6N9A

Crystal Structure of Thermotoga maritima threonylcarbamoyladenosine biosynthesis complex TsaB2D2E2 bound to ATP and carboxy-AMP

Summary for 6N9A

• Entry DOI: 10.2210/pdb6n9a/pdb
• Descriptor: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB, MAGNESIUM ION, tRNA N6-adenosine threonylcarbamoyltransferase, ... (11 entities in total)
• Functional Keywords: threonylcarbamoyl transfer complex, t6a biosynthesis, trna modification, biosynthetic protein
• Biological source: Thermotoga maritima; More
• Total number of polymer chains: 3
• Total formula weight: 79854.87

Authors

Swairjo, M.A.,Stec, B. (deposition date: 2018-12-01, release date: 2019-05-22, Last modification date: 2023-10-11)

Primary citation

Luthra, A.,Paranagama, N.,Swinehart, W.,Bayooz, S.,Phan, P.,Quach, V.,Schiffer, J.M.,Stec, B.,Iwata-Reuyl, D.,Swairjo, M.A.
Conformational communication mediates the reset step in t6A biosynthesis.
Nucleic Acids Res., 47:6551-6567, 2019

PubMed 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.

PubMed: 31114923
DOI: 10.1093/nar/gkz439

Experimental method

X-RAY DIFFRACTION (2.5 Å)