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 1.2 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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Predicted HD phosphohydrolase PhnZA228uncultured bacterium HF130_AEPn_1Mutation(s): 0 
Gene Names: ACU83550ALOHA_HF130_AEPn_1_06cphnZ
EC: 1.13.11.78
Find proteins for D0E8I5 (Uncultured bacterium HF130_AEPn_1)
Explore D0E8I5 
Go to UniProtKB:  D0E8I5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download CCD File 
A
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
FE
Query on FE

Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
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 

  • 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