Biochemical and Structural Characterization of a Schiff Base in the Radical-Mediated Biosynthesis of 4-Demethylwyosine by TYW1

Tsehai A.J. Grell, Anthony P. Young, Catherine L. Drennan, Vahe Bandarian

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

TYW1 is a radical S-adenosyl-l-methionine (SAM) enzyme that catalyzes the condensation of pyruvate and N-methylguanosine to form the posttranscriptional modification, 4-demethylwyosine, in situ on transfer RNA (tRNA). Two mechanisms have been proposed for this transformation, with one of the possible mechanisms invoking a Schiff base intermediate formed between a conserved lysine residue and pyruvate. Utilizing a combination of mass spectrometry and X-ray crystallography, we have obtained evidence to support the formation of a Schiff base lysine adduct in TYW1. When 13C labeled pyruvate is used, the mass shift of the adduct matches that of the labeled pyruvate, indicating that pyruvate is the source of the adduct. Furthermore, a crystal structure of TYW1 provides visualization of the Schiff base lysine-pyruvate adduct, which is positioned directly adjacent to the auxiliary [4Fe-4S] cluster. The adduct coordinates the unique iron of the auxiliary cluster through the lysine nitrogen and a carboxylate oxygen, reminiscent of how the radical SAM [4Fe-4S] cluster is coordinated by SAM. The structure provides insight into the binding site for tRNA and further suggests how radical SAM chemistry can be combined with Schiff base chemistry for RNA modification.

Original languageEnglish (US)
Pages (from-to)6842-6852
Number of pages11
JournalJournal of the American Chemical Society
Volume140
Issue number22
DOIs
StatePublished - Jun 6 2018
Externally publishedYes

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Schiff Bases
Biosynthesis
Pyruvic Acid
Methionine
Lysine
X ray crystallography
Binding sites
RNA
Mass spectrometry
Condensation
Visualization
Enzymes
Crystal structure
Iron
Transfer RNA
Nitrogen
Oxygen
X Ray Crystallography
4-demethylwyosine
Reactive Oxygen Species

ASJC Scopus subject areas

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

Cite this

Biochemical and Structural Characterization of a Schiff Base in the Radical-Mediated Biosynthesis of 4-Demethylwyosine by TYW1. / Grell, Tsehai A.J.; Young, Anthony P.; Drennan, Catherine L.; Bandarian, Vahe.

In: Journal of the American Chemical Society, Vol. 140, No. 22, 06.06.2018, p. 6842-6852.

Research output: Contribution to journalArticle

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