Paradigm Shift for Radical S-Adenosyl-l-methionine Reactions: The Organometallic Intermediate Ω Is Central to Catalysis

J Am Chem Soc. 2018 Jul 18;140(28):8634-8638. doi: 10.1021/jacs.8b04061. Epub 2018 Jul 6.

Abstract

Radical S-adenosyl-l-methionine (SAM) enzymes comprise a vast superfamily catalyzing diverse reactions essential to all life through homolytic SAM cleavage to liberate the highly reactive 5'-deoxyadenosyl radical (5'-dAdo·). Our recent observation of a catalytically competent organometallic intermediate Ω that forms during reaction of the radical SAM (RS) enzyme pyruvate formate-lyase activating-enzyme (PFL-AE) was therefore quite surprising, and led to the question of its broad relevance in the superfamily. We now show that Ω in PFL-AE forms as an intermediate under a variety of mixing order conditions, suggesting it is central to catalysis in this enzyme. We further demonstrate that Ω forms in a suite of RS enzymes chosen to span the totality of superfamily reaction types, implicating Ω as essential in catalysis across the RS superfamily. Finally, EPR and electron nuclear double resonance spectroscopy establish that Ω involves an Fe-C5' bond between 5'-dAdo· and the [4Fe-4S] cluster. An analogous organometallic bond is found in the well-known adenosylcobalamin (coenzyme B12) cofactor used to initiate radical reactions via a 5'-dAdo· intermediate. Liberation of a reactive 5'-dAdo· intermediate via homolytic metal-carbon bond cleavage thus appears to be similar for Ω and coenzyme B12. However, coenzyme B12 is involved in enzymes catalyzing only a small number (∼12) of distinct reactions, whereas the RS superfamily has more than 100 000 distinct sequences and over 80 reaction types characterized to date. The appearance of Ω across the RS superfamily therefore dramatically enlarges the sphere of bio-organometallic chemistry in Nature.

Publication types

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

MeSH terms

  • Acetyltransferases
  • Bacteria / chemistry
  • Bacteria / enzymology*
  • Bacteria / metabolism
  • Biocatalysis
  • Cobamides / chemistry
  • Cobamides / metabolism*
  • Deoxyadenosines / chemistry
  • Deoxyadenosines / metabolism*
  • Electron Spin Resonance Spectroscopy
  • Enzymes / chemistry
  • Enzymes / metabolism*
  • Escherichia coli / chemistry
  • Escherichia coli / enzymology
  • Escherichia coli / metabolism
  • Models, Molecular
  • Protein Conformation
  • S-Adenosylmethionine / chemistry
  • S-Adenosylmethionine / metabolism*

Substances

  • Cobamides
  • Deoxyadenosines
  • Enzymes
  • 5'-deoxyadenosine
  • S-Adenosylmethionine
  • Acetyltransferases
  • pyruvate formate-lyase activating enzyme
  • cobamamide