5I4R

Contact-dependent inhibition system from Escherichia coli NC101 - ternary CdiA/CdiI/EF-Tu complex (trypsin-modified)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs.

Michalska, K.Gucinski, G.C.Garza-Sanchez, F.Johnson, P.M.Stols, L.M.Eschenfeldt, W.H.Babnigg, G.Low, D.A.Goulding, C.W.Joachimiak, A.Hayes, C.S.

(2017) Nucleic Acids Res. 45: 10306-10320

  • DOI: 10.1093/nar/gkx700
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Contact-dependent growth inhibition (CDI) is a mechanism of inter-cellular competition in which Gram-negative bacteria exchange polymorphic toxins using type V secretion systems. Here, we present structures of the CDI toxin from Escherichia coli NC10 ...

    Contact-dependent growth inhibition (CDI) is a mechanism of inter-cellular competition in which Gram-negative bacteria exchange polymorphic toxins using type V secretion systems. Here, we present structures of the CDI toxin from Escherichia coli NC101 in ternary complex with its cognate immunity protein and elongation factor Tu (EF-Tu). The toxin binds exclusively to domain 2 of EF-Tu, partially overlapping the site that interacts with the 3'-end of aminoacyl-tRNA (aa-tRNA). The toxin exerts a unique ribonuclease activity that cleaves the single-stranded 3'-end from tRNAs that contain guanine discriminator nucleotides. EF-Tu is required to support this tRNase activity in vitro, suggesting the toxin specifically cleaves substrate in the context of GTP·EF-Tu·aa-tRNA complexes. However, superimposition of the toxin domain onto previously solved GTP·EF-Tu·aa-tRNA structures reveals potential steric clashes with both aa-tRNA and the switch I region of EF-Tu. Further, the toxin induces conformational changes in EF-Tu, displacing a β-hairpin loop that forms a critical salt-bridge contact with the 3'-terminal adenylate of aa-tRNA. Together, these observations suggest that the toxin remodels GTP·EF-Tu·aa-tRNA complexes to free the 3'-end of aa-tRNA for entry into the nuclease active site.


    Organizational Affiliation

    Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Contact-dependent inhibitor A
A, E
92N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Elongation factor Tu
C, G
45Escherichia coli O139:H28 (strain E24377A / ETEC)Mutation(s): 0 
Gene Names: tuf1
Find proteins for A7ZSL4 (Escherichia coli O139:H28 (strain E24377A / ETEC))
Go to UniProtKB:  A7ZSL4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Elongation factor Tu
D, H
335Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: tufA
Find proteins for P0CE47 (Escherichia coli (strain K12))
Go to UniProtKB:  P0CE47
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Contact-dependent inhibitor I
B, F
114Escherichia coliMutation(s): 0 
Find proteins for A0A192ETU5 (Escherichia coli)
Go to UniProtKB:  A0A192ETU5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
C, G
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.243 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 74.395α = 90.00
b = 128.354β = 109.58
c = 100.358γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
PHASERphasing
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM094585
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM102318

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence
  • Version 1.2: 2017-10-25
    Type: Database references