4TPG

Selectivity mechanism of a bacterial homologue of the human drug peptide transporters PepT1 and PepT2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.91 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Selectivity mechanism of a bacterial homolog of the human drug-peptide transporters PepT1 and PepT2.

Guettou, F.Quistgaard, E.M.Raba, M.Moberg, P.Low, C.Nordlund, P.

(2014) Nat.Struct.Mol.Biol. 21: 728

  • DOI: 10.1038/nsmb.2860
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Peptide transporters of the PepT family have key roles in the transport of di- and tripeptides across membranes as well as in the absorption of orally administered drugs in the small intestine. We have determined structures of a PepT transporter from ...

    Peptide transporters of the PepT family have key roles in the transport of di- and tripeptides across membranes as well as in the absorption of orally administered drugs in the small intestine. We have determined structures of a PepT transporter from Shewanella oneidensis (PepT(So2)) in complex with three different peptides. The peptides bind in a large cavity lined by residues that are highly conserved in human PepT1 and PepT2. The bound peptides adopt extended conformations with their N termini clamped into a conserved polar pocket. A positively charged patch allows differential interactions with the C-terminal carboxylates of di- and tripeptides. Here we identify three pockets for peptide side chain interactions, and our binding studies define differential roles of these pockets for the recognition of different subtypes of peptide side chains.


    Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proton:oligopeptide symporter POT family
A, B
523Shewanella oneidensis (strain MR-1)Mutation(s): 0 
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Major Facilitator Superfamily (MFS) Transporters
Protein: 
PepTSo Oligopeptide-proton symporter (POT family)
Find proteins for Q8EHE6 (Shewanella oneidensis (strain MR-1))
Go to UniProtKB:  Q8EHE6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ala-L-3-Br-Tyr-Ala
E
3N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
LMT
Query on LMT

Download SDF File 
Download CCD File 
A, B
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002092
Query on PRD_002092
E5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINEPolypeptide / Transport activator

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.91 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.261 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 82.890α = 90.00
b = 108.090β = 90.00
c = 206.830γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--
Swedish Cancer SocietySweden--
integrated EU project EDICTSweden--
NRF-CRP grantSingapore--

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-08-13
    Type: Database references
  • Version 1.2: 2014-08-27
    Type: Data collection
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence