1vy4

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Crystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing acylated tRNA-substrates in the A and P sites.

Structural highlights

1vy4 is a 20 chain structure with sequence from Escherichia coli, Thermus thermophilus HB8 and Synthetic construct. This structure supersedes the now removed PDB entries 4qcm, 4qcn, 4qco and 4qcp. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.6Å
Ligands:31H, 4SU, 5MC, 5MU, 7MG, F3N, K, MG, MIA, PSU, SF4, ZN
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RS5_THET8 With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01307_B]

Publication Abstract from PubMed

During peptide-bond formation on the ribosome, the alpha-amine of an aminoacyl-tRNA attacks the ester carbonyl carbon of a peptidyl-tRNA to yield a peptide lengthened by one amino acid. Although the ribosome's contribution to catalysis is predominantly entropic, the lack of high-resolution structural data for the complete active site in complex with full-length ligands has made it difficult to assess how the ribosome might influence the pathway of the reaction. Here, we present crystal structures of preattack and postcatalysis complexes of the Thermus thermophilus 70S ribosome at ~2.6-A resolution. These structures reveal a network of hydrogen bonds along which proton transfer could take place to ensure the concerted, rate-limiting formation of a tetrahedral intermediate. We propose that, unlike earlier models, the ribosome and the A-site tRNA facilitate the deprotonation of the nucleophile through the activation of a water molecule.

A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.,Polikanov YS, Steitz TA, Innis CA Nat Struct Mol Biol. 2014 Aug 17. doi: 10.1038/nsmb.2871. PMID:25132179[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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Citations
13 reviews cite this structure
Structure and Function of the Mitochondrial Ribosome.
Greber et al. (2016)
12 more
76 other articles
No citations found

See Also

References

  1. ↑ Polikanov YS, Steitz TA, Innis CA. A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome. Nat Struct Mol Biol. 2014 Aug 17. doi: 10.1038/nsmb.2871. PMID:25132179 doi:http://dx.doi.org/10.1038/nsmb.2871

Contents


PDB ID 1vy4

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