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Ligand 2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate

Basic Ligand Information

Molecular Structure

Related pathways

Pathway Source

Pathways

BRENDA

vitamin B1 metabolism

KEGG

Biosynthesis of cofactors, Thiamine metabolism

MetaCyc

4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis I, 4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis II, hydroxymethylpyrimidine salvage, thiamine diphosphate biosynthesis I (E. coli), thiamine diphosphate biosynthesis II (Bacillus), thiamine diphosphate biosynthesis III (Staphylococcus), thiamine diphosphate biosynthesis IV (eukaryotes), thiamine diphosphate salvage II, thiamine diphosphate salvage IV (yeast), thiamine phosphate formation from pyrithiamine and oxythiamine (yeast) more

Show all BRENDA pathways known for 2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate

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Roles as Enzyme Ligand

In Vivo Substrate in Enzyme-catalyzed Reactions (5 results)

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Show Natural Substrate (5 entries)

EC NUMBER

PROVEN IN VIVO REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

2.5.1.3

2-methyl-4-amino-5-diphosphomethylpyrimidine + 2-(4-methyl-1,3-thiazol-5-yl)ethyl phosphate = diphosphate + ?

639719, 639725, 639726, 639720

-

2.5.1.3

2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + (R,Z)-2-(2-carboxy-4-methylthiazol-5(2H)-ylidene)ethyl phosphate = diphosphate + thiamine phosphate + CO2

715306

-

2.5.1.3

2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate = diphosphate + thiamine phosphate + CO2

715306

-

2.5.1.3

2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + 4-methyl-5-(2-phosphono-oxyethyl)-thiazole = thiamine monophosphate + diphosphate

660270

-

2.5.1.3

2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + 4-methyl-5-(2-phosphono-oxyethyl)thiazole = diphosphate + thiamine phosphate

727098

-

2.5.1.3

5 entries

In Vivo Product in Enzyme-catalyzed Reactions (6 results)

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Show Natural Product (6 entries)

EC NUMBER

PROVEN IN VIVO REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

2.7.1.49

ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine = ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine

-

-

2.7.1.49

ATP + 4-amino-5-phosphomethyl-2-methylpyrimidine = ADP + 4-amino-5-diphosphomethyl-2-methylpyrimidine

-

-

2.7.4.7

ATP + (4-amino-2-methylpyrimidin-5-yl)methyl phosphate = ADP + (4-amino-2-methylpyrimidin-5-yl)methyl diphosphate

-

-

2.7.4.7

ATP + 2-methyl-4-amino-5-phosphomethylpyrimidine = ADP + 2-methyl-4-amino-5-diphosphomethylpyrimidine

641660, 641657, 639726

-

2.7.4.7

ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine = ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine

-

-

2.7.4.7

ATP + 4-amino-2-methyl-phosphomethylpyrimidine = ADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine

-

-

2.7.1.49

2 entries

2.7.4.7

4 entries

Substrate in Enzyme-catalyzed Reactions (9 results)

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Show Substrate (9 entries)

EC NUMBER

REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

2.5.1.3

2-methyl-4-amino-5-diphosphomethylpyrimidine + 2-(4-methyl-1,3-thiazol-5-yl)ethyl phosphate = diphosphate + ?

639719, 639725, 639726, 639720

-

2.5.1.3

2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + (R,Z)-2-(2-carboxy-4-methylthiazol-5(2H)-ylidene)ethyl phosphate = diphosphate + thiamine phosphate + CO2

715306

-

2.5.1.3

2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate = diphosphate + thiamine phosphate + CO2

715306

-

2.5.1.3

2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + 4-methyl-5-(2-phosphono-oxyethyl)-thiazole = ?

688400

-

2.5.1.3

2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + 4-methyl-5-(2-phosphono-oxyethyl)-thiazole = thiamine monophosphate + diphosphate

639724, 639727, 639722, 639723, 639721, 639719, 639720, 639725, 639726, 660270, 671621, 674302

-

2.5.1.3

2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + 4-methyl-5-(2-phosphono-oxyethyl)-thiazole = thiamine phosphate + diphosphate

723533, 721627

-

2.5.1.3

2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + 4-methyl-5-(2-phosphono-oxyethyl)thiazole = diphosphate + thiamine phosphate

727098

-

2.5.1.3

2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + 4-methyl-5-beta-hydroxyethylthiazole phosphate = thiamine phosphate + diphosphate

722984

-

2.5.1.3

4-amino-5-hydroxymethyl-2-methylpyrimidine diphosphate + 4-methyl-5-(2-hydroxyethyl)thiazole phosphate = thiamine monophosphate + diphosphate + phosphate

