6PMO

Co-crystal structure of the Geobacillus kaustophilus glyQ T-box riboswitch discriminator domain in complex with tRNA-Gly

Summary for 6PMO

• Entry DOI: 10.2210/pdb6pmo/pdb
• Related: 6POM
• Descriptor: tRNA-Gly, T-box riboswitch discriminator, IRIDIUM ION, ... (5 entities in total)
• Functional Keywords: riboswitch, trna, rna
• Biological source: Geobacillus kaustophilus; More
• Total number of polymer chains: 2
• Total formula weight: 48126.09

Authors

Li, S.,Zhang, J. (deposition date: 2019-07-02, release date: 2019-11-20, Last modification date: 2024-03-13)

Primary citation

Li, S.,Su, Z.,Lehmann, J.,Stamatopoulou, V.,Giarimoglou, N.,Henderson, F.E.,Fan, L.,Pintilie, G.D.,Zhang, K.,Chen, M.,Ludtke, S.J.,Wang, Y.X.,Stathopoulos, C.,Chiu, W.,Zhang, J.
Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions.
Nat.Struct.Mol.Biol., 26:1094-1105, 2019

PubMed Abstract: Amino acid availability in Gram-positive bacteria is monitored by T-box riboswitches. T-boxes directly bind tRNAs, assess their aminoacylation state, and regulate the transcription or translation of downstream genes to maintain nutritional homeostasis. Here, we report cocrystal and cryo-EM structures of Geobacillus kaustophilus and Bacillus subtilis T-box-tRNA complexes, detailing their multivalent, exquisitely selective interactions. The T-box forms a U-shaped molecular vise that clamps the tRNA, captures its 3' end using an elaborate 'discriminator' structure, and interrogates its aminoacylation state using a steric filter fashioned from a wobble base pair. In the absence of aminoacylation, T-boxes clutch tRNAs and form a continuously stacked central spine, permitting transcriptional readthrough or translation initiation. A modeled aminoacyl disrupts tRNA-T-box stacking, severing the central spine and blocking gene expression. Our data establish a universal mechanism of amino acid sensing on tRNAs and gene regulation by T-box riboswitches and exemplify how higher-order RNA-RNA interactions achieve multivalency and specificity.

PubMed: 31740854
DOI: 10.1038/s41594-019-0326-7

Experimental method

X-RAY DIFFRACTION (2.65703362888 Å)