5J43

CdiA-CT from uropathogenic Escherichia coli in complex with CysK


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Unraveling the essential role of CysK in CDI toxin activation.

Johnson, P.M.Beck, C.M.Morse, R.P.Garza-Sanchez, F.Low, D.A.Hayes, C.S.Goulding, C.W.

(2016) Proc Natl Acad Sci U S A 113: 9792-9797

  • DOI: 10.1073/pnas.1607112113
  • Primary Citation of Related Structures:  
    5J43, 5J5V

  • PubMed Abstract: 
  • Contact-dependent growth inhibition (CDI) is a widespread mechanism of bacterial competition. CDI(+) bacteria deliver the toxic C-terminal region of contact-dependent inhibition A proteins (CdiA-CT) into neighboring target bacteria and produce CDI im ...

    Contact-dependent growth inhibition (CDI) is a widespread mechanism of bacterial competition. CDI(+) bacteria deliver the toxic C-terminal region of contact-dependent inhibition A proteins (CdiA-CT) into neighboring target bacteria and produce CDI immunity proteins (CdiI) to protect against self-inhibition. The CdiA-CT(EC536) deployed by uropathogenic Escherichia coli 536 (EC536) is a bacterial toxin 28 (Ntox28) domain that only exhibits ribonuclease activity when bound to the cysteine biosynthetic enzyme O-acetylserine sulfhydrylase A (CysK). Here, we present crystal structures of the CysK/CdiA-CT(EC536) binary complex and the neutralized ternary complex of CysK/CdiA-CT/CdiI(EC536) CdiA-CT(EC536) inserts its C-terminal Gly-Tyr-Gly-Ile peptide tail into the active-site cleft of CysK to anchor the interaction. Remarkably, E. coli serine O-acetyltransferase uses a similar Gly-Asp-Gly-Ile motif to form the "cysteine synthase" complex with CysK. The cysteine synthase complex is found throughout bacteria, protozoa, and plants, indicating that CdiA-CT(EC536) exploits a highly conserved protein-protein interaction to promote its toxicity. CysK significantly increases CdiA-CT(EC536) thermostability and is required for toxin interaction with tRNA substrates. These observations suggest that CysK stabilizes the toxin fold, thereby organizing the nuclease active site for substrate recognition and catalysis. By contrast, Ntox28 domains from Gram-positive bacteria lack C-terminal Gly-Tyr-Gly-Ile motifs, suggesting that they do not interact with CysK. We show that the Ntox28 domain from Ruminococcus lactaris is significantly more thermostable than CdiA-CT(EC536), and its intrinsic tRNA-binding properties support CysK-independent nuclease activity. The striking differences between related Ntox28 domains suggest that CDI toxins may be under evolutionary pressure to maintain low global stability.


    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697; Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697 celia.goulding@uci.edu christopher.hayes@lifesci.ucsb.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cysteine synthase AAE323Escherichia coli O157:H7Mutation(s): 0 
Gene Names: cysKZ3680ECs3286
EC: 2.5.1.47 (PDB Primary Data), 4.5.1.5 (UniProt)
Find proteins for P0ABK5 (Escherichia coli (strain K12))
Explore P0ABK5 
Go to UniProtKB:  P0ABK5
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA nuclease CdiABF239Escherichia coli 536Mutation(s): 1 
Gene Names: cdiAECP_4580
EC: 3.1
Find proteins for Q0T963 (Escherichia coli O6:K15:H31 (strain 536 / UPEC))
Explore Q0T963 
Go to UniProtKB:  Q0T963
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A,EL-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.01α = 90
b = 64.01β = 90
c = 365.37γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
PHENIXphasing
PHENIXmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2017-04-12
    Changes: Database references
  • Version 1.2: 2017-05-03
    Changes: Non-polymer description