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 
  • R-Value Observed: 0.225 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 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: https://doi.org/10.15252/embr.201338403
  • Primary Citation of Related Structures:  
    4D2B, 4D2C, 4D2D

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Di-or tripeptide:H+ symporter491Streptococcus thermophilus LMG 18311Mutation(s): 0 
Gene Names: dtpTstu0970
Membrane Entity: Yes 
UniProt
Find proteins for Q5M4H8 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311))
Explore Q5M4H8 
Go to UniProtKB:  Q5M4H8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5M4H8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
78N
Query on 78N

Download Ideal Coordinates CCD File 
D [auth A],
G [auth A]
(2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
C18 H34 O4
BJMLBVHMHXYQFS-XZVRFQMRSA-N
78M
Query on 78M

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
E [auth A],
F [auth A]
(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
C18 H34 O4
BJMLBVHMHXYQFS-JJEJIETFSA-N
PHE
Query on PHE

Download Ideal Coordinates CCD File 
J [auth A]PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
H [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ALA
Query on ALA

Download Ideal Coordinates CCD File 
I [auth A]ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.06α = 90
b = 110.33β = 90
c = 110.74γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2014-08-13
    Changes: Database references
  • Version 2.0: 2018-02-21
    Changes: Advisory, Atomic model, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2019-09-25
    Changes: Data collection, Experimental preparation, Other
  • Version 2.2: 2023-12-20
    Changes: Data collection, Database references, Refinement description