3SCF

Fe(II)-HppE with S-HPP and NO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of regiospecificity of a mononuclear iron enzyme in antibiotic fosfomycin biosynthesis.

Yun, D.Dey, M.Higgins, L.J.Yan, F.Liu, H.W.Drennan, C.L.

(2011) J Am Chem Soc 133: 11262-11269

  • DOI: https://doi.org/10.1021/ja2025728
  • Primary Citation of Related Structures:  
    3SCF, 3SCG, 3SCH

  • PubMed Abstract: 

    Hydroxypropylphosphonic acid epoxidase (HppE) is an unusual mononuclear iron enzyme that uses dioxygen to catalyze the oxidative epoxidation of (S)-2-hydroxypropylphosphonic acid (S-HPP) in the biosynthesis of the antibiotic fosfomycin. Additionally, the enzyme converts the R-enantiomer of the substrate (R-HPP) to 2-oxo-propylphosphonic acid. To probe the mechanism of HppE regiospecificity, we determined three X-ray structures: R-HPP with inert cobalt-containing enzyme (Co(II)-HppE) at 2.1 Å resolution; R-HPP with active iron-containing enzyme (Fe(II)-HppE) at 3.0 Å resolution; and S-HPP-Fe(II)-HppE in complex with dioxygen mimic NO at 2.9 Å resolution. These structures, along with previously determined structures of S-HPP-HppE, identify the dioxygen binding site on iron and elegantly illustrate how HppE is able to recognize both substrate enantiomers to catalyze two completely distinct reactions.


  • Organizational Affiliation

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epoxidase
A, B, C
198Streptomyces wedmorensisMutation(s): 0 
Gene Names: fom4
UniProt
Find proteins for Q56185 (Streptomyces wedmorensis)
Explore Q56185 
Go to UniProtKB:  Q56185
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ56185
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S0H
Query on S0H

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
L [auth C]
(S)-2-HYDROXYPROPYLPHOSPHONIC ACID
C3 H9 O4 P
ZFVCONUOLQASEW-VKHMYHEASA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
M [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE2
Query on FE2

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B],
K [auth C]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
NO
Query on NO

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
NITRIC OXIDE
N O
ODUCDPQEXGNKDN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.661α = 90
b = 111.661β = 90
c = 152.158γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-10
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description