Structural Evidence for DUF512 as a Radical S-Adenosylmethionine Cobalamin-Binding Domain

Bo Wang, Amy E. Solinski, Matthew I. Radle, Olivia M. Peduzzi, Hayley L. Knox, Jiayuan Cui, Ravi K. Maurya, Neela H. Yennawar, Squire J. Booker

Research output: Contribution to journalArticlepeer-review

Abstract

Cobalamin (Cbl)-dependent radical S-adenosylmethionine (SAM) enzymes constitute a large subclass of radical SAM (RS) enzymes that use Cbl to catalyze various types of reactions, the most common of which are methylations. Most Cbl-dependent RS enzymes contain an N-terminal Rossmann fold that aids Cbl binding. Recently, it has been demonstrated that the methanogenesis marker protein 10 (Mmp10) requires Cbl to methylate an arginine residue in the α-subunit of methyl coenzyme M reductase. However, Mmp10 contains a Cbl-binding domain in the C-terminal region of its primary structure that does not share significant sequence similarity with canonical RS Cbl-binding domains. Bioinformatic analysis of Mmp10 identified DUF512 (Domain of Unknown Function 512) as a potential Cbl-binding domain in RS enzymes. In this paper, four randomly selected DUF512-containing proteins from various organisms were overexpressed, purified, and shown to bind Cbl. X-ray crystal structures of DUF512-containing proteins from Clostridium sporogenes and Pyrococcus furiosus were determined, confirming their C-terminal Cbl-binding domains. The structure of the DUF512-containing protein from C. sporogenes is the first of an RS enzyme containing a PDZ domain. Its RS domain has an unprecedented β3α4 core, whereas most RS enzymes adopt a (βα)6 core. The DUF512-containing protein from P. furiosus has no PDZ domain, but its RS domain also has an uncommon (βα)5 core.

Original languageEnglish (US)
Pages (from-to)319-330
Number of pages12
JournalACS Bio and Med Chem Au
Volume4
Issue number6
DOIs
StatePublished - Dec 18 2024

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology
  • Pharmaceutical Science
  • Drug Discovery

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