4ZYR

Crystal structure of E. coli Lactose permease G46W/G262W bound to p-nitrophenyl alpha-D-galactopyranoside (alpha-NPG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.312 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.259 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of LacY with an alpha-substituted galactoside: Connecting the binding site to the protonation site.

Kumar, H.Finer-Moore, J.S.Kaback, H.R.Stroud, R.M.

(2015) Proc.Natl.Acad.Sci.USA 112: 9004-9009

  • DOI: 10.1073/pnas.1509854112

  • PubMed Abstract: 
  • The X-ray crystal structure of a conformationally constrained mutant of the Escherichia coli lactose permease (the LacY double-Trp mutant Gly-46→Trp/Gly-262→Trp) with bound p-nitrophenyl-α-d-galactopyranoside (α-NPG), a high-affinity lactose analog, ...

    The X-ray crystal structure of a conformationally constrained mutant of the Escherichia coli lactose permease (the LacY double-Trp mutant Gly-46→Trp/Gly-262→Trp) with bound p-nitrophenyl-α-d-galactopyranoside (α-NPG), a high-affinity lactose analog, is described. With the exception of Glu-126 (helix IV), side chains Trp-151 (helix V), Glu-269 (helix VIII), Arg-144 (helix V), His-322 (helix X), and Asn-272 (helix VIII) interact directly with the galactopyranosyl ring of α-NPG to provide specificity, as indicated by biochemical studies and shown directly by X-ray crystallography. In contrast, Phe-20, Met-23, and Phe-27 (helix I) are within van der Waals distance of the benzyl moiety of the analog and thereby increase binding affinity nonspecifically. Thus, the specificity of LacY for sugar is determined solely by side-chain interactions with the galactopyranosyl ring, whereas affinity is increased by nonspecific hydrophobic interactions with the anomeric substituent.


    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 permease
A, B
417Escherichia coli (strain K12)Mutation(s): 2 
Gene Names: lacY
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Major Facilitator Superfamily (MFS) Transporters
Protein: 
LacY Lactose Permease Transporter (C154G mutant)
Find proteins for P02920 (Escherichia coli (strain K12))
Go to UniProtKB:  P02920
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9PG
Query on 9PG

Download SDF File 
Download CCD File 
A, B
4-nitrophenyl alpha-D-galactopyranoside
C12 H15 N O8
IFBHRQDFSNCLOZ-IIRVCBMXSA-N
 Ligand Interaction
BNG
Query on BNG

Download SDF File 
Download CCD File 
A, B
B-NONYLGLUCOSIDE
C15 H30 O6
QFAPUKLCALRPLH-UXXRCYHCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.312 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.259 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 103.150α = 90.00
b = 121.990β = 90.00
c = 266.090γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PHENIXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR37GM024485
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesDK069463
National Science Foundation (United States)United StatesMCB-1129551

Revision History 

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2015-08-05
    Type: Database references
  • Version 1.2: 2015-08-12
    Type: Derived calculations
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Derived calculations