxamine 5'-phosphate + H2O = pyridoxamine + phosphate

-

-

3.1.3.74

pyridoxamine 5'-phosphate + H2O = pyridoxamine + phosphate

-

-

Inhibitor in Enzyme-catalyzed Reactions (12 results)

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Show Inhibitors (12 entries)

EC NUMBER

COMMENTARY

LITERATURE

ENZYME 3D STRUCTURE

1.1.1.107

-

80781

-

1.1.99.9

-

287852

-

1.2.1.21

approx. 0.1 mM, 22% inhibition of isozyme A

390214

-

2.4.1.1

weak inhibition of phosphorylase I, not II

488269

-

2.4.1.160

competitive inhibitor of pyridoxine glucosylation

488674

-

2.7.1.35

-

641408

1rft, 3D-view

2.7.1.35

effective competitive inhibitor

641407

1rft, 3D-view

2.7.1.35

2 entries

3.1.2.6

-

37432

-

3.2.1.26

-

136067, 136133

-

3.2.1.26

10 mM, 28% inhibition of invertase I, 65% inhibition of invertase II

136110

-

3.2.1.26

10 mM, 85% inhibition

136087

-

3.2.1.26

3 entries

4.4.1.5

-

37432

-

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

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

EC NUMBER

ENZYME 3D STRUCTURE

1.1.3.12

4ha6, 3D-view

2.6.1.30

2z9v, 3D-view

2.7.1.35

1rft, 3D-view

Enzyme Kinetic Parameters

k_cat Value (Turnover Number) (14 results)

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Show Turnover Number (14 entries)

EC NUMBER

TURNOVER NUMBER [1/S]

TURNOVER NUMBER MAXIMUM [1/S]

COMMENTARY

LITERATURE

2.6.1.30

0.77

-

mutant E68G, pH 9.0, 30°C

687694

2.6.1.30

0.78

-

mutant E68A, pH 9.0, 30°C

687694

2.6.1.30

2

8

-

671864

2.6.1.30

2

8

30°C, pH 9.0

671864

2.6.1.30

2

8

mutant R336A, pH 9.0, 30°C

687694

2.6.1.30

2

8

wild-type, pH 9.0, 30°C

687694

2.7.1.35

0.03

-

pH 6.5, 30°C

662440

2.7.1.35

0.097

-

pH 8.5, 37°C

759183

2.7.1.35

0.3

-

with MgATP2- as substrate, pH 7.3, 37°C

663303

2.7.1.35

0.4

-

kinase 1 with ZnATP2- as substrate, pH 7.3, 37°C

663303

2.7.1.35

0.7

-

kinase 1 with MgATP2- as substrate, pH 7.3, 37°C

663303

2.7.1.35

0.79

-

in 70 mM potassium phosphate buffer, pH 6.2

673580

2.7.1.35

0.79

-

pH 6.2, 37°C

673580

2.7.1.35

127

-

recombinant enzyme, in HEPES/MgCl2 pH 7.4, 0.15 mM ZnCl2, at 37°C

723219

2.6.1.30

6 entries

2.7.1.35

8 entries

K_M Value (24 results)

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Show KM Value (24 entries)

EC NUMBER

KM VALUE [MM]

KM VALUE MAXIMUM [MM]

COMMENTARY

LITERATURE

2.4.1.160

0.26

-

-

488674

2.6.1.30

0.013

-

pH 8.9, 25°C

639957

2.6.1.30

0.043

-

pH 8.5, 37°C

639956

2.6.1.30

0.044

-

-

671864

2.6.1.30

0.044

-

30°C, pH 9.0

671864

2.6.1.30

0.044

-

wild-type, pH 9.0, 30°C

687694

2.6.1.30

0.09

-

pH 8.5, 37°C

739366

2.6.1.30

0.1

-

mutant R336A, pH 9.0, 30°C

687694

2.6.1.30

0.35

-

with 3-hydroxy-4-aminomethylpyridine, pH 8.9, 25°C

639957

2.6.1.30

1.3

-

mutant E68A, pH 9.0, 30°C

687694

2.6.1.30

2.5

-

mutant E68G, pH 9.0, 30°C

687694

2.6.1.31

0.7

-

pH 8.5, 37°C

639961

2.6.1.31

2.3

-

pH 8.5, 37°C

639961

2.7.1.35

0.006

-

pH 6.5

641417

2.7.1.35

0.0062

-

-

641406

2.7.1.35

0.01

-

kinase 1 with ZnATP2- as substrate, pH 7.3, 37°C

663303

2.7.1.35

0.03

-

kinase 1 with MgATP2- as substrate, pH 7.3, 37°C

663303

2.7.1.35

0.035

-

with MgATP2- as substrate, pH 7.3, 37°C

663303

2.7.1.35

0.0594

-

recombinant enzyme, apparent value, in HEPES/MgCl2 pH 7.4, 0.15 mM ZnCl2, at 37°C