671903

-

2.5.1.3

9 entries

Product in Enzyme-catalyzed Reactions (7 results)

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Show Product (7 entries)

EC NUMBER

REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

2.7.1.49

ATP + 2-methyl-4-amino-5-phosphomethylpyrimidine = ADP + 2-methyl-4-amino-5-diphosphomethylpyrimidine

-

-

2.7.1.49

ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine = ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine

-

-

2.7.1.49

ATP + 4-amino-5-phosphomethyl-2-methylpyrimidine = ADP + 4-amino-5-diphosphomethyl-2-methylpyrimidine

-

-

2.7.4.7

ATP + (4-amino-2-methylpyrimidin-5-yl)methyl phosphate = ADP + (4-amino-2-methylpyrimidin-5-yl)methyl diphosphate

-

-

2.7.4.7

ATP + 2-methyl-4-amino-5-phosphomethylpyrimidine = ADP + 2-methyl-4-amino-5-diphosphomethylpyrimidine

645187, 641660, 641657, 639726

-

2.7.4.7

ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine = ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine

-

-

2.7.4.7

ATP + 4-amino-2-methyl-phosphomethylpyrimidine = ADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine

-

-

2.7.1.49

3 entries

2.7.4.7

4 entries

Inhibitor in Enzyme-catalyzed Reactions (1 result)

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Show Inhibitors (1 entry)

EC NUMBER

COMMENTARY

LITERATURE

ENZYME 3D STRUCTURE

2.5.1.3

uncompetitive

671903

-

Enzyme Kinetic Parameters

K_M Value (4 results)

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Show KM Value (4 entries)

EC NUMBER

KM VALUE [MM]

KM VALUE MAXIMUM [MM]

COMMENTARY

LITERATURE

2.5.1.3

0.0007

-

wild type enzyme, in buffer containing 50 mM phosphate and 10 mM MgSO4, at pH 8.0 and 37°C

722984

2.5.1.3

0.00085

-

-

639722, 639723

2.5.1.3

0.001

-

pH 9.2, 37°C

639721

2.5.1.3

0.0128

-

37°C, pH 8.0

671903

2.5.1.3

4 entries

K_i Value (1 result)

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Show KI Value (1 entry)

EC NUMBER

KI VALUE [MM]

KI VALUE MAXIMUM [MM]

COMMENTARY

LITERATURE

2.5.1.3

0.0148

-

37°C, pH 8.0

671903

References & Links

Literature References (22)

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Show Reference (22 entries)

BRENDA REFERENCE ID

PUBMED ID

TITLE

YEAR

AUTHORS

JOURNAL

VOLUME

PAGES

639719

13807175

The biosynthesis of thiamine. 2. Fractionation of enzyme system and identification of thiazole monophosphate and thiamine monophosphate as intermediates

1960

Camiener, G.W.; Brown, G.M.

J. Biol. Chem.

235

2411-2417

639720

8394314

Copurification of hydroxyethylthiazole kinase and thiamine-phosphate pyrophosphorylase of Saccharomyces cerevisiae: characterization of hydroxyethylthiazole kinase as a bifunctional enzyme in the thiamine biosynthetic pathway

1993

Kawasaki, Y.

J. Bacteriol.

175

5153-5158

639721

14463407

The enzymatic synthesis of thiamine monophosphate

1961

Leder, I.G.

J. Biol. Chem.

236

3066-3071

639722

4580841

Purification and properties of thiaminephosphate pyrophosphorylase of Escherichia coli

1973

Kayama, Y.; Kawasaki, T.

Arch. Biochem. Biophys.

158

242-248

639723

374983

Thiamine phosphate pyrophosphorylase

1979

Kawasaki, T.

Methods Enzymol.

62

69-73

639724

11513588

Mechanistic studies on thiamin phosphate synthase: evidence for a dissociative mechanism

2001

Reddick, J.J.; Nicewonger, R.; Begley, T.P.

Biochemistry

40

10095-10102

639725

7982968

Isolation and characterization of the THI6 gene encoding a bifunctional thiamin-phosphate pyrophosphorylase/hydroxyethylthiazole kinase from Saccharomyces cerevisiae

1994

Nosaka, K.; Nishimura, H.; Kawasaki, Y.; Tsujihara, T.; Iwashima, A.

J. Biol. Chem.

269

30510-30516

639726

9700068

A Brassica cDNA clone encoding a bifunctional hydroxymethylpyrimidine kinase/thiamin-phosphate pyrophosphorylase involved in thiamin biosynthesis

1998

Kim, Y.S.; Nosaka, K.; Downs, D.M.; Kwak, J.M.; Park, D.; Chung, I.K.; Nam, H.G.

