5E3E

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

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

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

(2017) Nucleic Acids Res 45: 5013-5025

  • DOI: 10.1093/nar/gkx230
  • Primary Citation of Related Structures:  
    5E3E

  • 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 domain ...

    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.


    Organizational Affiliation

    Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA 92697, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CdiI immunity proteinACE104Yersinia kristensenii ATCC 33638Mutation(s): 0 
Gene Names: ykris0001_13520
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Large exoprotein involved in heme utilization or adhesionBDF114Yersinia kristensenii ATCC 33638Mutation(s): 0 
Gene Names: ykris0001_13530
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download CCD File 
B, E
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,C,EL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 
  • Space Group: P 1
  • Diffraction Data DOI: 10.18430/M35E3E Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.89α = 78.25
b = 57.146β = 90.21
c = 64.302γ = 79.11
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SBC-Collectdata collection
HKL-3000data scaling
HKL-3000phasing
HKL-3000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM094585
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5U01GM102318

Revision History 

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2017-02-15
    Changes: Database references
  • Version 1.2: 2017-02-22
    Changes: Structure summary
  • Version 1.3: 2017-03-01
    Changes: Structure summary
  • Version 1.4: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.5: 2017-10-04
    Changes: Database references
  • Version 1.6: 2019-12-25
    Changes: Author supporting evidence