8QLK

Crystal structure of the pneumococcal Substrate-binding protein AliB in complex with Peptide 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular and structural basis of oligopeptide recognition by the Ami transporter system in pneumococci.

Alcorlo, M.Abdullah, M.R.Steil, L.Sotomayor, F.Lopez-de Oro, L.de Castro, S.Velazquez, S.Kohler, T.P.Jimenez, E.Medina, A.Uson, I.Keller, L.E.Bradshaw, J.L.McDaniel, L.S.Camarasa, M.J.Volker, U.Hammerschmidt, S.Hermoso, J.A.

(2024) PLoS Pathog 20: e1011883-e1011883

  • DOI: https://doi.org/10.1371/journal.ppat.1011883
  • Primary Citation of Related Structures:  
    8A42, 8QLC, 8QLG, 8QLH, 8QLJ, 8QLK, 8QLM, 8QLV, 8QM0

  • PubMed Abstract: 

    ATP-binding cassette (ABC) transport systems are crucial for bacteria to ensure sufficient uptake of nutrients that are not produced de novo or improve the energy balance. The cell surface of the pathobiont Streptococcus pneumoniae (pneumococcus) is decorated with a substantial array of ABC transporters, critically influencing nasopharyngeal colonization and invasive infections. Given the auxotrophic nature of pneumococci for certain amino acids, the Ami ABC transporter system, orchestrating oligopeptide uptake, becomes indispensable in host compartments lacking amino acids. The system comprises five exposed Oligopeptide Binding Proteins (OBPs) and four proteins building the ABC transporter channel. Here, we present a structural analysis of all the OBPs in this system. Multiple crystallographic structures, capturing both open and closed conformations along with complexes involving chemically synthesized peptides, have been solved at high resolution providing insights into the molecular basis of their diverse peptide specificities. Mass spectrometry analysis of oligopeptides demonstrates the unexpected remarkable promiscuity of some of these proteins when expressed in Escherichia coli, displaying affinity for a wide range of peptides. Finally, a model is proposed for the complete Ami transport system in complex with its various OBPs. We further disclosed, through in silico modelling, some essential structural changes facilitating oligopeptide transport into the cellular cytoplasm. Thus, the structural analysis of the Ami system provides valuable insights into the mechanism and specificity of oligopeptide binding by the different OBPs, shedding light on the intricacies of the uptake mechanism and the in vivo implications for this human pathogen.


  • Organizational Affiliation

    Department of Crystallography and Structural Biology, Institute of Physical-Chemistry "Blas Cabrera", Spanish National Research Council (CSIC), Madrid; Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oligopeptide-binding protein AliB626Streptococcus pneumoniaeMutation(s): 0 
Gene Names: aliBspr1382
UniProt
Find proteins for P0A4G1 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore P0A4G1 
Go to UniProtKB:  P0A4G1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A4G1
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-ILE-GLN-SER-GLU-LYS-ALA-ARG-LYS-HIS-ASN11synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.976α = 90
b = 111.501β = 108.04
c = 56.28γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2020-115331GB-I00

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release
  • Version 1.1: 2024-07-03
    Changes: Database references