Plant Mol. Biol.

37

955-966

639727

10350464

Crystal structure of thiamin phosphate synthase from Bacillus subtilis at 1.25 A resolution

1999

Chiu, H.J.; Reddick, J.J.; Begley, T.P.; Ealick, S.E.

Biochemistry

38

6460-6470

641657

-

The biosynthesis of thiamine. III. Mechanism of enzymatic formation of the pyrophosphate ester of 2-methyl-4-amino-5-hydroxymethylpyrimidine

1961

Lewin, L.M.; Brown, G.M.

J. Biol. Chem.

236

2768-2771

641660

-

Overexpression, purification and characterization of two pyrimidine kinases involved in the biosynthesis of thiamin: 4-amino-5-hydroxymethyl-2-methylpyrimidine kinase and 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase

1998

Reddick, J.J.; Kinsland, C.; Nicewonger, R.; Christian, T.; Downs, D.M.; Winkler, M.E.; Begley, T.P.

Tetrahedron

54

15983-15991

645187

11839308

Crystal structure of 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase from Salmonella typhimurium at 2.3.ANG. resolution

2002

Cheng, G.; Bennett, E.M.; Begley, T.P.; Ealick, S.E.

Structure

10

225-235

660270

15051042

Thiamine binding and metabolism in germinating seeds of selected cereals and legumes

2004

Golda, A.; Szyniarowski, P.; Ostrowska, K.; Kozik, A.; Rapala-Kozik, M.

Plant Physiol. Biochem.

42

187-195

671621

17174261

Determination of the genetic, molecular, and biochemical basis of the Arabidopsis thaliana thiamin auxotroph th1

2007

Ajjawi, I.; Tsegaye, Y.; Shintani, D.

Arch. Biochem. Biophys.

459

107-114

671903

17696876

Molecular characterization of thi3 gene involved in thiamine biosynthesis in Zea mays: cDNA sequence and enzymatic and structural properties of recombinant bifunctional protein with 4-amino-5-hydroxymethyl-2-methylpyrimidine (phosphate) kinase and thiamin

2007

Rapala-Kozik, M.; Olczak, M.; Ostrowska, K.; Starosta, A.; Kozik, A.

Biochem. J.

408

149-159

674302

16952958

Thiamine is synthesized by a salvage pathway in Rhizobium leguminosarum bv. viciae strain 3841

2006

Karunakaran, R.; Ebert, K.; Harvey, S.; Leonard, M.E.; Ramachandran, V.; Poole, P.S.

J. Bacteriol.

188

6661-6668

688400

18178222

Sensitive genome-wide screen for low secondary enzymatic activities: the YjbQ family shows thiamin phosphate synthase activity

2008

Morett, E.; Saab-Rincon, G.; Olvera, L.; Olvera, M.; Flores, H.; Grande, R.

J. Mol. Biol.

376

839-853

715306

21534620

A missing enzyme in thiamin thiazole biosynthesis: identification of TenI as a thiazole tautomerase

2011

Hazra, A.B.; Han, Y.; Chatterjee, A.; Zhang, Y.; Lai, R.Y.; Ealick, S.E.; Begley, T.P.

J. Am. Chem. Soc.

133

9311-9319

721627

20968298

Domain organization in Candida glabrata THI6, a bifunctional enzyme required for thiamin biosynthesis in eukaryotes

2010

Paul, D.; Chatterjee, A.; Begley, T.P.; Ealick, S.E.

Biochemistry

49

9922-9934

722984

22226942

Evolutionary walk between (beta/alpha)8 barrels: catalytic migration from triosephosphate isomerase to thiamin phosphate synthase

2012

Saab-Rincon, G.; Olvera, L.; Olvera, M.; Rudino-Pinera, E.; Benites, E.; Soberon, X.; Morett, E.

J. Mol. Biol.

416

255-270

723533

21818324

Identification of inhibitors against Mycobacterium tuberculosis thiamin phosphate synthase, an important target for the development of anti-TB drugs

2011

Khare, G.; Kar, R.; Tyagi, A.K.

PLoS ONE

6

e22441

727098

24583237

Enzymatic and structural characterization of an archaeal thiamin phosphate synthase

2014

Hayashi, M.; Kobayashi, K.; Esaki, H.; Konno, H.; Akaji, K.; Tazuya, K.; Yamada, K.; Nakabayashi, T.; Nosaka, K.

Biochim. Biophys. Acta

1844

803-809

Links to other databases for 2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate

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Show Links (1 entry)