EMD-31655

Single-particle
3.3 Å
EMD-31655 Deposition: 09/08/2021
Map released: 06/04/2022
Last modified: 12/06/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-31655

T.thermophilus 30S ribosome with KsgA, class K1k2

EMD-31655

Single-particle
3.3 Å
EMD-31655 Deposition: 09/08/2021
Map released: 06/04/2022
Last modified: 12/06/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Thermus thermophilus HB8, Bacillus subtilis (strain 168)
Sample: 30S ribosomal with bound KsgA, a RNA methyltransferase at position 2
Fitted models: 7v2l (Avg. Q-score: 0.524)

Deposition Authors: Raina R , Singh J
Decoding the Mechanism of Specific RNA Targeting by Ribosomal Methyltransferases.
Singh J , Raina R , Vinothkumar KR, Anand R
(2022) ACS Chem Biol , 17 , 829 - 839
PUBMED: 35316014
DOI: doi:10.1021/acschembio.1c00732
ISSN: 1554-8937
Abstract:
Methylation of specific nucleotides is integral for ribosomal biogenesis and also serves as a common mechanism to confer antibiotic resistance by pathogenic bacteria. Here, by determining the high-resolution structure of the 30S-KsgA complex by cryo-electron microscopy, a state was captured, where KsgA juxtaposes between helices h44 and h45 of the 30S ribosome, separating them, thereby enabling remodeling of the surrounded rRNA and allowing the cognate site to enter the methylation pocket. With the structure as a guide, several mutant versions of the ribosomes, where interacting bases in the catalytic helix h45 and surrounding helices h44, h24, and h27, were mutated and evaluated for their methylation efficiency revealing factors that direct the enzyme to its cognate site with high fidelity. The biochemical studies show that the three-dimensional environment of the ribosome enables the interaction of select loop regions in KsgA with the ribosome helices paramount to maintain selectivity.