8ARE

Crystal structure of the peptide binding protein, OppA, from Bacillus subtilis in complex with a PhrE-derived pentapeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.252 

Starting Model: other
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Literature

Peptide transport in Bacillus subtilis - structure and specificity in the extracellular solute binding proteins OppA and DppE.

Hughes, A.M.Darby, J.F.Dodson, E.J.Wilson, S.J.Turkenburg, J.P.Thomas, G.H.Wilkinson, A.J.

(2022) Microbiology (Reading) 168

  • DOI: https://doi.org/10.1099/mic.0.001274
  • Primary Citation of Related Structures:  
    8ARE, 8ARN, 8AY0, 8AZB

  • PubMed Abstract: 

    Peptide transporters play important nutritional and cell signalling roles in Bacillus subtilis, which are pronounced during stationary phase adaptations and development. Three high-affinity ATP-binding cassette (ABC) family transporters are involved in peptide uptake - the oligopeptide permease (Opp), another peptide permease (App) and a less well-characterized dipeptide permease (Dpp). Here we report crystal structures of the extracellular substrate binding proteins, OppA and DppE, which serve the Opp and Dpp systems, respectively. The structure of OppA was determined in complex with endogenous peptides, modelled as Ser-Asn-Ser-Ser, and with the sporulation-promoting peptide Ser-Arg-Asn-Val-Thr, which bind with K d values of 0.4 and 2 µM, respectively, as measured by isothermal titration calorimetry. Differential scanning fluorescence experiments with a wider panel of ligands showed that OppA has highest affinity for tetra- and penta-peptides. The structure of DppE revealed the unexpected presence of a murein tripeptide (MTP) ligand, l-Ala-d-Glu- meso -DAP, in the peptide binding groove. The mode of MTP binding in DppE is different to that observed in the murein peptide binding protein, MppA, from Escherichia coli , suggesting independent evolution of these proteins from an OppA-like precursor. The presence of MTP in DppE points to a role for Dpp in the uptake and recycling of cell wall peptides, a conclusion that is supported by analysis of the genomic context of dpp , which revealed adjacent genes encoding enzymes involved in muropeptide catabolism in a gene organization that is widely conserved in Firmicutes .


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oligopeptide-binding protein OppA525Bacillus subtilis subsp. subtilis str. 168Mutation(s): 3 
Gene Names: oppAspo0KABSU11430
UniProt
Find proteins for P24141 (Bacillus subtilis (strain 168))
Explore P24141 
Go to UniProtKB:  P24141
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24141
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatase RapE inhibitor5Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: phrEBSU25840
UniProt
Find proteins for O32025 (Bacillus subtilis (strain 168))
Explore O32025 
Go to UniProtKB:  O32025
Entity Groups  
UniProt GroupO32025
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.252 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.861α = 90
b = 63.689β = 114.352
c = 100.06γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
ELVESdata processing
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Data collection, Refinement description