6I3G

Crystal structure of a putative peptide binding protein AppA from Clostridium difficile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the putative peptide-binding protein AppA from Clostridium difficile.

Hughes, A.Wilson, S.Dodson, E.J.Turkenburg, J.P.Wilkinson, A.J.

(2019) Acta Crystallogr F Struct Biol Commun 75: 246-253

  • DOI: https://doi.org/10.1107/S2053230X1900178X
  • Primary Citation of Related Structures:  
    6I3G

  • PubMed Abstract: 

    Peptides play an important signalling role in Bacillus subtilis, where their uptake by one of two ABC-type oligopeptide transporters, Opp and App, is required for efficient sporulation. Homologues of these transporters in Clostridium difficile have been characterized, but their role, and hence that of peptides, in regulating sporulation in this organism is less clear. Here, the oligopeptide-binding receptor proteins for these transporters, CdAppA and CdOppA, have been purified and partially characterized, and the crystal structure of CdAppA has been determined in an open unliganded form. Peptide binding to either protein could not be observed in Thermofluor assays with a set of ten peptides of varying lengths and compositions. Re-examination of the protein sequences together with structure comparisons prompts the proposal that CdAppA is not a versatile peptide-binding protein but instead may bind a restricted set of peptides. Meanwhile, CdOppA is likely to be the receptor protein for a nickel-uptake system.


  • Organizational Affiliation

    Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ABC transporter, substrate-binding protein, family 5490Clostridioides difficileMutation(s): 0 
Gene Names: appAappA_1BGU81_05565BN1095_250054BN1096_520027BN1097_680156SAMEA3374989_00890
UniProt
Find proteins for A0A069AL86 (Clostridioides difficile)
Explore A0A069AL86 
Go to UniProtKB:  A0A069AL86
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A069AL86
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.525α = 90
b = 106.094β = 90
c = 109.515γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MrBUMPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J014443/1

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references