723219

2.7.1.35

0.06

-

pH 8.5, 37°C

759183

2.7.1.35

0.126

-

in 70 mM potassium phosphate buffer, pH 6.2

673580

2.7.1.35

0.126

-

pH 6.2, 37°C

673580

2.7.1.35

0.1818

-

recombinant enzyme, pH 7.5, 37°C

759346

2.6.1.30

10 entries

2.6.1.31

2 entries

2.7.1.35

10 entries

2.7.1.49

2.4

-

pH 6.2, 37°C

641658

References & Links

Literature References (49)

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Show Reference (49 entries)

BRENDA REFERENCE ID

PUBMED ID

TITLE

YEAR

AUTHORS

JOURNAL

VOLUME

PAGES

37432

7417280

Inhibitors of glyoxalase enzymes

1980

Oray, B.; Norton, S.J.

Biochem. Biophys. Res. Commun.

95

624-629

80781

4306030

The bacterial oxidation of vitamin B6. VI. Pyridoxal dehydrogenase and 4-pyridoxolactonase

1969

Burg, R.W.; Snell, E.E.

J. Biol. Chem.

244

2585-2589

136067

-

Partial purification and properties of invertase from Carica papaya fruits

1988

Lopez, M.E.; Vattuone, M.A.; Sampietro, A.R.

Phytochemistry

27

3077-3081

136087

16664223

Wheat invertases. Characterization of cell wall-bound and soluble forms

1985

Krishnan, H.B.; Blanchette, J.T.; Okita, T.W.

Plant Physiol.

78

241-245

136110

-

Invertases in oat seedlings

1980

Pressey, R.; Avants, J.K.

Plant Physiol.

65

135-140

136133

-

Purification and properties of an extracellular invertase from Azotobacter chroococcum

1991

De la Vega, M.G.; Cejudo, F.J.; Paneque, A.

Enzyme Microb. Technol.

13

267-271

287851

5769992

The bacterial oxidation of vitamin B6. V. The enzymatic formation of pyridoxal and isopyridoxal from pyridoxine

1969

Sundaram, T.K.; Snell, E.E.

J. Biol. Chem.

244

2577-2584

287852

3533935

Enzymes of vitamin B6 degradation. Purification and properties of pyridoxine 5-dehydrogenase (oxidase)

1986

Jong, Y.J.; Nelson, M.J.K.; Snell, E.E.

J. Biol. Chem.

261

15102-15105

390214

-

Control of glycolaldehyde dehydrogenase in vitamin B6 biosynthesis in Escherichia coli B

1978

Morita, H.; Tani, Y.; Ogata, K.

Agric. Biol. Chem.

42

69-73

488269

-

Kinetic properties of two starch phosphorylases from pea seeds

1973

Matheson, N.K.; Richardson, R.H.

Phytochemistry

17

195-200

488674

6217302

Specificity of a particulate glucosyltransferase in seedlings of Pisum sativum L. which catalyzes the formation of 5-O-(beta-D-glucopyranosyl)pyridoxine

1982

Tadera, K.; Yagi, F.; Kobayashi, A.

J. Nutr. Sci. Vitaminol.

28

359-366

637633

-

Studies on vitamin b6 metabolism in microorganisms. Part X. Further purification and characterization of pyridoxamine 5'-phosphate-alpha-ketoglutarate transaminase from Clostridium kainantoi

1972

Tani, Y.; Ukita, M.; Ogata, K.

Agric. Biol. Chem.

36

181-188

639956

14004227

Enzymatic transamination pf pyridoxamine. II. Crystalline pyridoxamine-pyruvate transaminase

1962

Wada, H.; Snell, E.E.

J. Biol. Chem.

237

133-137

639957

5650371

Relation of structure to activity of pyridoxal analogs as substrates for pyridoxamine pyruvate transaminase

1968

Ayling, J.E.; Snell, E.E.

Biochemistry

7

1626-1636

639958

-

Effect of pH and temperature on kinetic parameters of pyridoxamine-pyruvate transaminase

1978

Ford, J.B.

J. Ala. Acad. Sci.

49

16-30

639959

21680

Pyridoxamine-pyruvate transaminase. 1. Determination of the active site stoichiometry and the pH dependence of the dissociation constant for 5-deoxypyridoxal

1977

Gilmer, P.J.; McIntire, W.S.; Kirsch, J.F.

