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TitleDecoding the Mechanism of Specific RNA Targeting by Ribosomal Methyltransferases.
Journal, issue, pagesACS Chem Biol, Vol. 17, Issue 4, Page 829-839, Year 2022
Publish dateApr 15, 2022
AuthorsJuhi Singh / Rahul Raina / Kutti R Vinothkumar / Ruchi Anand /
PubMed AbstractMethylation 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- ...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.
External linksACS Chem Biol / PubMed:35316014
MethodsEM (single particle)
Resolution3.24 - 3.6 Å
Structure data

31655

7v2l

EMDB-31655, PDB-7v2l:
T.thermophilus 30S ribosome with KsgA, class K1k2
Method: EM (single particle) / Resolution: 3.3 Å

31656

7v2m

EMDB-31656, PDB-7v2m:
T.thermophilus 30S ribosome with KsgA, class K1k4
Method: EM (single particle) / Resolution: 3.4 Å

31657

7v2n

EMDB-31657, PDB-7v2n:
T.thermophilus 30S ribosome with KsgA, class K2
Method: EM (single particle) / Resolution: 3.6 Å

31658

7v2o

EMDB-31658, PDB-7v2o:
T.thermophilus 30S ribosome with KsgA, class K4
Method: EM (single particle) / Resolution: 3.5 Å

31659

7v2p

EMDB-31659, PDB-7v2p:
T.thermophilus 30S ribosome with KsgA, class K5
Method: EM (single particle) / Resolution: 3.3 Å

31660

7v2q

EMDB-31660, PDB-7v2q:
T.thermophilus 30S ribosome with KsgA, class K6
Method: EM (single particle) / Resolution: 3.24 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • thermus thermophilus hb8 (bacteria)
  • bacillus subtilis (strain 168) (bacteria)
KeywordsRIBOSOME / 30S subunit / KsgA / rRNA methyltransferase

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