5J5V

CdiA-CT from uropathogenic Escherichia coli in complex with cognate immunity protein and CysK


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.196 

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:  

  • 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;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cysteine synthase A
A, D
323Escherichia coli O157:H7Mutation(s): 1 
Gene Names: cysK
EC: 2.5.1.47
Find proteins for P0ABK6 (Escherichia coli O157:H7)
Go to UniProtKB:  P0ABK6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
tRNA nuclease CdiA
B, E
228Escherichia coli O6:K15:H31 (strain 536 / UPEC)Mutation(s): 0 
Gene Names: cdiA
EC: 3.1.-.-
Find proteins for Q0T963 (Escherichia coli O6:K15:H31 (strain 536 / UPEC))
Go to UniProtKB:  Q0T963
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Immunity protein CdiI
C, F
138Escherichia coli O6:K15:H31 (strain 536 / UPEC)Mutation(s): 0 
Gene Names: cdiI
Find proteins for Q0T964 (Escherichia coli O6:K15:H31 (strain 536 / UPEC))
Go to UniProtKB:  Q0T964
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
B, C, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
LLP
Query on LLP
A, D
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.196 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 81.251α = 90.00
b = 195.539β = 90.00
c = 175.061γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
HKL-2000data reduction
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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