PDBsum entry 5e3e

Toxin

PDB id: 5e3e

Contents

Protein chains

99 a.a.

114 a.a.

94 a.a.

Metals

_NA ×2

Waters ×436

PDB id:

5e3e

Name:

Toxin

Title:

Crystal structure of cdia-ct/cdii complex from y. Kristensenii 33638

Structure:

Cdii immunity protein. Chain: a, c, e. Engineered: yes. Other_details: sequence identical to unp reference c4tss4 but with longer open reading frame at n-terminus. Large exoprotein involved in heme utilization or adhesion. Chain: b, d, f. Engineered: yes. Other_details: the cloned fragment starts from m0 preceding v1 (v3116

Source:

Yersinia kristensenii atcc 33638. Organism_taxid: 527012. Gene: ykris0001_13520. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: ykris0001_13530.

Resolution:

1.70Å R-factor: 0.174 R-free: 0.202

Authors:

K.Michalska,G.Joachimiak,R.Jedrzejczak,C.W.Goulding,A.Joachimiak, Structure-Function Analysis Of Polymorphic Cdi Toxin-Immunity Protein Complexes (Uc4cdi),Midwest Center For Structural Genomics (Mcsg)

Key ref:

G.Batot et al. (2017). The CDI toxin of Yersinia kristensenii is a novel bacterial member of the RNase A superfamily. Nucleic Acids Res, 45, 5013-5025. PubMed id: 28398546

Date:

02-Oct-15 Release date: 25-Nov-15

Protein chains

C4TSS4  (C4TSS4_YERKR) -

Protein chains

C4TSS5  (C4TSS5_YERKR) -

Protein chain

C4TSS4  (C4TSS4_YERKR) -

Nucleic Acids Res 45:5013-5025 (2017)

PubMed id: 28398546

The CDI toxin of Yersinia kristensenii is a novel bacterial member of the RNase A superfamily.

G.Batot, K.Michalska, G.Ekberg, E.M.Irimpan, G.Joachimiak, R.Jedrzejczak, G.Babnigg, C.S.Hayes, A.Joachimiak, C.W.Goulding.

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.