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
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 2.0 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:  
    6ABP, 7ABP, 8ABP

  • 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 means of site-directed mutagenesis, equilibrium and rapid kinetic binding techniques, and X-ray crystallography ...

    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: 
    • 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
    • Novel Stereospecificity of the L-Arabinose-Binding Protein
      Quiocho, F.A., Vyas, N.K.
      (1984) Nature 310: 381
    • 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
    • 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
    • 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
    • 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
    • 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 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
    • 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 U S A 73: 2186

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-ARABINOSE-BINDING PROTEINA306Escherichia coliMutation(s): 0 
UniProt
Find proteins for P02924 (Escherichia coli (strain K12))
Explore P02924 
Go to UniProtKB:  P02924
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAL (Subject of Investigation/LOI)
Query on GAL

Download Ideal Coordinates CCD File 
C [auth A]beta-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
GLA (Subject of Investigation/LOI)
Query on GLA

Download Ideal Coordinates CCD File 
B [auth A]alpha-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GLA Binding MOAD:  8ABP Kd: 10 (nM) from 1 assay(s)
GAL Binding MOAD:  8ABP Kd: 10 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.62α = 90
b = 71.93β = 90
c = 78.09γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1991-10-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Structure summary