5I4R

Contact-dependent inhibition system from Escherichia coli NC101 - ternary CdiA/CdiI/EF-Tu complex (trypsin-modified)

Summary for 5I4R

• Entry DOI: 10.2210/pdb5i4r/pdb
• Descriptor: Contact-dependent inhibitor A, Elongation factor Tu, Contact-dependent inhibitor I, ... (5 entities in total)
• Functional Keywords: toxin, antitoxin, elongation factor, structural genomics, psi-biology, midwest center for structural genomics, mcsg, structure-function analysis of polymorphic cdi toxin-immunity protein complexes, uc4cdi, toxin-antitoxin complex, toxin/antitoxin
• Biological source: Escherichia coli NC101; More
• Total number of polymer chains: 8
• Total formula weight: 133836.14

Authors

Michalska, K.,Stols, L.,Eschenfeldt, W.,Hayes, C.S.,Goulding, C.W.,Joachimiak, A.,Midwest Center for Structural Genomics (MCSG),Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI) (deposition date: 2016-02-12, release date: 2017-06-28, Last modification date: 2024-10-30)

Primary citation

Michalska, K.,Gucinski, G.C.,Garza-Sanchez, F.,Johnson, P.M.,Stols, L.M.,Eschenfeldt, W.H.,Babnigg, G.,Low, D.A.,Goulding, C.W.,Joachimiak, A.,Hayes, C.S.
Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs.
Nucleic Acids Res., 45:10306-10320, 2017

PubMed Abstract: Contact-dependent growth inhibition (CDI) is a mechanism of inter-cellular competition in which Gram-negative bacteria exchange polymorphic toxins using type V secretion systems. Here, we present structures of the CDI toxin from Escherichia coli NC101 in ternary complex with its cognate immunity protein and elongation factor Tu (EF-Tu). The toxin binds exclusively to domain 2 of EF-Tu, partially overlapping the site that interacts with the 3'-end of aminoacyl-tRNA (aa-tRNA). The toxin exerts a unique ribonuclease activity that cleaves the single-stranded 3'-end from tRNAs that contain guanine discriminator nucleotides. EF-Tu is required to support this tRNase activity in vitro, suggesting the toxin specifically cleaves substrate in the context of GTP·EF-Tu·aa-tRNA complexes. However, superimposition of the toxin domain onto previously solved GTP·EF-Tu·aa-tRNA structures reveals potential steric clashes with both aa-tRNA and the switch I region of EF-Tu. Further, the toxin induces conformational changes in EF-Tu, displacing a β-hairpin loop that forms a critical salt-bridge contact with the 3'-terminal adenylate of aa-tRNA. Together, these observations suggest that the toxin remodels GTP·EF-Tu·aa-tRNA complexes to free the 3'-end of aa-tRNA for entry into the nuclease active site.

PubMed: 28973472
DOI: 10.1093/nar/gkx700

Experimental method

X-RAY DIFFRACTION (3.3 Å)