Biochemistry

16

5241-5246

639960

21681

Pyridoxamine-pyruvate transaminase. 2. Temperature-jump and stopped-flow kinetic investigation of the rates and mechanism of the reaction of 5-deoxypyridoxal with the enzyme

1977

Gilmer, P.J.; Kirsch, J.F.

Biochemistry

16

5246-5253

639961

14004226

Enzymatic transamination of pyridoxamine. I. With oxaloacetate and alpha-ketoglutarate

1962

Wada, H.; Snell, E.E.

J. Biol. Chem.

237

127-132

639962

14189882

Pyridoxamine-oxaloacetic transaminase of rat kidney

1964

Wu, H.L.C.; Mason, M.

J. Biol. Chem.

239

1492-1497

641406

3018716

Purification and characterization of pyridoxal kinase from human erythrocytes

1986

Kerry, J.A.; Kwok, F.

Prep. Biochem.

16

199-216

641407

13789

Pyridoxine kinase activity in human erythrocytes and leukocytes: assay and properties

1976

Solomon, L.R.; Hillman, R.S.

Biochem. Med.

16

223-233

641408

238769

Purification and characterization of human erythrocyte pyridoxine kinase

1975

Chern, C.J.; Beutler, E.

Clin. Chim. Acta

61

353-365

641417

3015616

Brain pyridoxal kinase. Purification and characterization

1986

Kerry, J.A.; Rohde, M.; Kwok, F.

Eur. J. Biochem.

158

581-585

641418

221500

Brain pyridoxal kinase. Purification, substrate specificities, and sensitized photodestruction of an essential histidine

1979

Kwok, F.; Churchich, J.E.

J. Biol. Chem.

254

6489-6495

641424

9354586

Mechanisms of the inhibition of human erythrocyte pyridoxal kinase by drugs

1997

Laine-Cessac, P.; Cailleux, A.; Allain, P.

Biochem. Pharmacol.

54

863-870

641429

11983425

Study of substrate-enzyme interaction between immobilized pyridoxamine and recombinant porcine pyridoxal kinase using surface plasmon resonance biosensor

2002

Fong, C.C.; Lai, W.P.; Leung, Y.C.; Lo, S.C.; Wong, M.S.; Yang, M.

Biochim. Biophys. Acta

1596

95-107

641658

2540841

Purification and properties of hydroxymethylpyrimidine kinase from Escherichia coli

1989

Mizote, T.; Nakayama, H.

Biochim. Biophys. Acta

991

109-113

662007

14973012

Characterization of two kinases involved in thiamine pyrophosphate and pyridoxal phosphate biosynthesis in Bacillus subtilis: 4-amino-5-hydroxymethyl-2methylpyrimidine kinase and pyridoxal kinase

2004

Park, J.H.; Burns, K.; Kinsland, C.; Begley, T.P.

J. Bacteriol.

186

1571-1573

662200

14722069

Conformational changes in the reaction of pyridoxal kinase

2004

Li, M.H.; Kwok, F.; Chang, W.R.; Liu, S.Q.; Lo, S.C.; Zhang, J.P.; Jiang, T.; Liang, D.C.

J. Biol. Chem.

279

17459-17465

662402

15985434

Crystal structure of pyridoxal kinase in complex with roscovitine and derivatives

2005

Tang, L.; Li, M.H.; Cao, P.; Wang, F.; Chang, W.R.; Bach, S.; Reinhardt, J.; Ferandin, Y.; Galons, H.; Wan, Y.; Gray, N.; Meijer, L.; Jiang, T.; Liang, D.C.

J. Biol. Chem.

280

31220-31229

662440

15590634

Analysis of the vitamin B6 biosynthesis pathway in the human malaria parasite Plasmodium falciparum

2005

Wrenger, C.; Eschbach, M.L.; Muller, I.B.; Warnecke, D.; Walter, R.D.

J. Biol. Chem.

280

5242-5248

663303

15249053

Expression, purification, and kinetic constants for human and Escherichia coli pyridoxal kinases

2004

di Salvo, M.L.; Hunt, S.; Schirch, V.

Protein Expr. Purif.

36

300-306

670891

-

Vitamin B6 degradation by pyridoxamine-pyruvate transaminase and pyridoxine 4-oxidase from Ochrobactrum anthropi- and Enterobacter cloacae-like bacteria

2005

Yanee, T.; Suwanna, N.; Sineenat, S.

Science Asia

31

307-311

671140

17012797

Cloning, purification and preliminary crystallographic analysis of a putative pyridoxal kinase from Bacillus subtilis

2006

Newman, J.A.; Das, S.K.; Sedelnikova, S.E.; Rice, D.W.

