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

Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):18874-9. doi: 10.1073/pnas.1315927110. Epub 2013 Nov 6.


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.

Keywords: C-H activation; PhnY; nonheme diiron enzymes; structural genomics; superoxo intermediate.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacteria / enzymology*
  • Catalysis
  • Crystallography, X-Ray
  • Escherichia coli
  • Inositol Oxygenase / chemistry*
  • Inositol Oxygenase / genetics
  • Inositol Oxygenase / metabolism*
  • Models, Molecular*
  • Molecular Structure
  • Organophosphonates / metabolism*
  • Phylogeny
  • Protein Conformation*
  • Spectroscopy, Mossbauer


  • Organophosphonates
  • Inositol Oxygenase

Associated data

  • PDB/4N6W
  • PDB/4N71