7V2P

T.thermophilus 30S ribosome with KsgA, class K5

Summary for 7V2P

• Entry DOI: 10.2210/pdb7v2p/pdb
• EMDB information: 31655 31656 31657 31658 31659 31660
• Descriptor: 16s ribosomal RNA, 30S ribosomal protein S10, 30S ribosomal protein S11, ... (23 entities in total)
• Functional Keywords: 30s subunit, ksga, rrna methyltransferase, ribosome
• Biological source: Bacillus subtilis (strain 168); More
• Total number of polymer chains: 22
• Total formula weight: 817114.25

Authors

Raina, R.,Singh, J.,Anand, R.,Vinothkumar, K.R. (deposition date: 2021-08-09, release date: 2022-04-06, Last modification date: 2024-06-12)

Primary citation

Singh, J.,Raina, R.,Vinothkumar, K.R.,Anand, R.
Decoding the Mechanism of Specific RNA Targeting by Ribosomal Methyltransferases.
Acs Chem.Biol., 17:829-839, 2022

PubMed 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.

PubMed: 35316014
DOI: 10.1021/acschembio.1c00732

Experimental method

ELECTRON MICROSCOPY (3.3 Å)