3AMU

Crystal structure of the TiaS-tRNA(Ile2)-AMPCPP-agmatine complex

Summary for 3AMU

• Entry DOI: 10.2210/pdb3amu/pdb
• Related: 3AMT 3AU7
• Descriptor: Putative uncharacterized protein, RNA (78-MER), DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER, ... (4 entities in total)
• Functional Keywords: tias, trna(ile2), modification, rna binding protein-rna complex, rna binding protein/rna
• Biological source: Archaeoglobus fulgidus; More
• Cellular location: Cytoplasm (Potential): O28025
• Total number of polymer chains: 2
• Total formula weight: 76302.18

Authors

Numata, T.,Osawa, T. (deposition date: 2010-08-23, release date: 2011-10-19, Last modification date: 2023-11-01)

Primary citation

Osawa, T.,Kimura, S.,Terasaka, N.,Inanaga, H.,Suzuki, T.,Numata, T.
Structural basis of tRNA agmatinylation essential for AUA codon decoding
Nat.Struct.Mol.Biol., 18:1275-1280, 2011

PubMed 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.

PubMed: 22002223
DOI: 10.1038/nsmb.2144

Experimental method

X-RAY DIFFRACTION (3.1 Å)