6MPF

Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a 2-thiocytidine (s2C32) and inosine (I34) modified anticodon stem loop (ASL) of Escherichia coli transfer RNA Arginine 1 (TRNAARG1) bound to an mRNA with an CGC-codon in the A-site and paromomycin

Summary for 6MPF

• Entry DOI: 10.2210/pdb6mpf/pdb
• Descriptor: 16S rRNA, 30S ribosomal protein S10, 30S ribosomal protein S11, ... (26 entities in total)
• Functional Keywords: 2-thiocytidine, inosine, transfer rna, trna, ribosome, 30s, translation, anticodon
• Biological source: Thermus thermophilus HB8 (strain HB8 / ATCC 27634 / DSM 579); More
• Total number of polymer chains: 23
• Total formula weight: 771222.05

Authors

Cantara, W.A.,DeMirci, H.,Agris, P.F. (deposition date: 2018-10-05, release date: 2019-04-24, Last modification date: 2023-10-11)

Primary citation

Vangaveti, S.,Cantara, W.A.,Spears, J.L.,DeMirci, H.,Murphy IV, F.V.,Ranganathan, S.V.,Sarachan, K.L.,Agris, P.F.
A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine.
J.Mol.Biol., 432:913-929, 2020

PubMed Abstract: Three of six arginine codons (CGU, CGC, and CGA) are decoded by two Escherichia coli tRNA isoacceptors. The anticodon stem and loop (ASL) domains of tRNA and tRNA both contain inosine and 2-methyladenosine modifications at positions 34 (I) and 37 (mA). tRNA is also modified from cytidine to 2-thiocytidine at position 32 (sC). The sC modification is known to negate wobble codon recognition of the rare CGA codon by an unknown mechanism, while still allowing decoding of CGU and CGC. Substitution of sC for C in the Saccharomyces cerevisiae tRNA anticodon stem and loop domain (ASL) negates wobble decoding of its synonymous A-ending codon, suggesting that this function of sC at position 32 is a generalizable property. X-ray crystal structures of variously modified ASL and ASL constructs bound to cognate and wobble codons on the ribosome revealed the disruption of a CA cross-loop interaction but failed to fully explain the means by which sC restricts I wobbling. Computational studies revealed that the adoption of a spatially broad inosine-adenosine base pair at the wobble position of the codon cannot be maintained simultaneously with the canonical ASL U-turn motif. CA cross-loop interactions are required for stability of the anticodon/codon interaction in the ribosomal A-site.

PubMed: 31945376
DOI: 10.1016/j.jmb.2019.12.016

Experimental method

X-RAY DIFFRACTION (3.33 Å)