Conformational Communication Mediates the Reset Step in T6A Biosynthesis

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2019 May 23

PMID 31114923

Citations 17

Authors

Amit Luthra

Naduni Paranagama

William Swinehart

Susan Bayooz

Phuc Phan

Vanessa Quach

Jamie M Schiffer

Boguslaw Stec

Dirk Iwata-Reuyl

Manal A Swairjo

Affiliations

Soon will be listed here.

Abstract

The universally conserved N6-threonylcarbamoyladenosine (t6A) modification of tRNA is essential for translational fidelity. In bacteria, t6A biosynthesis starts with the TsaC/TsaC2-catalyzed synthesis of the intermediate threonylcarbamoyl adenylate (TC-AMP), followed by transfer of the threonylcarbamoyl (TC) moiety to adenine-37 of tRNA by the TC-transfer complex comprised of TsaB, TsaD and TsaE subunits and possessing an ATPase activity required for multi-turnover of the t6A cycle. We report a 2.5-Å crystal structure of the T. maritima TC-transfer complex (TmTsaB2D2E2) bound to Mg2+-ATP in the ATPase site, and substrate analog carboxy-AMP in the TC-transfer site. Site directed mutagenesis results show that residues in the conserved Switch I and Switch II motifs of TsaE mediate the ATP hydrolysis-driven reactivation/reset step of the t6A cycle. Further, SAXS analysis of the TmTsaB2D2-tRNA complex in solution reveals bound tRNA lodged in the TsaE binding cavity, confirming our previous biochemical data. Based on the crystal structure and molecular docking of TC-AMP and adenine-37 in the TC-transfer site, we propose a model for the mechanism of TC transfer by this universal biosynthetic system.

Citing Articles

Structures of KEOPS bound to tRNA reveal functional roles of the kinase Bud32.

Ona Chuquimarca S, Beenstock J, Daou S, Porat J, Keszei A, Yin J Nat Commun. 2024; 15(1):10633.

PMID: 39639027 PMC: 11621456. DOI: 10.1038/s41467-024-54787-w.

The archaeal KEOPS complex possesses a functional Gon7 homolog and has an essential function independent of the cellular tA modification level.

Wu P, Gan Q, Zhang X, Yang Y, Xiao Y, She Q mLife. 2024; 2(1):11-27.

PMID: 38818338 PMC: 10989989. DOI: 10.1002/mlf2.12051.

Molecular basis of A. thaliana KEOPS complex in biosynthesizing tRNA t6A.

Zheng X, Su C, Duan L, Jin M, Sun Y, Zhu L Nucleic Acids Res. 2024; 52(8):4523-4540.

PMID: 38477398 PMC: 11077089. DOI: 10.1093/nar/gkae179.

Structure-function analysis of an ancient TsaD-TsaC-SUA5-TcdA modular enzyme reveals a prototype of tRNA t6A and ct6A synthetases.

Jin M, Zhang Z, Yu Z, Chen W, Wang X, Lei D Nucleic Acids Res. 2023; 51(16):8711-8729.

PMID: 37427786 PMC: 10484737. DOI: 10.1093/nar/gkad587.

The life and times of a tRNA.

Phizicky E, Hopper A RNA. 2023; 29(7):898-957.

PMID: 37055150 PMC: 10275265. DOI: 10.1261/rna.079620.123.

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