Structural Basis for Methyl-donor-dependent and Sequence-specific Binding to TRNA Substrates by Knotted Methyltransferase TrmD

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2015 Jul 18

PMID 26183229

Citations 37

Authors

Takuhiro Ito

Isao Masuda

Ken-Ichi Yoshida

Sakurako Goto-Ito

Shun-Ichi Sekine

Se Won Suh

Ya-Ming Hou

Shigeyuki Yokoyama

Affiliations

Soon will be listed here.

Abstract

The deep trefoil knot architecture is unique to the SpoU and tRNA methyltransferase D (TrmD) (SPOUT) family of methyltransferases (MTases) in all three domains of life. In bacteria, TrmD catalyzes the N(1)-methylguanosine (m(1)G) modification at position 37 in transfer RNAs (tRNAs) with the (36)GG(37) sequence, using S-adenosyl-l-methionine (AdoMet) as the methyl donor. The m(1)G37-modified tRNA functions properly to prevent +1 frameshift errors on the ribosome. Here we report the crystal structure of the TrmD homodimer in complex with a substrate tRNA and an AdoMet analog. Our structural analysis revealed the mechanism by which TrmD binds the substrate tRNA in an AdoMet-dependent manner. The trefoil-knot center, which is structurally conserved among SPOUT MTases, accommodates the adenosine moiety of AdoMet by loosening/retightening of the knot. The TrmD-specific regions surrounding the trefoil knot recognize the methionine moiety of AdoMet, and thereby establish the entire TrmD structure for global interactions with tRNA and sequential and specific accommodations of G37 and G36, resulting in the synthesis of m(1)G37-tRNA.

Citing Articles

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