4D2D

Structure of a tri peptide bound POT family peptide transporter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for Polyspecificity in the Pot Family of Proton-Coupled Oligopeptide Transporters.

Lyons, J.A.Parker, J.L.Solcan, N.Brinth, A.Li, D.Shah, S.T.Caffrey, M.Newstead, S.

(2014) EMBO Rep 15: 886

  • DOI: 10.15252/embr.201338403
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • An enigma in the field of peptide transport is the structural basis for ligand promiscuity, as exemplified by PepT1, the mammalian plasma membrane peptide transporter. Here, we present crystal structures of di- and tripeptide-bound complexes of a bac ...

    An enigma in the field of peptide transport is the structural basis for ligand promiscuity, as exemplified by PepT1, the mammalian plasma membrane peptide transporter. Here, we present crystal structures of di- and tripeptide-bound complexes of a bacterial homologue of PepT1, which reveal at least two mechanisms for peptide recognition that operate within a single, centrally located binding site. The dipeptide was orientated laterally in the binding site, whereas the tripeptide revealed an alternative vertical binding mode. The co-crystal structures combined with functional studies reveal that biochemically distinct peptide-binding sites likely operate within the POT/PTR family of proton-coupled symporters and suggest that transport promiscuity has arisen in part through the ability of the binding site to accommodate peptides in multiple orientations for transport.


    Organizational Affiliation

    Department of Biochemistry, University of Oxford, Oxford, UK simon.newstead@bioch.ox.ac.uk martin.caffrey@tcd.ie.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DI-OR TRIPEPTIDE\:H+ SYMPORTER
A
491Streptococcus thermophilus LMG 18311Mutation(s): 0 
Gene Names: dtpTstu0970
Find proteins for Q5M4H8 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311))
Go to UniProtKB:  Q5M4H8
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ALANINE-TRIPEPTIDE
B
3synthetic constructMutation(s): 0 
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
78M
Query on 78M

Download CCD File 
A
(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
C18 H34 O4
BJMLBVHMHXYQFS-JJEJIETFSA-N
 Ligand Interaction
78N
Query on 78N

Download CCD File 
A
(2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
C18 H34 O4
BJMLBVHMHXYQFS-XZVRFQMRSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.38α = 90
b = 110.7β = 90
c = 110.62γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2014-08-13
    Changes: Database references
  • Version 1.2: 2019-09-25
    Changes: Data collection, Experimental preparation, Other