4APS | pdb_00004aps

Crystal structure of a POT family peptide transporter in an inward open conformation.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.289 (Depositor), 0.323 (DCC) 
  • R-Value Work: 
    0.272 (Depositor) 
  • R-Value Observed: 
    0.273 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Alternating Access Mechanism in the Pot Family of Oligopeptide Transporters.

Solcan, N.Kwok, J.Fowler, P.W.Cameron, A.D.Drew, D.Iwata, S.Newstead, S.

(2012) EMBO J 31: 3411

  • DOI: https://doi.org/10.1038/emboj.2012.157
  • Primary Citation Related Structures: 
    4APS

  • PubMed Abstract: 

    Short chain peptides are actively transported across membranes as an efficient route for dietary protein absorption and for maintaining cellular homeostasis. In mammals, peptide transport occurs via PepT1 and PepT2, which belong to the proton-dependent oligopeptide transporter, or POT family. The recent crystal structure of a bacterial POT transporter confirmed that they belong to the major facilitator superfamily of secondary active transporters. Despite the functional characterization of POT family members in bacteria, fungi and mammals, a detailed model for peptide recognition and transport remains unavailable. In this study, we report the 3.3-Å resolution crystal structure and functional characterization of a POT family transporter from the bacterium Streptococcus thermophilus. Crystallized in an inward open conformation the structure identifies a hinge-like movement within the C-terminal half of the transporter that facilitates opening of an intracellular gate controlling access to a central peptide-binding site. Our associated functional data support a model for peptide transport that highlights the importance of salt bridge interactions in orchestrating alternating access within the POT family.


  • Organizational Affiliation
    • Department of Biochemistry, University of Oxford, Oxford, UK.

Macromolecule Content 

  • Total Structure Weight: 107.55 kDa 
  • Atom Count: 6,891 
  • Modeled Residue Count: 892 
  • Deposited Residue Count: 982 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DI-OR TRIPEPTIDE H+ SYMPORTER
A, B
491Streptococcus thermophilus LMG 18311Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q5M4H8 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311))
Explore Q5M4H8 
Go to UniProtKB:  Q5M4H8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5M4H8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD

Query on CD



Download:Ideal Coordinates CCD File
C [auth B]CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.289 (Depositor), 0.323 (DCC) 
  • R-Value Work:  0.272 (Depositor) 
  • R-Value Observed: 0.273 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.39α = 90
b = 112.99β = 90
c = 215.49γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
Aimlessdata scaling
SHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-13
    Type: Initial release
  • Version 1.1: 2012-08-29
    Changes: Database references
  • Version 1.2: 2012-10-31
    Changes: Other
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other