6OFQ

ABC transporter-associated periplasmic binding protein DppA from Helicobacter pylori in complex with peptide STSA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular Basis of Unexpected Specificity of ABC Transporter-Associated Substrate-Binding Protein DppA from Helicobacter pylori.

Rahman, M.M.Machuca, M.A.Khan, M.F.Barlow, C.K.Schittenhelm, R.B.Roujeinikova, A.

(2019) J.Bacteriol. 201: --

  • DOI: 10.1128/JB.00400-19
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The gastric pathogen <i>Helicobacter pylori </i> has limited ability to use carbohydrates as a carbon source, relying instead on exogenous amino acids and peptides. Uptake of certain peptides by <i>H. pylori </i> requires an ABC transporter annotat ...

    The gastric pathogen Helicobacter pylori has limited ability to use carbohydrates as a carbon source, relying instead on exogenous amino acids and peptides. Uptake of certain peptides by H. pylori requires an ABC transporter annotated dipeptide permease (Dpp). The transporter specificity is determined by its cognate substrate-binding protein DppA that captures ligands in the periplasm and delivers them to the permease. Here, we show that, unlike previously characterized DppA proteins, H. pylori DppA binds, with micromolar affinity, peptides of diverse amino acid sequences, ranging between two and eight residues in length. We present analysis of the 1.45-Å resolution crystal structure of its complex with the tetrapeptide STSA, which provides a structural rationale for the observed broad specificity. Analysis of the molecular surface revealed a ligand-binding pocket that is large enough to accommodate peptides of up to nine residues in length. The structure suggests that H. pylori DppA is able to recognize a wide range of peptide sequences by forming interactions primarily with the peptide main-chain atoms. The loop that terminates the peptide-binding pocket in DppAs from other bacteria is significantly shorter in the H. pylori protein, providing an explanation for its ability to bind longer peptides. The subsites accommodating the two N-terminal residues of the peptide ligand make the most contribution to the protein-ligand binding energy, in agreement with the observation that dipeptides bind with affinity close to that of longer peptides. IMPORTANCE The World Health Organization listed Helicobacter pylori as a high priority pathogen for antibiotic development. The potential of using peptide transporters in drug design is well recognized. We discovered that the substrate-binding protein of the ABC transporter for peptides termed dipeptide permease, is an unusual member of its family in that it directly binds peptides of diverse amino acid sequences, ranging between two and eight residues in length. We also provided a structural rationale for the observed broad specificity. Since the ability to import peptides as a source of carbon is critical for H. pylori , our findings will inform drug design strategies based on inhibition or fusion of membrane-impermeant antimicrobials with peptides.


    Organizational Affiliation

    Infection and Immunity Program, Monash Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia anna.roujeinikova@monash.edu.,Monash Proteomics and Metabolomics Facility, and Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,Infection and Immunity Program, Monash Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heme-binding protein A / AI-2 binding protein A
A
533Helicobacter pylori SS1Mutation(s): 0 
Gene Names: hbpA
Find proteins for A0A1U9ISL1 (Helicobacter pylori SS1)
Go to UniProtKB:  A0A1U9ISL1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SER-THR-SER-ALA
B
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.147 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 64.120α = 90.00
b = 75.770β = 90.00
c = 128.370γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-08-21
    Type: Initial release
  • Version 1.1: 2019-10-02
    Type: Data collection, Database references