1XOC

The structure of the oligopeptide-binding protein, AppA, from Bacillus subtilis in complex with a nonapeptide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The structure of the oligopeptide-binding protein, AppA, from Bacillus subtilis in complex with a nonapeptide.

Levdikov, V.M.Blagova, E.V.Brannigan, J.A.Wright, L.Vagin, A.A.Wilkinson, A.J.

(2005) J.Mol.Biol. 345: 879-892

  • DOI: 10.1016/j.jmb.2004.10.089

  • PubMed Abstract: 
  • Besides their role as a source of amino acids for Bacillus subtilis, exogenous peptides play important roles in the signalling pathways leading to the development of competence and sporulation. B.subtilis has three peptide transport systems all belon ...

    Besides their role as a source of amino acids for Bacillus subtilis, exogenous peptides play important roles in the signalling pathways leading to the development of competence and sporulation. B.subtilis has three peptide transport systems all belonging to the ATP-binding cassette family, a dipeptide permease (Dpp) and two oligopeptide permeases (Opp and App) with overlapping specificity. These comprise a membrane-spanning channel through which the peptide passes, a pair of ATPases which couple ATP hydrolysis to peptide translocation and a lipid-modified, membrane-anchored extracellular "binding-protein" that serves as the receptor for the system. Here, we present the crystal structure of a soluble form of the peptide-binding protein AppA, which has been solved to 1.6 A spacing by anomalous scattering and molecular replacement methods. The structure reveals a protein made of two distinct lobes with a topology similar to those of DppA from Escherichia coli and OppA from Salmonella typhimurium. Examination of the interlobe region reveals an enlarged pocket, containing electron density defining a nonapeptide ligand. The main-chain of the peptide is well defined and makes a series of polar contacts with the protein including salt-bridges at both its termini. The side-chain density is ambiguous in places, consistent with the interpretation that a population of peptides is bound, whose average electron density resembles the amino acid sequence N-VDSKNTSSW-C.


    Related Citations: 
    • Crystallization of the oligopeptide-binding protein AppA from Bacillus subtilis.
      Wright, L.,Blagova, E.,Levdikov, V.M.,Brannigan, J.A.,Pattenden, R.J.,Chambers, J.,Wilkinson, A.J.
      (2004) Acta Crystallogr.,Sect.D 60: 175


    Organizational Affiliation

    Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oligopeptide-binding protein appA
A
520Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: appA
Find proteins for P42061 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42061
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nonapeptide VDSKNTSSW
B
9N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 120.955α = 90.00
b = 90.779β = 90.00
c = 54.719γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
MLPHAREphasing
REFMACrefinement
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-01-25
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2014-09-10
    Type: Database references