PXD071262

PXD071262 is an original dataset announced via ProteomeXchange.

Title	Anticodon loop remodeling and D-stem shape drive the specific recognition of ANN-decoding tRNAs for t6A modification
Description	N6-threonylcarbamoyladenosine (t6A) is a universal tRNA modification essential for translational fidelity. The modification is installed at position 37 of ANN-decoding tRNAs (N is A, U, G or C) by transfer of a threonylcarbamoyl moiety from a pathway intermediate, catalyzed in bacteria by the TsaBD complex. Despite the strict requirement for the 36-UAA-38 sequence in substrate tRNAs, the structural basis for this specificity has remained unclear. We determined cryo-EM structures of the Thermotoga maritima t6A synthase bound to unmodified and to natively modified tRNA carrying the t6A37 modification, at a nominal resolution of 3.2 Å. In both structures, A37 is positioned in the active site, and the anticodon loop is remodeled into a zig-zag conformation not previously observed in tRNA, stabilized by conserved interactions with the RNA backbone at the TsaD/TsaB interface. The wobble and middle anticodon bases occupy shallow surface pockets without base-specific contacts, explaining tolerance to base identity at these positions. In contrast, U36 and A38 are recognized indirectly through formation of a base triple with U32. Additional D-stem contacts provide a second mode of indirect readout. Together with mutagenesis data, the structures reveal the molecular basis for restriction of t6A37 to ANN-decoding tRNAs and the requirement for A38.
HostingRepository	PRIDE
AnnounceDate	2026-05-28
AnnouncementXML	Submission_2026-05-28_04:14:00.841.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chi Kong Chan
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: NEWT:562;
ModificationList	No PTMs are included in the dataset
Instrument	6550 iFunnel Q-TOF LC/MS

Revision	Datetime	Status	ChangeLog Entry
0	2025-11-26 08:11:15	ID requested
⏵ 1	2026-05-28 04:14:01	announced

Dataset with its publication pending

submitter keyword: cryo-EM,tRNA, TsaB2D2, t6A

Peter C Dedon
contact affiliation	Underwood-Prescott Professor, Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 56-731 Cambridge, MA 02139-4307
contact email	pcdedon@mit.edu
lab head
Chi Kong Chan
contact affiliation	Department of Biological Engineering, Massachusetts Institute of Technology
contact email	mckchan@mit.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD071262
     1. Label: PRIDE project
     2. Name: Anticodon loop remodeling and D-stem shape drive the specific recognition of ANN-decoding tRNAs for t6A modification