Acta Crystallogr. Sect. F

F62

1006-1009

671864

16545075

Molecular cloning, expression and characterization of pyridoxamine-pyruvate aminotransferase

2006

Yoshikane, Y.; Yokochi, N.; Ohnishi, K.; Hayashi, H.; Yagi, T.

Biochem. J.

396

499-507

673580

17250738

The human pyridoxal kinase, a plausible target for ginkgotoxin from Ginkgo biloba

2007

Kaestner, U.; Hallmen, C.; Wiese, M.; Leistner, E.; Drewke, C.

FEBS J.

274

1036-1045

675407

16978644

The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parallel emergence of enzyme activity during evolution

2006

Newman, J.A.; Das, S.K.; Sedelnikova, S.E.; Rice, D.W.

J. Mol. Biol.

363

520-530

677029

17766369

Crystal Structure of human pyridoxal kinase: Structural basis of M+ and M2+ activation

2007

Musayev, F.N.; Di Salvo, M.L.; Ko, T.P.; Gandhi, A.K.; Goswami, A.; Schirch, V.; Safo, M.K.

Protein Sci.

16

2184-2194

687694

17989071

Crystal structure of pyridoxamine-pyruvate aminotransferase from Mesorhizobium loti MAFF303099

2008

Yoshikane, Y.; Yokochi, N.; Yamasaki, M.; Mizutani, K.; Ohnishi, K.; Mikami, B.; Hayashi, H.; Yagi, T.

J. Biol. Chem.

283

1120-1127

706419

19197387

Poisoning pyridoxal 5-phosphate-dependent enzymes: a new strategy to target the malaria parasite Plasmodium falciparum

2009

Mueller, I.B.; Wu, F.; Bergmann, B.; Knoeckel, J.; Walter, R.D.; Gehring, H.; Wrenger, C.

PLoS ONE

4

e4406

722999

-

Engineering Mesorhizobium loti pyridoxamine-pyruvate aminotransferase for production of pyridoxamine with L-glutamate as an amino donor

2010

Yoshikane, Y.; Tamura, A.; Yokochi, N.; Ellouze, K.; Yamamura, E.; Mizunaga, H.; Fujimoto, N.; Sakamoto, K.; Sawa, Y.; Yagi, T.

J. Mol. Catal. B

67

104-110

723219

22857512

Chemical, genetic and structural assessment of pyridoxal kinase as a drug target in the African trypanosome

2012

Jones, D.C.; Alphey, M.S.; Wyllie, S.; Fairlamb, A.H.

Mol. Microbiol.

86

51-64

723449

23321022

The SOS4 pyridoxal kinase is required for maintenance of vitamin B6-mediated processes in chloroplasts

2013

Rueschhoff, E.E.; Gillikin, J.W.; Sederoff, H.W.; Daub, M.E.

Plant Physiol. Biochem.

63

281-291

723578

22879864

Crystal structures of human pyridoxal kinase in complex with the neurotoxins, ginkgotoxin and theophylline: insights into pyridoxal kinase inhibition

2012

Gandhi, A.K.; Desai, J.V.; Ghatge, M.S.; di Salvo, M.L.; Di Biase, S.; Danso-Danquah, R.; Musayev, F.N.; Contestabile, R.; Schirch, V.; Safo, M.K.

PLoS ONE

7

e40954

739366

100020636

Enzymatic transamination of pyridoxamine in tobacco plants

2013

Huang, S.; Zhang, J.; Wu, M.; Wu, Q.; Huang, L.

Plant Sci.

212

55-59

758844

30928491

Discovery of pyridoxal reductase activity as part of human vitamin B6 metabolism

2019

Ramos, R.J.; Albersen, M.; Vringer, E.; Bosma, M.; Zwakenberg, S.; Zwartkruis, F.; Jans, J.J.M.; Verhoeven-Duif, N.M.

Biochim. Biophys. Acta

1863

1088-1097

759183

31116912

Structural and functional studies on Salmonella typhimurium pyridoxal kinase the first structural evidence for the formation of Schiff base with the substrate

2019

Deka, G.; Kalyani, J.N.; Jahangir, F.B.; Sabharwal, P.; Savithri, H.S.; Murthy, M.R.N.

FEBS J.

286

3684-3700

759346

32105687

Structural attributes and substrate specificity of pyridoxal kinase from Leishmania donovani

2020

Are, S.; Gatreddi, S.; Jakkula, P.; Qureshi, I.A.

Int. J. Biol. Macromol.

152

812-827

759524

30057158

Bioconversion of pyridoxine to pyridoxamine through pyridoxal using a Rhodococcus expression system

2019

Yamamura, E.T.

J. Biosci. Bioeng.

127

79-84

Links to other databases for pyridoxamine

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Show Links (1 entry)

ChEBI

PubChem

-