2XUT | pdb_00002xut

Crystal structure of a proton dependent oligopeptide (POT) family transporter.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.62 Å
  • R-Value Free: 
    0.296 (Depositor), 0.347 (DCC) 
  • R-Value Work: 
    0.277 (Depositor), 0.323 (DCC) 
  • R-Value Observed: 
    0.278 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2XUT

This is version 1.4 of the entry. See complete history

Literature

Crystal Structure of a Prokaryotic Homologue of the Mammalian Oligopeptide-Proton Symporters, Pept1 and Pept2.

Newstead, S.Drew, D.Cameron, A.D.Postis, V.L.Xia, X.Fowler, P.W.Ingram, J.C.Carpenter, E.P.Sansom, M.S.P.McPherson, M.J.Baldwin, S.A.Iwata, S.

(2011) EMBO J 30: 417

  • DOI: https://doi.org/10.1038/emboj.2010.309
  • Primary Citation Related Structures: 
    2XUT

  • PubMed Abstract: 

    PepT1 and PepT2 are major facilitator superfamily (MFS) transporters that utilize a proton gradient to drive the uptake of di- and tri-peptides in the small intestine and kidney, respectively. They are the major routes by which we absorb dietary nitrogen and many orally administered drugs. Here, we present the crystal structure of PepT(So), a functionally similar prokaryotic homologue of the mammalian peptide transporters from Shewanella oneidensis. This structure, refined using data up to 3.6 Å resolution, reveals a ligand-bound occluded state for the MFS and provides new insights into a general transport mechanism. We have located the peptide-binding site in a central hydrophilic cavity, which occludes a bound ligand from both sides of the membrane. Residues thought to be involved in proton coupling have also been identified near the extracellular gate of the cavity. Based on these findings and associated kinetic data, we propose that PepT(So) represents a sound model system for understanding mammalian peptide transport as catalysed by PepT1 and PepT2.


  • Organizational Affiliation
    • Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College London, London, UK. simon.newstead@bioch.ox.ac.uk

Macromolecule Content 

  • Total Structure Weight: 173.05 kDa 
  • Atom Count: 10,533 
  • Modeled Residue Count: 1,368 
  • Deposited Residue Count: 1,572 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTON/PEPTIDE SYMPORTER FAMILY PROTEIN
A, B, C
524Shewanella oneidensis MR-1Mutation(s): 2 
Membrane Entity: Yes 
UniProt
Find proteins for Q8EKT7 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1))
Explore Q8EKT7 
Go to UniProtKB:  Q8EKT7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8EKT7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.62 Å
  • R-Value Free:  0.296 (Depositor), 0.347 (DCC) 
  • R-Value Work:  0.277 (Depositor), 0.323 (DCC) 
  • R-Value Observed: 0.278 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.4α = 90
b = 159.4β = 90
c = 152.94γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-15
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Source and taxonomy
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Other