4Q65

Structure of the E. coli Peptide Transporter YbgH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 

wwPDB Validation   3D Report Full Report


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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
  • Primary Citation of Related Structures:  
    4Q65

  • 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 conformations during substrate transport ...

    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

    National Laboratory of Macromolecules, National Center of Protein Science Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China. Electronic address: zhangc@ibp.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dipeptide permease DA493Escherichia coli K-12Mutation(s): 1 
Gene Names: dtpDybgHb0709JW0699
Membrane Entity: Yes 
UniProt
Find proteins for P75742 (Escherichia coli (strain K12))
Explore P75742 
Go to UniProtKB:  P75742
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.035α = 90
b = 109.448β = 90
c = 76.659γ = 90
Software Package:
Software NamePurpose
SHELXSphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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