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TitleStructural basis for HflXr-mediated antibiotic resistance in Listeria monocytogenes.
Journal, issue, pagesNucleic Acids Res, Vol. 50, Issue 19, Page 11285-11300, Year 2022
Publish dateOct 27, 2022
AuthorsTimm O Koller / Kathryn J Turnbull / Karolis Vaitkevicius / Caillan Crowe-McAuliffe / Mohammad Roghanian / Ondřej Bulvas / Jose A Nakamoto / Tatsuaki Kurata / Christina Julius / Gemma C Atkinson / Jörgen Johansson / Vasili Hauryliuk / Daniel N Wilson /
PubMed AbstractHflX is a ubiquitous bacterial GTPase that splits and recycles stressed ribosomes. In addition to HflX, Listeria monocytogenes contains a second HflX homolog, HflXr. Unlike HflX, HflXr confers ...HflX is a ubiquitous bacterial GTPase that splits and recycles stressed ribosomes. In addition to HflX, Listeria monocytogenes contains a second HflX homolog, HflXr. Unlike HflX, HflXr confers resistance to macrolide and lincosamide antibiotics by an experimentally unexplored mechanism. Here, we have determined cryo-EM structures of L. monocytogenes HflXr-50S and HflX-50S complexes as well as L. monocytogenes 70S ribosomes in the presence and absence of the lincosamide lincomycin. While the overall geometry of HflXr on the 50S subunit is similar to that of HflX, a loop within the N-terminal domain of HflXr, which is two amino acids longer than in HflX, reaches deeper into the peptidyltransferase center. Moreover, unlike HflX, the binding of HflXr induces conformational changes within adjacent rRNA nucleotides that would be incompatible with drug binding. These findings suggest that HflXr confers resistance using an allosteric ribosome protection mechanism, rather than by simply splitting and recycling antibiotic-stalled ribosomes.
External linksNucleic Acids Res / PubMed:36300626 / PubMed Central
MethodsEM (single particle)
Resolution2.1 - 3.1 Å
Structure data

15161

8a57

EMDB-15161, PDB-8a57:
Cryo-EM structure of HflXr bound to the Listeria monocytogenes 50S ribosomal subunit.
Method: EM (single particle) / Resolution: 2.3 Å

15175

8a5i

EMDB-15175, PDB-8a5i:
Cryo-EM structure of Lincomycin bound to the Listeria monocytogenes 50S ribosomal subunit.
Method: EM (single particle) / Resolution: 2.3 Å

15204

8a63

EMDB-15204, PDB-8a63:
Cryo-EM structure of Listeria monocytogenes 50S ribosomal subunit.
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-15670: Cryo-EM volume of HflX bound to the Listeria monocytogenes 50S ribosomal subunit
Method: EM (single particle) / Resolution: 2.76 Å

EMDB-15864: Cryo-EM map of lincomycin bound to the Listeria monocytogenes 50S ribosomal subunit.
Method: EM (single particle) / Resolution: 2.1 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-SPD:
SPERMIDINE / Spermidine

ChemComp-MG:
Unknown entry

ChemComp-PUT:
1,4-DIAMINOBUTANE / Putrescine

ChemComp-K:
Unknown entry

ChemComp-GNP:
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp, GMPPNP, energy-carrying molecule analogue*YM / 5'-Guanylyl imidodiphosphate

ChemComp-3QB:
LINCOMYCIN / antibiotic*YM / Lincomycin

ChemComp-HOH:
WATER / Water

Source
  • Listeria monocytogenes E (bacteria)
  • listeria monocytogenes egd-e (bacteria)
KeywordsRIBOSOME / Listeria monocytogenes / HflXr / 50S / antibiotic resistance / Lincomycin / antibiotic

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