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: 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 ...

    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.


    Related Citations: 
    • Target highlights in CASP13: Experimental target structures through the eyes of their authors.
      Lepore, R., Kryshtafovych, A., Alahuhta, M., Veraszto, H.A., Bomble, Y.J., Bufton, J.C., Bullock, A.N., Caba, C., Cao, H., Davies, O.R., Desfosses, A., Dunne, M., Fidelis, K., Goulding, C.W., Gurusaran, M., Gutsche, I., Harding, C.J., Hartmann, M.D., Hayes, C.S., Joachimiak, A., Leiman, P.G., Loppnau, P., Lovering, A.L., Lunin, V.V., Michalska, K., Mir-Sanchis, I., Mitra, A., Moult, J., Phillips Jr., G.N., Pinkas, D.M., Rice, P.A., Tong, Y., Topf, M., Walton, J.D., Schwede, T.
      (2019) Proteins --: --

    Organizational Affiliation

    Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA; Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA. Electronic address: chayes@lifesci.ucsb.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CdiAACEG126Klebsiella pneumoniae 342Mutation(s): 0 
Gene Names: KPK_4110
Find proteins for B5Y0C2 (Klebsiella pneumoniae (strain 342))
Explore B5Y0C2 
Go to UniProtKB:  B5Y0C2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CdiIBDFH116Klebsiella pneumoniae 342Mutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,C,E,GL-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 

  • 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