6CP9

Contact-dependent growth inhibition toxin - immunity protein complex from Klebsiella pneumoniae 342


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Convergent Evolution of the Barnase/EndoU/Colicin/RelE (BECR) Fold in Antibacterial tRNase Toxins.

Gucinski, G.C.Michalska, K.Garza-Sanchez, F.Eschenfeldt, W.H.Stols, L.Nguyen, J.Y.Goulding, C.W.Joachimiak, A.Hayes, C.S.

(2019) Structure 27: 1660

  • DOI: https://doi.org/10.1016/j.str.2019.08.010
  • Primary Citation of Related Structures:  
    6CP8, 6CP9

  • PubMed Abstract: 

    Contact-dependent growth inhibition (CDI) is a form of interbacterial competition mediated by CdiB-CdiA two-partner secretion systems. CdiA effector proteins carry polymorphic C-terminal toxin domains (CdiA-CT), which are neutralized by specific CdiI immunity proteins to prevent self-inhibition. Here, we present the crystal structures of CdiA-CT⋅CdiI complexes from Klebsiella pneumoniae 342 and Escherichia coli 3006. The toxins adopt related folds that resemble the ribonuclease domain of colicin D, and both are isoacceptor-specific tRNases that cleave the acceptor stem of deacylated tRNA GAU Ile . Although the toxins are similar in structure and substrate specificity, CdiA-CT Kp342 activity requires translation factors EF-Tu and EF-Ts, whereas CdiA-CT EC3006 is intrinsically active. Furthermore, the corresponding immunity proteins are unrelated in sequence and structure. CdiI Kp342 forms a dimeric β sandwich, whereas CdiI EC3006 is an α-solenoid monomer. Given that toxin-immunity genes co-evolve as linked pairs, these observations suggest that the similarities in toxin structure and activity reflect functional convergence.


  • Organizational Affiliation

    Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CdiA
A, C, E, G
126Klebsiella pneumoniae 342Mutation(s): 0 
Gene Names: KPK_4110
UniProt
Find proteins for B5Y0C2 (Klebsiella pneumoniae (strain 342))
Explore B5Y0C2 
Go to UniProtKB:  B5Y0C2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5Y0C2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CdiI
B, D, F, H
116Klebsiella pneumoniae 342Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, C, E, G
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.643α = 90
b = 145.446β = 90
c = 84.281γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SBC-Collectdata collection

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 StatesGM102318
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM115586

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-04-10
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2019-10-23
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-20
    Changes: Database references
  • Version 1.4: 2020-01-01
    Changes: Author supporting evidence