Summary information and primary citation

PDB-id
3amt; SNAP-derived features in text and JSON formats; DNAproDB
Class
RNA binding protein-RNA
Method
X-ray (2.9 Å)
Summary
Crystal structure of the tias-trna(ile2)-atp complex
Reference
Osawa T, Kimura S, Terasaka N, Inanaga H, Suzuki T, Numata T (2011): "Structural basis of tRNA agmatinylation essential for AUA codon decoding." Nat.Struct.Mol.Biol., 18, 1275-1280. doi: 10.1038/nsmb.2144.
Abstract
The cytidine at the first position of the anticodon (C34) in the AUA codon-specific archaeal tRNA(Ile2) is modified to 2-agmatinylcytidine (agm(2)C or agmatidine), an agmatine-conjugated cytidine derivative, which is crucial for the precise decoding of the genetic code. Agm(2)C is synthesized by tRNA(Ile)-agm(2)C synthetase (TiaS) in an ATP-dependent manner. Here we present the crystal structures of the Archaeoglobus fulgidus TiaS-tRNA(Ile2) complexed with ATP, or with AMPCPP and agmatine, revealing a previously unknown kinase module required for activating C34 by phosphorylation, and showing the molecular mechanism by which TiaS discriminates between tRNA(Ile2) and tRNA(Met). In the TiaS-tRNA(Ile2)-ATP complex, C34 is trapped within a pocket far away from the ATP-binding site. In the agmatine-containing crystals, C34 is located near the AMPCPP γ-phosphate in the kinase module, demonstrating that agmatine is essential for placing C34 in the active site. These observations also provide the structural dynamics for agm(2)C formation.

Cartoon-block schematics in six views (download the tarball)

PyMOL session file Download PDB file View in 3Dmol.js