4Q65

Structure of the E. coli Peptide Transporter YbgH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal Structure of the E. coli Peptide Transporter YbgH

Zhao, Y.Mao, G.Liu, M.Zhang, L.Wang, X.Zhang, X.C.

(2014) Structure --: --

  • DOI: 10.1016/j.str.2014.06.008

  • PubMed Abstract: 
  • E. coli YbgH belongs to the family of proton-dependent oligopeptide transporters (POTs), a subfamily of the major facilitator superfamily (MFS) of secondary active transporters. Like other MFS transporters, POT proteins switch between two major confo ...

    E. coli YbgH belongs to the family of proton-dependent oligopeptide transporters (POTs), a subfamily of the major facilitator superfamily (MFS) of secondary active transporters. Like other MFS transporters, POT proteins switch between two major conformations during substrate transport. Apart from possessing a canonical 12-helix, two-domain transmembrane (TM) core, prokaryotic POT proteins usually have two TM helices inserted between the two domains. Here we determined the crystal structure of YbgH in its inward-facing conformation. Our structure-based functional studies investigated the roles of both the POT signature motif 2 and the inserted interdomain TM helix pair in the stabilization and regulation of the major conformational change in MFS/POT transporters. Furthermore, of all the proton-titratable amino acid residues, Glu21 is the only conserved one (among POTs) located in the central cavity and is critical for in vivo transport. Together, our results support the notion that MFS symporters utilize a transport mechanism based on substrate-protonation coupling.


    Organizational Affiliation

    School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China; National Laboratory of Macromolecules, National Center of Protein Science Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dipeptide permease D
A
493Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: dtpD (ybgH)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Major Facilitator Superfamily (MFS) Transporters
Protein: 
YbgH peptide transporter (POT family), inward facing conformation
Find proteins for P75742 (Escherichia coli (strain K12))
Go to UniProtKB:  P75742
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.258 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 94.035α = 90.00
b = 109.448β = 90.00
c = 76.659γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-13
    Type: Initial release