2VK2

Crystal structure of a galactofuranose binding protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Furanose-Specific Sugar Transport: Characterization of a Bacterial Galactofuranose-Binding Protein.

Horler, R.S.P.Muller, A.Williamson, D.C.Potts, J.R.Wilson, K.S.Thomas, G.H.

(2009) J.Biol.Chem. 284: 31156

  • DOI: 10.1074/jbc.M109.054296

  • PubMed Abstract: 
  • The widespread utilization of sugars by microbes is reflected in the diversity and multiplicity of cellular transporters used to acquire these compounds from the environment. The model bacterium Escherichia coli has numerous transporters that allow i ...

    The widespread utilization of sugars by microbes is reflected in the diversity and multiplicity of cellular transporters used to acquire these compounds from the environment. The model bacterium Escherichia coli has numerous transporters that allow it to take up hexoses and pentoses, which recognize the more abundant pyranose forms of these sugars. Here we report the biochemical and structural characterization of a transporter protein YtfQ from E. coli that forms part of an uncharacterized ABC transporter system. Remarkably the crystal structure of this protein, solved to 1.2 A using x-ray crystallography, revealed that YtfQ binds a single molecule of galactofuranose in its ligand binding pocket. Selective binding of galactofuranose over galactopyranose was also observed using NMR methods that determined the form of the sugar released from the protein. The pattern of expression of the ytfQRTyjfF operon encoding this transporter mirrors that of the high affinity galactopyranose transporter of E. coli, suggesting that this bacterium has evolved complementary transporters that enable it to use all the available galactose present during carbon limiting conditions.


    Organizational Affiliation

    Department of Biology, University of York, York YO10 5YW, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ABC TRANSPORTER PERIPLASMIC-BINDING PROTEIN YTFQ
A
306Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ytfQ
Find proteins for P39325 (Escherichia coli (strain K12))
Go to UniProtKB:  P39325
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GZL
Query on GZL

Download SDF File 
Download CCD File 
A
BETA-D-GALACTOFURANOSE
C6 H12 O6
AVVWPBAENSWJCB-DGPNFKTASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GZLKd: 130 nM BINDINGMOAD
GZLKd: 130 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.745α = 90.00
b = 51.535β = 90.00
c = 116.091γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance