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TitleMechanism of activation of contact-dependent growth inhibition tRNase toxin by the amino acid biogenesis factor CysK in the bacterial competition system.
Journal, issue, pagesNucleic Acids Res, Vol. 53, Issue 1, Year 2025
Publish dateJan 7, 2025
AuthorsZhaohang Feng / Yuka Yashiro / Kozo Tomita /
PubMed AbstractContact-dependent growth inhibition (CDI) is a bacterial competition mechanism, wherein the C-terminal toxin domain of CdiA protein (CdiA-CT) is transferred from one bacterium to another, impeding ...Contact-dependent growth inhibition (CDI) is a bacterial competition mechanism, wherein the C-terminal toxin domain of CdiA protein (CdiA-CT) is transferred from one bacterium to another, impeding the growth of the toxin recipient. In uropathogenic Escherichia coli 536, CdiA-CT (CdiA-CTEC536) is a tRNA anticodon endonuclease that requires a cysteine biogenesis factor, CysK, for its activity. However, the mechanism underlying tRNA recognition and cleavage by CdiA-CTEC536 remains unresolved. Here, we present the cryo-EM structure of the CysK:CdiA-CTEC536:tRNA ternary complex. The interaction between CdiA-CTEC536 and CysK stabilizes the CdiA-CTEC536 structure and facilitates tRNA binding and the formation of the CdiA-CTEC536 catalytic core structure. The bottom-half of the tRNA interacts exclusively with CdiA-CTEC536 and the α-helices of CdiA-CTEC536 engage with the minor and major grooves of the bottom-half of tRNA, positioning the tRNA anticodon loop at the CdiA-CTEC536 catalytic site for tRNA cleavage. Thus, CysK serves as a platform facilitating the recognition and cleavage of substrate tRNAs by CdiA-CTEC536.
External linksNucleic Acids Res / PubMed:39228374 / PubMed Central
MethodsEM (single particle)
Resolution2.6 - 3.04 Å
Structure data

60561

8zyc

EMDB-60561, PDB-8zyc:
Cryo-EM structure of uropathogenic Escherichia coli CysK:CdiA:tRNA complex A
Method: EM (single particle) / Resolution: 2.99 Å

60562

8zyd

EMDB-60562, PDB-8zyd:
Cryo-EM structure of uropathogenic Escherichia coli CysK:CdiA:tRNA complex B
Method: EM (single particle) / Resolution: 3.04 Å

EMDB-60563: Cryo-EM structure of uropathogenic Escherichia coli 2:1 CysK:CdiA complex
Method: EM (single particle) / Resolution: 2.6 Å

EMDB-60564: Cryo-EM structure of uropathogenic Escherichia coli 2:2 CysK:CdiA complex
Method: EM (single particle) / Resolution: 2.78 Å

Chemicals

ChemComp-MG:
Unknown entry

Source
  • escherichia coli 536 (bacteria)
  • escherichia coli (E. coli)
KeywordsTOXIN / RNase / Complex / Contact-dependent growth inhibition

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