2VGX

Structure of the Yersinia enterocolitica Type III Secretion Translocator Chaperone SycD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the Yersinia Enterocolitica Type III Secretion Chaperone Sycd

Buttner, C.R.Sorg, I.Cornelis, G.R.Heinz, D.W.Niemann, H.H.

(2008) J.Mol.Biol. 375: 997

  • DOI: 10.1016/j.jmb.2007.11.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Many Gram-negative bacteria use a type III secretion (T3S) system to directly inject effector molecules into eucaryotic cells in order to establish a symbiotic or pathogenic relationship with their host. The translocation of many T3S proteins require ...

    Many Gram-negative bacteria use a type III secretion (T3S) system to directly inject effector molecules into eucaryotic cells in order to establish a symbiotic or pathogenic relationship with their host. The translocation of many T3S proteins requires specialized chaperones from the bacterial cytosol. SycD belongs to a class of T3S chaperones that assists the secretion of pore-forming translocators and, specifically chaperones the translocators YopB and YopD from enteropathogenic Yersinia enterocolitica. In addition, SycD is involved in the regulation of virulence factor biosynthesis and secretion. In this study, we present two crystal structures of Y. enterocolitica SycD at 1.95 and 2.6 A resolution, the first experimental structures of a T3S class II chaperone specific for translocators. The fold of SycD is entirely alpha-helical and reveals three tetratricopeptide repeat-like motifs that had been predicted from amino acid sequence. In both structures, SycD forms dimers utilizing residues from the first tetratricopeptide repeat motif. Using site-directed mutagenesis and size exclusion chromatography, we verified that SycD forms head-to-head homodimers in solution. Although in both structures, dimerization largely depends on the same residues, the two assemblies represent alternative dimers that exhibit different monomer orientations and overall shape. In these two distinct head-to-head dimers, both the concave and the convex surface of each monomer are accessible for interactions with the SycD binding partners YopB and YopD. A SycD variant carrying two point mutations in the dimerization interface is properly folded but defective in dimerization. Expression of this stable SycD monomer in Yersinia does not rescue the phenotype of a sycD null mutant, suggesting a physiological relevance of the dimerization interface.


    Organizational Affiliation

    Division of Structural Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHAPERONE SYCD
A
148Yersinia enterocoliticaMutation(s): 0 
Gene Names: sycD
Find proteins for O87496 (Yersinia enterocolitica)
Go to UniProtKB:  O87496
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CHAPERONE SYCD
B
148Yersinia enterocoliticaMutation(s): 0 
Gene Names: sycD
Find proteins for O87496 (Yersinia enterocolitica)
Go to UniProtKB:  O87496
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
A, B
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 107.247α = 90.00
b = 32.979β = 122.34
c = 96.731γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-04
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-04-03
    Type: Data collection, Derived calculations, Experimental preparation, Other