PDBsum entry 1g6c

Transferase

PDB id: 1g6c

Contents

Protein chains

226 a.a. *

Ligands

IFP ×2

POP ×2

TZP ×2

Metals

_MG ×2

Waters ×293

* Residue conservation analysis

PDB id:

1g6c

Name:

Transferase

Title:

Thiamin phosphate synthase

Structure:

Thiamin phosphate synthase. Chain: a, b. Engineered: yes. Mutation: yes. Other_details: complexed with 2-trifluoromethyl-5-methylene-5h- pyrimidin-4-ylideneamine, 4-methyl-5-hydroxyethylthiazole phosphate and pyrophosphate

Source:

Bacillus subtilis. Organism_taxid: 1423. Gene: thic. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

1.40Å R-factor: 0.215 R-free: 0.237

Authors:

D.H.Peapus,H.-J.Chiu,N.Campobasso,J.J.Reddick,T.P.Begley,S.E.Ealick

Key ref:

D.H.Peapus et al. (2001). Structural characterization of the enzyme-substrate, enzyme-intermediate, and enzyme-product complexes of thiamin phosphate synthase. Biochemistry, 40, 10103-10114. PubMed id: 11513589 DOI: 10.1021/bi0104726

Date:

03-Nov-00 Release date: 26-Sep-01

Protein chains

P39594  (THIE_BACSU) -  Thiamine-phosphate synthase from Bacillus subtilis (strain 168)

Seq: 222 a.a.

Struc: 226 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.5.1.3 - thiamine phosphate synthase.
• Reaction:
  1. 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2 H⁺ = thiamine phosphate + CO2 + diphosphate
  2. 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate + 4-amino-2-methyl- 5-(diphosphooxymethyl)pyrimidine + 2 H⁺ = thiamine phosphate + CO2 + diphosphate
  3. 4-methyl-5-(2-phosphooxyethyl)-thiazole + 4-amino-2-methyl-5- (diphosphooxymethyl)pyrimidine + H⁺ = thiamine phosphate + diphosphate

2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2 × H(+) = thiamine phosphate + CO2 (Bound ligand (Het Group name = POP) corresponds exactly) + diphosphate (Bound ligand (Het Group name = TZP) matches with 59.09% similarity)

2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate + 4-amino-2-methyl- 5-(diphosphooxymethyl)pyrimidine + 2 × H(+) = thiamine phosphate + CO2 (Bound ligand (Het Group name = POP) corresponds exactly) + diphosphate (Bound ligand (Het Group name = TZP) matches with 59.09% similarity)

4-methyl-5-(2-phosphooxyethyl)-thiazole + 4-amino-2-methyl-5- (diphosphooxymethyl)pyrimidine + H(+) = thiamine phosphate (Bound ligand (Het Group name = POP) corresponds exactly) + diphosphate (Bound ligand (Het Group name = TZP) matches with 59.09% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/bi0104726

Biochemistry 40:10103-10114 (2001)

PubMed id: 11513589

Structural characterization of the enzyme-substrate, enzyme-intermediate, and enzyme-product complexes of thiamin phosphate synthase.

D.H.Peapus, H.J.Chiu, N.Campobasso, J.J.Reddick, T.P.Begley, S.E.Ealick.

ABSTRACT

Thiamin phosphate synthase catalyzes the formation of thiamin phosphate from 4-amino-5-(hydroxymethyl)-2-methylpyrimidine pyrophosphate and 5-(hydroxyethyl)-4-methylthiazole phosphate. Several lines of evidence suggest that the reaction proceeds via a dissociative mechanism. The previously determined crystal structure of thiamin phosphate synthase in complex with the reaction products, thiamin phosphate and magnesium pyrophosphate, provided a view of the active site and suggested a number of additional experiments. We report here seven new crystal structures primarily involving crystals of S130A thiamin phosphate synthase soaked in solutions containing substrates or products. We prepared S130A thiamin phosphate synthase with the intent of characterizing the enzyme-substrate complex. Surprisingly, in three thiamin phosphate synthase structures, the active site density cannot be modeled as either substrates or products. For these structures, the best fit to the electron density is provided by a model that consists of independent pyrimidine, pyrophosphate, and thiazole phosphate fragments, consistent with a carbenium ion intermediate. The resulting carbenium ion is likely to be further stabilized by proton transfer from the pyrimidine amino group to the pyrophosphate to give the pyrimidine iminemethide, which we believe is the species that is observed in the crystal structures.