8ABP

SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES OF AN ARABINOSE-BINDING PROTEIN MUTANT (MET108LEU) WHICH EXHIBITS ENHANCED AFFINITY AND ALTERED SPECIFICITY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Sugar-binding and crystallographic studies of an arabinose-binding protein mutant (Met108Leu) that exhibits enhanced affinity and altered specificity.

Vermersch, P.S.Lemon, D.D.Tesmer, J.J.Quiocho, F.A.

(1991) Biochemistry 30: 6861-6866

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In addition to hydrogen bonds, van der Waals forces contribute to the affinity of protein-carbohydrate interactions. Nonpolar van der Waals contacts in the complexes of the L-arabinose-binding protein (ABP) with monosaccharides have been studied by m ...

    In addition to hydrogen bonds, van der Waals forces contribute to the affinity of protein-carbohydrate interactions. Nonpolar van der Waals contacts in the complexes of the L-arabinose-binding protein (ABP) with monosaccharides have been studied by means of site-directed mutagenesis, equilibrium and rapid kinetic binding techniques, and X-ray crystallography. ABP, a periplasmic transport receptor of Escherichia coli, binds L-arabinose, D-galactose, and D-fucose with preferential affinity in the order of Ara greater than Gal much greater than Fuc. Well-refined, high-resolution structures of ABP complexed with the three sugars revealed that the structural differences in the ABP-sugar complexes are localized around C5 of the sugars, where the equatorial H of Ara has been substituted for CH3 (Fuc) or CH2OH (Gal). The side chain of Met108 undergoes a sterically dictated, ligand-specific, conformational change to optimize nonpolar interactions between its methyl group and the sugar. We found that the Met108Leu ABP binds Gal tighter than wild-type ABP binds Ara and exhibits a preference for ligand in the order of Gal much greater than Fuc greater than Ara. The differences in affinity can be attributed to differences in the dissociation rates of the ABP-sugar complexes. We have refined at better than 1.7-A resolution the crystal structures of the Met108Leu ABP complexed with each of the sugars and offer a molecular explanation for the altered binding properties.


    Related Citations: 
    • Location of the Sugar-Binding Site of L-Arabinose-Binding Protein. Sugar Derivative Syntheses, Sugar Binding Specificity, and Difference Fourier Analyses
      Newcomer, M.E.,Miller /III, D.M.,Quiocho, F.A.
      (1979) J.Biol.Chem. 254: 7529
    • The Thiol Group of the L-Arabinose-Binding Protein. Chromophoric Labeling and Chemical Identification of the Sugar-Binding Site
      Miller /III, D.M.,Newcomer, M.E.,Quiocho, F.A.
      (1979) J.Biol.Chem. 254: 7521
    • Structure of L-Arabinose-Binding Protein from Escherichia Coli at 5 Angstroms Resolution and Preliminary Results at 3.5 Angstroms
      Phillips Jr., G.N.,Mahajan, V.K.,Siu, A.K.Q.,Quiocho, F.A.
      (1976) Proc.Natl.Acad.Sci.USA 73: 2186
    • Novel Stereospecificity of the L-Arabinose-Binding Protein
      Quiocho, F.A.,Vyas, N.K.
      (1984) Nature 310: 381
    • Substrate Specificity and Affinity of a Protein Modulated by Bound Water Molecules
      Quiocho, F.A.,Wilson, D.K.,Vyas, N.K.
      (1989) Nature 340: 404
    • The 2.8-Angstroms Resolution Structure of the L-Arabinose-Binding Protein from Escherichia Coli
      Quiocho, F.A.,Gilliland, G.L.,Phillips Jr., G.N.
      (1977) J.Biol.Chem. 252: 5142
    • Hinge-Bending in L-Arabinose-Binding Protein. The "Venus'S-Flytrap" Model
      Mao, B.,Pear, M.R.,Mccammon, J.A.,Quiocho, F.A.
      (1982) J.Biol.Chem. 257: 1131
    • The Radius of Gyration of L-Arabinose-Binding Protein Decreases Upon Binding of Ligand
      Newcomer, M.E.,Lewis, B.A.,Quiocho, F.A.
      (1981) J.Biol.Chem. 256: 13218
    • Structure of the L-Arabinose-Binding Protein from Escherichia Coli at 2.4 Angstroms Resolution
      Gilliland, G.L.,Quiocho, F.A.
      (1981) J.Mol.Biol. 146: 341
    • L-Arabinose-Binding Protein-Sugar Complex at 2.4 Angstroms Resolution. Stereochemistry and Evidence for a Structural Change
      Newcomer, M.E.,Gilliand, G.L.,Quiocho, F.A.
      (1981) J.Biol.Chem. 256: 13213


    Organizational Affiliation

    Howard Hughes Medical Institute Baylor College of Medicine, Houston, Texas 77030.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-ARABINOSE-BINDING PROTEIN
A
306Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: araF
Find proteins for P02924 (Escherichia coli (strain K12))
Go to UniProtKB:  P02924
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAL
Query on GAL

Download SDF File 
Download CCD File 
A
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
GLA
Query on GLA

Download SDF File 
Download CCD File 
A
ALPHA D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GALKd: 10 nM BINDINGMOAD
GLAKd: 10 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.620α = 90.00
b = 71.930β = 90.00
c = 78.090γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1991-10-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance