Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme

Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16137-41. doi: 10.1073/pnas.0806640105. Epub 2008 Oct 13.

Abstract

Pyruvate formate-lyase activating enzyme generates a stable and catalytically essential glycyl radical on G(734) of pyruvate formate-lyase via the direct, stereospecific abstraction of a hydrogen atom from pyruvate formate-lyase. The activase performs this remarkable feat by using an iron-sulfur cluster and S-adenosylmethionine (AdoMet), thus placing it among the AdoMet radical superfamily of enzymes. We report here structures of the substrate-free and substrate-bound forms of pyruvate formate-lyase-activating enzyme, the first structures of an AdoMet radical activase. To obtain the substrate-bound structure, we have used a peptide substrate, the 7-mer RVSGYAV, which contains the sequence surrounding G(734). Our structures provide fundamental insights into the interactions between the activase and the G(734) loop of pyruvate formate-lyase and provide a structural basis for direct and stereospecific H atom abstraction from the buried G(734) of pyruvate formate-lyase.

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

  • Acetyltransferases
  • Crystallography, X-Ray
  • Enzymes / chemistry*
  • Enzymes / genetics
  • Enzymes / metabolism*
  • Free Radicals / chemistry
  • Free Radicals / metabolism
  • Glycine / chemistry
  • Glycine / genetics
  • Models, Molecular
  • Protein Binding
  • Protein Folding
  • Protein Structure, Quaternary
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Substrate Specificity

Substances

  • Enzymes
  • Free Radicals
  • Acetyltransferases
  • pyruvate formate-lyase activating enzyme
  • Glycine

Associated data

  • PDB/3C8F
  • PDB/3CB8