5E3E

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.5 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

  • 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 Molecular Biology & Biochemistry, University of California Irvine, Irvine, CA 92697, USA.,Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.,Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA.,Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9625, USA.,Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA 93106-9625, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.,Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA 92697, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CdiI immunity protein
A, C, E
104N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Large exoprotein involved in heme utilization or adhesion
B, D, F
114N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 48.890α = 78.25
b = 57.146β = 90.21
c = 64.302γ = 79.11
Software Package:
Software NamePurpose
HKL-3000data scaling
SBC-Collectdata collection
PHENIXrefinement
REFMACrefinement
HKL-3000phasing
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM094585
National Institutes of Health/National Institute of General Medical SciencesUnited States5U01GM102318

Revision History 

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