4N6W

X-Ray Crystal Structure of Citrate-bound PhnZ


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Organophosphonate-degrading PhnZ reveals an emerging family of HD domain mixed-valent diiron oxygenases.

Worsdorfer, B.Lingaraju, M.Yennawar, N.H.Boal, A.K.Krebs, C.Bollinger, J.M.Pandelia, M.E.

(2013) Proc Natl Acad Sci U S A 110: 18874-18879

  • DOI: https://doi.org/10.1073/pnas.1315927110
  • Primary Citation of Related Structures:  
    4N6W, 4N71

  • PubMed Abstract: 

    The founding members of the HD-domain protein superfamily are phosphohydrolases, and newly discovered members are generally annotated as such. However, myo-inositol oxygenase (MIOX) exemplifies a second, very different function that has evolved within the common scaffold of this superfamily. A recently discovered HD protein, PhnZ, catalyzes conversion of 2-amino-1-hydroxyethylphosphonate to glycine and phosphate, culminating a bacterial pathway for the utilization of environmentally abundant 2-aminoethylphosphonate. Using Mössbauer and EPR spectroscopies, X-ray crystallography, and activity measurements, we show here that, like MIOX, PhnZ employs a mixed-valent Fe(II)/Fe(III) cofactor for the O2-dependent oxidative cleavage of its substrate. Phylogenetic analysis suggests that many more HD proteins may catalyze yet-unknown oxygenation reactions using this hitherto exceptional Fe(II)/Fe(III) cofactor. The results demonstrate that the catalytic repertoire of the HD superfamily extends well beyond phosphohydrolysis and suggest that the mechanism used by MIOX and PhnZ may be a common strategy for oxidative C-X bond cleavage.


  • Organizational Affiliation

    Departments of Chemistry, and Biochemistry and Molecular Biology, and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Predicted HD phosphohydrolase PhnZ228uncultured bacterium HF130_AEPn_1Mutation(s): 0 
Gene Names: ACU83550ALOHA_HF130_AEPn_1_06c
UniProt
Find proteins for D0E8I5 (Uncultured bacterium HF130_AEPn_1)
Explore D0E8I5 
Go to UniProtKB:  D0E8I5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0E8I5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.871α = 90
b = 68.871β = 90
c = 98.842γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SHARPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-27
    Type: Initial release
  • Version 1.1: 2013-12-11
    Changes: Structure summary
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations