1G69

THIAMIN PHOSPHATE SYNTHASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

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

(2001) Biochemistry 40: 10103-10114

  • Primary Citation of Related Structures:  1G4E, 1G4P, 1G4S, 1G4T, 1G67, 1G6C

  • PubMed 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 ...

    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.


    Related Citations: 
    • Crystal Structure of Thiamin Phosphate Synthase from Bacillus subtilis at 1.25A Resolution
      Chiu, H.-J.,Reddick, J.J.,Begley, T.P.,Ealick, S.E.
      (1999) Biochemistry 38: 6460
    • CHARACTERIZATION OF THE BACILLUS SUBTILIS THIC OPERON INVOLVED IN THIAMINE BIOSYNTHESIS
      ZHANG, Y.,TAYLOR, S.V.,CHIU, H.-J.,BEGLEY, T.P.
      (1997) J.BACTERIOL. 179: 3030


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THIAMIN PHOSPHATE SYNTHASE
A, B
228Bacillus subtilis (strain 168)Gene Names: thiE (thiC, ywbK)
EC: 2.5.1.3
Find proteins for P39594 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P39594
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP

Download SDF File 
Download CCD File 
A, B
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
ICP
Query on ICP

Download SDF File 
Download CCD File 
A, B
2-METHYL-5-METHYLENE-5H-PYRIMIDIN-4-YLIDENEAMINE
4-IMINO-5-METHIDYL-2-METHYLPYRIMIDINE
C6 H7 N3
AXFPKNUSOMMYRV-UHFFFAOYSA-N
 Ligand Interaction
TZP
Query on TZP

Download SDF File 
Download CCD File 
A, B
4-METHYL-5-HYDROXYETHYLTHIAZOLE PHOSPHATE
C6 H10 N O4 P S
OCYMERZCMYJQQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.215 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 76.480α = 90.00
b = 76.480β = 90.00
c = 139.880γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-09-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance