8ZYC
Cryo-EM structure of uropathogenic Escherichia coli CysK:CdiA:tRNA complex A
Summary for 8ZYC
| Entry DOI | 10.2210/pdb8zyc/pdb |
| EMDB information | 60561 |
| Descriptor | Cysteine synthase A, tRNA nuclease CdiA, tRNAIleGAU, ... (4 entities in total) |
| Functional Keywords | rnase, complex, contact-dependent growth inhibition, toxin |
| Biological source | Escherichia coli More |
| Total number of polymer chains | 4 |
| Total formula weight | 119744.10 |
| Authors | Feng, Z.,Yashiro, Y.,Tomita, K. (deposition date: 2024-06-17, release date: 2024-08-21, Last modification date: 2025-03-05) |
| Primary citation | Feng, Z.,Yashiro, Y.,Tomita, K. Mechanism of activation of contact-dependent growth inhibition tRNase toxin by the amino acid biogenesis factor CysK in the bacterial competition system. Nucleic Acids Res., 53:-, 2025 Cited by PubMed Abstract: 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. PubMed: 39228374DOI: 10.1093/nar/gkae735 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.99 Å) |
Structure validation
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