Thiamine phosphate synthase

 

Thiamin phosphate synthase catalyses the formation of thiamin phosphate from 4-amino-5-(hydroxymethyl)-2-methylpyrimidine pyrophosphate and 5-(hydroxyethyl-4-methylthiazole phosphate, in the penultimate step of the biosynthesis of thiamin phosphate.

 

Reference Protein and Structure

Sequence
P39594 UniProt (2.5.1.3) IPR034291 (Sequence Homologues) (PDB Homologues)
Biological species
Bacillus subtilis subsp. subtilis str. 168 (Bacteria) Uniprot
PDB
2tps - THIAMIN PHOSPHATE SYNTHASE (1.25 Å) PDBe PDBsum 2tps
Catalytic CATH Domains
3.20.20.70 CATHdb (see all for 2tps)
Cofactors
Magnesium(2+) (1)
Click To Show Structure

Enzyme Reaction (EC:2.5.1.3)

4-methyl-5-(2-phosphonatooxyethyl)thiazole(2-)
CHEBI:58296ChEBI
+
4-amino-2-methyl-5-diphosphonatooxymethylpyrimidine(3-)
CHEBI:57841ChEBI
+
hydron
CHEBI:15378ChEBI
→
thiamine(1+) monophosphate(2-)
CHEBI:37575ChEBI
+
diphosphate(3-)
CHEBI:33019ChEBI
Alternative enzyme names: TMP-PPase, Thiamine monophosphate pyrophosphorylase, Thiamine phosphate pyrophosphorylase, Thiamine-phosphate pyrophosphorylase, TMP pyrophosphorylase, Thiamine-phosphate synthase, TMP diphosphorylase, Thiamine-phosphate diphosphorylase, ThiE (gene name), TH1 (gene name), THI6 (gene name), 2-methyl-4-amino-5-hydroxymethylpyrimidine-diphosphate:4-methyl-5-(2-phosphoethyl)thiazole 2-methyl-4-aminopyrimidine-5-methenyltransferase,

Enzyme Mechanism

Introduction

The reaction of thiamin phosphate synthase occurs by a dissociative SN1 mechanism. Ser 130 activates the pyrophosphate as a leaving group and transition state stabilisation is maintained by a magnesium cation. The ionised group is then able to react with 5-(hydroxyethyl-4-methylthiazole phosphate to give thiamin phosphate. The carbocation intermediate is stabilised by the counterion and a hydrogen bond between the pyrimidine amino group and the pyrophosphate.

Catalytic Residues Roles

UniProt PDB* (2tps)
Ser117 Ser130(122)A Activates the pyrophosphate to act as a leaving group. enhance reactivity, electrostatic stabiliser
Arg46, Lys146 Arg59(51)A, Lys159(151)A Help stabilise the reactive intermediates formed during the course of the reaction. electrostatic stabiliser
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

rate-determining step, unimolecular elimination by the conjugate base, overall reactant used, overall product formed, bimolecular nucleophilic addition

References

  1. Peapus DH et al. (2001), Biochemistry, 40, 10103-10114. Structural Characterization of the Enzyme−Substrate, Enzyme−Intermediate, and Enzyme−Product Complexes of Thiamin Phosphate Synthase†,‡. DOI:10.1021/bi0104726. PMID:11513589.
  2. Jurgenson CT et al. (2009), Annu Rev Biochem, 78, 569-603. The Structural and Biochemical Foundations of Thiamin Biosynthesis. DOI:10.1146/annurev.biochem.78.072407.102340. PMID:19348578.
  3. Reddick JJ et al. (2001), Biochemistry, 40, 10095-10102. Mechanistic Studies on Thiamin Phosphate Synthase:  Evidence for a Dissociative Mechanism†. DOI:10.1021/bi010267q. PMID:11513588.
  4. Chiu HJ et al. (1999), Biochemistry, 38, 6460-6470. Crystal Structure of Thiamin Phosphate Synthase fromBacillus subtilisat 1.25 Å Resolution†,‡. DOI:10.1021/bi982903z. PMID:10350464.

Step 1. Ser130 activates the pyrophosphate as a leaving group and transition state stabilisation is maintained by a magnesium cation.

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Catalytic Residues Roles

Residue Roles
Arg59(51)A electrostatic stabiliser
Ser130(122)A electrostatic stabiliser
Lys159(151)A electrostatic stabiliser
Ser130(122)A enhance reactivity

Chemical Components

rate-determining step, ingold: unimolecular elimination by the conjugate base, overall reactant used, overall product formed

Step 2. The ionised carbocation is then able to react with 5-(hydroxyethyl-4-methylthiazole phosphate to give thiamin phosphate. The intermediate is stabilised by a hydrogen bond between the pyrimidine amino group and the pyrophosphate.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Arg59(51)A electrostatic stabiliser
Ser130(122)A electrostatic stabiliser
Lys159(151)A electrostatic stabiliser

Chemical Components

ingold: bimolecular nucleophilic addition, overall product formed
Download: Image, Marvin File

Step 1. Ser130 activates the pyrophosphate as a leaving group and transition state stabilisation is maintained by a magnesium cation.

Step 2. The ionised carbocation is then able to react with 5-(hydroxyethyl-4-methylthiazole phosphate to give thiamin phosphate. The intermediate is stabilised by a hydrogen bond between the pyrimidine amino group and the pyrophosphate.

Products.

Contributors

Sophie T. Williams, Craig Porter, Gary McDowell, Gemma L. Holliday, Charity Hornby