5E3E

Crystal structure of CdiA-CT/CdiI complex from Y. kristensenii 33638

Summary for 5E3E

• Entry DOI: 10.2210/pdb5e3e/pdb
• Descriptor: CdiI immunity protein, Large exoprotein involved in heme utilization or adhesion, SODIUM ION, ... (4 entities in total)
• Functional Keywords: toxin, nuclease, immunity protein, structural genomics, psi-biology, midwest center for structural genomics, mcsg, uc4cdi, structure-function analysis of polymorphic cdi toxin-immunity protein complexes
• Biological source: Yersinia kristensenii ATCC 33638; More
• Total number of polymer chains: 6
• Total formula weight: 74689.24

Authors

Michalska, K.,Joachimiak, G.,Jedrzejczak, R.,Goulding, C.W.,Joachimiak, A.,Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI),Midwest Center for Structural Genomics (MCSG) (deposition date: 2015-10-02, release date: 2015-11-25, Last modification date: 2024-10-30)

Primary citation

Batot, G.,Michalska, K.,Ekberg, G.,Irimpan, E.M.,Joachimiak, G.,Jedrzejczak, R.,Babnigg, G.,Hayes, C.S.,Joachimiak, A.,Goulding, C.W.
The CDI toxin of Yersinia kristensenii is a novel bacterial member of the RNase A superfamily.
Nucleic Acids Res., 45:5013-5025, 2017

PubMed Abstract: Contact-dependent growth inhibition (CDI) is an important mechanism of inter-bacterial competition found in many Gram-negative pathogens. CDI+ cells express cell-surface CdiA proteins that bind neighboring bacteria and deliver C-terminal toxin domains (CdiA-CT) to inhibit target-cell growth. CDI+ bacteria also produce CdiI immunity proteins, which specifically neutralize cognate CdiA-CT toxins to prevent self-inhibition. Here, we present the crystal structure of the CdiA-CT/CdiIYkris complex from Yersinia kristensenii ATCC 33638. CdiA-CTYkris adopts the same fold as angiogenin and other RNase A paralogs, but the toxin does not share sequence similarity with these nucleases and lacks the characteristic disulfide bonds of the superfamily. Consistent with the structural homology, CdiA-CTYkris has potent RNase activity in vitro and in vivo. Structure-guided mutagenesis reveals that His175, Arg186, Thr276 and Tyr278 contribute to CdiA-CTYkris activity, suggesting that these residues participate in substrate binding and/or catalysis. CdiIYkris binds directly over the putative active site and likely neutralizes toxicity by blocking access to RNA substrates. Significantly, CdiA-CTYkris is the first non-vertebrate protein found to possess the RNase A superfamily fold, and homologs of this toxin are associated with secretion systems in many Gram-negative and Gram-positive bacteria. These observations suggest that RNase A-like toxins are commonly deployed in inter-bacterial competition.

PubMed: 28398546
DOI: 10.1093/nar/gkx230

Experimental method

X-RAY DIFFRACTION (1.7 Å)