4OAA

Crystal structure of E. coli lactose permease G46W,G262W bound to sugar


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of sugar-bound LacY.

Kumar, H.Kasho, V.Smirnova, I.Finer-Moore, J.S.Kaback, H.R.Stroud, R.M.

(2014) Proc.Natl.Acad.Sci.USA 111: 1784-1788

  • DOI: 10.1073/pnas.1324141111

  • PubMed Abstract: 
  • Here we describe the X-ray crystal structure of a double-Trp mutant (Gly46→Trp/Gly262→Trp) of the lactose permease of Escherichia coli (LacY) with a bound, high-affinity lactose analog. Although thought to be arrested in an open-outward conformation, ...

    Here we describe the X-ray crystal structure of a double-Trp mutant (Gly46→Trp/Gly262→Trp) of the lactose permease of Escherichia coli (LacY) with a bound, high-affinity lactose analog. Although thought to be arrested in an open-outward conformation, the structure is almost occluded and is partially open to the periplasmic side; the cytoplasmic side is tightly sealed. Surprisingly, the opening on the periplasmic side is sufficiently narrow that sugar cannot get in or out of the binding site. Clearly defined density for a bound sugar is observed at the apex of the almost occluded cavity in the middle of the protein, and the side chains shown to ligate the galactopyranoside strongly confirm more than two decades of biochemical and spectroscopic findings. Comparison of the current structure with a previous structure of LacY with a covalently bound inactivator suggests that the galactopyranoside must be fully ligated to induce an occluded conformation. We conclude that protonated LacY binds D-galactopyranosides specifically, inducing an occluded state that can open to either side of the membrane.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lactose/galactose transporter
A, B
417N/AMutation(s): 2 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TDG
Query on TDG

Download SDF File 
Download CCD File 
A, B
THIODIGALACTOSIDE
C12 H22 O10 S
SYKYBMOFPMXDRQ-ZFDCCPEWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.257 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 101.560α = 90.00
b = 121.940β = 90.00
c = 264.010γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
ELVESrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-29
    Type: Initial release
  • Version 1.1: 2014-02-26
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description
  • Version 1.3: 2019-07-17
    Type: Data collection, Refinement description