Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.29 kDa 
• Atom Count: 3753 
• Residue Count: 388 
• Unique protein chains: 1

2BNM

The structure of Hydroxypropylphosphonic acid epoxidase from S. wedmorenis.

• DOI: 10.2210/pdb2BNM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces wedmorensis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-03-29 Released: 2005-10-05 
• Deposition Author(s): McLuskey, K., Cameron, S., Hunter, W.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.230 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

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 U S A 102: 14221

• PubMed: 16186494 
• DOI: 10.1073/pnas.0504314102
• Structures With Same Primary Citation


• 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-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.

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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 Struct Biol Cryst Commun 61: 534

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
EPOXIDASE	A, B	198	Streptomyces wedmorensis	Mutation(s): 0  Gene Names: hppE, fom4 EC: 1.11.1.23
Find proteins for Q56185 (Streptomyces wedmorensis) Explore Q56185  Go to UniProtKB:  Q56185

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.230 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.363	α = 90
b = 86.363	β = 90
c = 221.44	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-03-29 
• Released Date: 2005-10-05 
Deposition Author(s): McLuskey, K., Cameron, S., Hunter, W.N.

Revision History 

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