2W0R | pdb_00002w0r

Crystal structure of the mutated N263D YscU C-terminal domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.225 (Depositor) 
  • R-Value Work: 
    0.201 (Depositor) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2W0R

This is version 1.4 of the entry. See complete history

Literature

Structure of the Type III Secretion Recognition Protein Yscu from Yersinia Enterocolitica

Wiesand, U.Sorg, I.Amstutz, M.Wagner, S.Van Den Heuvel, J.Luehrs, T.Cornelis, G.R.Heinz, D.W.

(2009) J Mol Biology 385: 854

  • DOI: https://doi.org/10.1016/j.jmb.2008.10.034
  • Primary Citation Related Structures: 
    2V5G, 2W0R

  • PubMed Abstract: 

    The inner-membrane protein YscU has an important role during the assembly of the Yersinia enterocolitica type III secretion injectisome. Its cytoplasmic domain (YscU(C)) recognizes translocators as individual substrates in the export hierarchy. Activation of YscU entails autocleavage at a conserved NPTH motif. Modification of this motif markedly changes the properties of YscU, including translocator export cessation and production of longer injectisome needles. We determined the crystal structures of the uncleaved variants N263A and N263D of YscU(C) at 2.05 A and 1.55 A resolution, respectively. The globular domain is found to consist of a central, mixed beta-sheet surrounded by alpha-helices. The NPTH motif forms a type II beta-turn connecting two beta-strands. NMR analysis of cleaved and uncleaved YscU(C) indicates that the global structure of the protein is retained in cleaved YscU(C). The structure of YscU(C) variant N263D reveals that wild type YscU(C) is poised for cleavage due to an optimal reaction geometry for nucleophilic attack of the scissile bond by the side chain of Asn263. In vivo analysis of N263Q and H266A/R314A YscU variants showed a phenotype that combines the absence of translocator secretion with normal needle-length control. Comparing the structure of YscU to those of related proteins reveals that the linker domain between the N-terminal transmembrane domain and the autocleavage domain can switch from an extended to a largely alpha-helical conformation, allowing for optimal positioning of the autocleavage domain during injectisome assembly.


  • Organizational Affiliation
    • Division of Structural Biology, Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany.

Macromolecule Content 

  • Total Structure Weight: 16.92 kDa 
  • Atom Count: 1,239 
  • Modeled Residue Count: 122 
  • Deposited Residue Count: 144 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
YSCU144Yersinia enterocoliticaMutation(s): 1 
UniProt
Find proteins for Q56844 (Yersinia enterocolitica W22703)
Explore Q56844 
Go to UniProtKB:  Q56844
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ56844
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.225 (Depositor) 
  • R-Value Work:  0.201 (Depositor) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.473α = 90
b = 66.473β = 90
c = 68.113γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-04
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description