3CJC

Actin dimer cross-linked by V. cholerae MARTX toxin and complexed with DNase I and Gelsolin-segment 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Connecting actin monomers by iso-peptide bond is a toxicity mechanism of the Vibrio cholerae MARTX toxin.

Kudryashov, D.S.Durer, Z.A.Ytterberg, A.J.Sawaya, M.R.Pashkov, I.Prochazkova, K.Yeates, T.O.Loo, R.R.Loo, J.A.Satchell, K.J.Reisler, E.

(2008) Proc Natl Acad Sci U S A 105: 18537-18542

  • DOI: 10.1073/pnas.0808082105
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The Gram-negative bacterium Vibrio cholerae is the causative agent of a severe diarrheal disease that afflicts three to five million persons annually, causing up to 200,000 deaths. Nearly all V. cholerae strains produce a large multifunctional-autopr ...

    The Gram-negative bacterium Vibrio cholerae is the causative agent of a severe diarrheal disease that afflicts three to five million persons annually, causing up to 200,000 deaths. Nearly all V. cholerae strains produce a large multifunctional-autoprocessing RTX toxin (MARTX(Vc)), which contributes significantly to the pathogenesis of cholera in model systems. The actin cross-linking domain (ACD) of MARTX(Vc) directly catalyzes a covalent cross-linking of monomeric G-actin into oligomeric chains and causes cell rounding, but the nature of the cross-linked bond and the mechanism of the actin cytoskeleton disruption remained elusive. To elucidate the mechanism of ACD action and effect on actin, we identified the covalent cross-link bond between actin protomers using limited proteolysis, X-ray crystallography, and mass spectrometry. We report here that ACD catalyzes the formation of an intermolecular iso-peptide bond between residues E270 and K50 located in the hydrophobic and the DNaseI-binding loops of actin, respectively. Mutagenesis studies confirm that no other residues on actin can be cross-linked by ACD both in vitro and in vivo. This cross-linking locks actin protomers into an orientation different from that of F-actin, resulting in strong inhibition of actin polymerization. This report describes a microbial toxin mechanism acting via iso-peptide bond cross-linking between host proteins and is, to the best of our knowledge, the only known example of a peptide linkage between nonterminal glutamate and lysine side chains.


    Organizational Affiliation

    Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Actin, alpha skeletal muscle
A
377Oryctolagus cuniculusMutation(s): 0 
Gene Names: ACTA1ACTA
Find proteins for P68135 (Oryctolagus cuniculus)
Go to UniProtKB:  P68135

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Deoxyribonuclease-1
D
260Bos taurusMutation(s): 0 
Gene Names: DNASE1DNL1
EC: 3.1.21.1
Find proteins for P00639 (Bos taurus)
Go to UniProtKB:  P00639

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Gelsolin
G
125Homo sapiensMutation(s): 0 
Gene Names: GSN
Find proteins for P06396 (Homo sapiens)
Go to UniProtKB:  P06396
NIH Common Fund Data Resources
PHAROS  P06396
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, D, G
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, G
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.303α = 90
b = 108.566β = 90
c = 133.761γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
BOSdata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description