1ZZC | pdb_00001zzc

Crystal Structure of CoII HppE in Complex with Tris Buffer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.242 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1ZZC

This is version 1.3 of the entry. See complete history

Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 43.08 kDa 
  • Atom Count: 2,933 
  • Modeled Residue Count: 358 
  • Deposited Residue Count: 396 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
hydroxypropylphosphonic acid epoxidase
A, B
198Streptomyces wedmorensisMutation(s): 0 
Gene Names: fom4
EC: 1.14 (PDB Primary Data), 1.11.1.23 (UniProt)
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.242 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
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
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

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