1IXQ

Enzyme-Phosphate2 Complex of Pyridoxine 5'-Phosphate synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Enzyme-ligand complexes of pyridoxine 5'-phosphate synthase: implications for substrate binding and catalysis

Garrido-Franco, M.Laber, B.Huber, R.Clausen, T.

(2002) J.MOL.BIOL. 321: 601-612

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pyridoxine 5'-phosphate (PNP) synthase is the last enzyme in the de novo biosynthesis of vitamin B(6) catalyzing the complicated ring-closure reaction between 1-deoxy-D-xylulose-5-phosphate and 1-amino-acetone-3-phosphate. Here we present the crystal ...

    Pyridoxine 5'-phosphate (PNP) synthase is the last enzyme in the de novo biosynthesis of vitamin B(6) catalyzing the complicated ring-closure reaction between 1-deoxy-D-xylulose-5-phosphate and 1-amino-acetone-3-phosphate. Here we present the crystal structures of four PNP synthase complexes with substrates and substrate analogs. While the overall fold of the enzyme is conserved in all complexes, characteristic readjustments were observed in the active site. The complementary structural information allowed us to postulate a detailed reaction mechanism. The observed binding mode of substrates indicates how the first reaction intermediate, the Schiff-base conjugate, is formed. The most important mechanistic features are the presence of two phosphate-binding sites with distinct affinities and the existence of a water relay system for the release of reaction water molecules. Furthermore, the complexes provide the basis to rationalize the open-closed transition of a flexible loop located on the C-terminal side of the TIM-barrel. Binding of both substrate molecules to the active site seems to be a prerequisite to trigger this transition. Highly conserved mechanistically important residues in the PNP synthase family imply a similar active site organization and reaction mechanism for all family members. Due to the exclusive presence of PNP synthase in a subset of eubacteria, including several well-known pathogens, and due to its outstanding physiological importance for these organisms, the enzyme appears to be a promising novel target for antibacterial drug design.


    Related Citations: 
    • Structural Basis for the Function of Pyridoxine 5'-Phosphate Synthase
      Garrido-Franco, M.,Laber, B.,Huber, R.,Clausen, T.
      (2001) Structure 9: 245
    • Crystallization and preliminary X-ray crystallographic analysis of PdxJ, the pyridoxine 5'-phosphate synthesizing enzyme
      Garrido-Franco, M.,Huber, R.,Schmidt, F.S.,Laber, B.,Clausen, T.
      (2000) Acta Crystallogr.,Sect.D 56: 1045


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, Planegg-Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyridoxine 5'-phosphate Synthase
A, B, C, D
242Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: pdxJ
EC: 2.6.99.2
Find proteins for P0A794 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A794
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.222 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 130.900α = 90.00
b = 155.400β = 90.00
c = 129.000γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
CCP4data scaling
SCALAdata scaling
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-11
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance