4TPH

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.254 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    4TPH, 4TPJ, 4TPG

  • 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 Shewanella oneidensis (PepT(So2)) in complex with three different peptides ...

    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

    1] Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden. [2] School of Biological Sciences, Nanyang Technological University, Singapore. [3] Institute of Molecular and Cell Biology, A* STAR, Singapore.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proton:oligopeptide symporter POT familyA, B523Shewanella oneidensis MR-1Mutation(s): 0 
Gene Names: SO_1277
Membrane Entity: Yes 
UniProt
Find proteins for Q8EHE6 (Shewanella oneidensis (strain MR-1))
Explore Q8EHE6 
Go to UniProtKB:  Q8EHE6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LMT (Subject of Investigation/LOI)
Query on LMT

Download Ideal Coordinates CCD File 
D [auth A], G [auth B], H [auth B]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
DBY (Subject of Investigation/LOI)
Query on DBY

Download Ideal Coordinates CCD File 
F [auth A]3,5 DIBROMOTYROSINE
C9 H9 Br2 N O3
COESHZUDRKCEPA-ZETCQYMHSA-N
 Ligand Interaction
ALA
Query on ALA

Download Ideal Coordinates CCD File 
E [auth A]ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.254 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.65α = 90
b = 107.68β = 90
c = 204.21γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--
Swedish Cancer SocietySweden--
EDICTSweden--
NRF-CRPSingapore--

Revision History  (Full details and data files)

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