The Elusive 5′-Deoxyadenosyl Radical: Captured and Characterized by Electron Paramagnetic Resonance and Electron Nuclear Double Resonance Spectroscopies

Hao Yang, Elizabeth C. McDaniel, Stella Impano, Amanda S. Byer, Richard J. Jodts, Kenichi Yokoyama, William E. Broderick, Joan B. Broderick*, Brian M. Hoffman

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

26 Scopus citations

Abstract

The 5′-deoxyadenosyl radical (5′-dAdo·) abstracts a substrate H atom as the first step in radical-based transformations catalyzed by adenosylcobalamin-dependent and radical S-adenosyl-l-methionine (RS) enzymes. Notwithstanding its central biological role, 5′-dAdo· has eluded characterization despite efforts spanning more than a half-century. Here, we report generation of 5′-dAdo· in a RS enzyme active site at 12 K using a novel approach involving cryogenic photoinduced electron transfer from the [4Fe-4S]+ cluster to the coordinated S-adenosylmethionine (SAM) to induce homolytic S-C5′ bond cleavage. We unequivocally reveal the structure of this long-sought radical species through the use of electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) spectroscopies with isotopic labeling, complemented by density-functional computations: a planar C5′ (2pπ) radical (∼70% spin occupancy); the C5′(H)2 plane is rotated by ∼37° (experiment)/39° (DFT) relative to the C5′-C4′-(C4′-H) plane, placing a C5′-H antiperiplanar to the ribose-ring oxygen, which helps stabilize the radical against elimination of the 4′-H. The agreement between from experiment and in vacuo DFT indicates that the conformation is intrinsic to 5-dAdo· itself, and not determined by its environment.

Original languageEnglish (US)
Pages (from-to)12139-12146
Number of pages8
JournalJournal of the American Chemical Society
Volume141
Issue number30
DOIs
StatePublished - Jul 31 2019

ASJC Scopus subject areas

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

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