Biological Assembly 1  

 3D View: Structure | Electron Density

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 120766.86 
• Atom Count: 6218 
• Residue Count: 1124 
• Unique protein chains: 2

5J43

CdiA-CT from uropathogenic Escherichia coli in complex with CysK

• DOI: 10.2210/pdb5J43/pdb

• Classification: TOXIN
• Organism(s): Escherichia coli (strain K12), Escherichia coli O6:K15:H31 (strain 536 / UPEC)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 1 


• Deposited: 2016-03-31 Released: 2016-07-27 
• Deposition Author(s): Morse, R.P., Goulding, C.W., Johnson, P.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.224 
• R-Value Work: 0.200 

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

• PubMed: 27531961 
• DOI: 10.1073/pnas.1607112113
• Primary Citation of Related Structures:  
  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 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
Molecule	Chains	Sequence Length	Organism	Details
Cysteine synthase A	E, A	323	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: cysK (cysZ) EC: 2.5.1.47
Find proteins for P0ABK5 (Escherichia coli (strain K12)) Go to UniProtKB:  P0ABK5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
tRNA nuclease CdiA	F, B	239	Escherichia coli O6:K15:H31 (strain 536 / UPEC)	Mutation(s): 1  Gene Names: cdiA EC: 3.1.-.-
Find proteins for Q0T963 (Escherichia coli O6:K15:H31 (strain 536 / UPEC)) Go to UniProtKB:  Q0T963

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, E	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.224 
• R-Value Work: 0.200 
• Space Group: P 4₁

Unit Cell:

Length (Å)	Angle (°)
a = 64.010	α = 90.00
b = 64.010	β = 90.00
c = 365.370	γ = 90.00

Software Package:

Software Name	Purpose
iMOSFLM	data reduction
PHENIX	phasing
PHENIX	model building
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-03-31 
• Released Date: 2016-07-27 
• Deposition Author(s): Morse, R.P., Goulding, C.W., Johnson, P.M.

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