Crystal Structure of CoII HppE in Complex with Tris Buffer

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 

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Structural insight into antibiotic fosfomycin biosynthesis by a mononuclear iron enzyme

Higgins, L.J.Yan, F.Liu, P.Liu, H.W.Drennan, C.L.

(2005) Nature 437: 838-844

  • DOI: https://doi.org/10.1038/nature03924
  • Primary Citation of Related Structures:  
    1ZZ6, 1ZZ7, 1ZZ8, 1ZZ9, 1ZZB, 1ZZC

  • PubMed Abstract: 

    The biosynthetic pathway of the clinically important antibiotic fosfomycin uses enzymes that catalyse reactions without precedent in biology. Among these is hydroxypropylphosphonic acid epoxidase, which represents a new subfamily of non-haem mononuclear iron enzymes. Here we present six X-ray structures of this enzyme: the apoenzyme at 2.0 A resolution; a native Fe(II)-bound form at 2.4 A resolution; a tris(hydroxymethyl)aminomethane-Co(II)-enzyme complex structure at 1.8 A resolution; a substrate-Co(II)-enzyme complex structure at 2.5 A resolution; and two substrate-Fe(II)-enzyme complexes at 2.1 and 2.3 A resolution. These structural data lead us to suggest how this enzyme is able to recognize and respond to its substrate with a conformational change that protects the radical-based intermediates formed during catalysis. Comparisons with other family members suggest why substrate binding is able to prime iron for dioxygen binding in the absence of alpha-ketoglutarate (a co-substrate required by many mononuclear iron enzymes), and how the unique epoxidation reaction of hydroxypropylphosphonic acid epoxidase may occur.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
hydroxypropylphosphonic acid epoxidase
A, B
198Streptomyces wedmorensisMutation(s): 0 
Gene Names: fom4
EC: 1.14
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.36α = 90
b = 86.36β = 90
c = 220.17γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-07-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations