4D2C

Structure of a di peptide bound POT family peptide transporter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 2.0 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
  • Primary Citation of Related Structures:  

  • 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

    Schools of Medicine and Biochemistry & Immunology, Trinity College Dublin, Dublin, Ireland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Di-or tripeptide:H+ symporter
A
491Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)Mutation(s): 0 
Gene Names: dtpT
Find proteins for Q5M4H8 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311))
Go to UniProtKB:  Q5M4H8
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
78M
Query on 78M

Download SDF File 
Download CCD File 
A
(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
7.8 MONOACYLGLYCEROL
C18 H34 O4
BJMLBVHMHXYQFS-JJEJIETFSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
78N
Query on 78N

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

Download SDF File 
Download CCD File 
A
PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
 Ligand Interaction
ALA
Query on ALA

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Download CCD File 
A
ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.222 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 102.060α = 90.00
b = 110.330β = 90.00
c = 110.740γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
PHENIXrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2014-08-13
    Type: Database references
  • Version 2.0: 2018-02-21
    Type: Advisory, Atomic model, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary