2BNM

The structure of Hydroxypropylphosphonic acid epoxidase from S. wedmorenis.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and Reactivity of Hydroxypropylphosphonic Acid Epoxidase in Fosfomycin Biosynthesis by a Cation- and Flavin-Dependent Mechanism.

Mcluskey, K.Cameron, S.Hammerschmidt, F.Hunter, W.N.

(2005) Proc.Natl.Acad.Sci.USA 102: 14221

  • DOI: 10.1073/pnas.0504314102
  • Primary Citation of Related Structures:  2BNN, 2BNO

  • PubMed Abstract: 
  • The biosynthesis of fosfomycin, an oxirane antibiotic in clinical use, involves a unique epoxidation catalyzed by (S)-2-hydroxypropylphosphonic acid epoxidase (HPPE). The reaction is essentially dehydrogenation of a secondary alcohol. A high-resoluti ...

    The biosynthesis of fosfomycin, an oxirane antibiotic in clinical use, involves a unique epoxidation catalyzed by (S)-2-hydroxypropylphosphonic acid epoxidase (HPPE). The reaction is essentially dehydrogenation of a secondary alcohol. A high-resolution crystallographic analysis reveals that the HPPE subunit displays a two-domain combination. The C-terminal or catalytic domain has the cupin fold that binds a divalent cation, whereas the N-terminal domain carries a helix-turn-helix motif with putative DNA-binding helices positioned 34 A apart. The structure of HPPE serves as a model for numerous proteins, of ill-defined function, predicted to be transcription factors but carrying a cupin domain at the C terminus. Structure-reactivity analyses reveal conformational changes near the catalytic center driven by the presence or absence of ligand, that HPPE is a Zn(2+)/Fe(2+)-dependent epoxidase, proof that flavin mononucleotide is required for catalysis, and allow us to propose a simple mechanism that is compatible with previous experimental data. The participation of the redox inert Zn(2+) in the mechanism is surprising and indicates that Lewis acid properties of the metal ions are sufficient to polarize the substrate and, aided by flavin mononucleotide reduction, facilitate the epoxidation.


    Related Citations: 
    • Initiating a Crystallographic Analysis of Recombinant (S)-2-Hydroxypropylphosphonic Acid Epoxidase from Streptomyces Wedmorensis.
      Cameron, S.,Mcluskey, K.,Chamberlayne, R.,Hallyburton, I.,Hunter, W.N.
      (2005) Acta Crystallogr.,Sect.F 61: 534


    Organizational Affiliation

    Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EPOXIDASE
A, B
198Streptomyces wedmorensisGene Names: hppE (fom4)
EC: 1.11.1.23
Find proteins for Q56185 (Streptomyces wedmorensis)
Go to UniProtKB:  Q56185
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.188 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 86.363α = 90.00
b = 86.363β = 90.00
c = 221.440γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-05
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance