1ABF

SUBSTRATE SPECIFICITY AND AFFINITY OF A PROTEIN MODULATED BY BOUND WATER MOLECULES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.134 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Substrate specificity and affinity of a protein modulated by bound water molecules.

Quiocho, F.A.Wilson, D.K.Vyas, N.K.

(1989) Nature 340: 404-407

  • DOI: 10.1038/340404a0
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Water molecules influence molecular interactions in all biological systems, yet it is extremely difficult to understand their effects in precise atomic detail. Here we present evidence, based on highly refined atomic structures of the complexes of th ...

    Water molecules influence molecular interactions in all biological systems, yet it is extremely difficult to understand their effects in precise atomic detail. Here we present evidence, based on highly refined atomic structures of the complexes of the L-arabinose-binding protein with L-arabinose, D-fucose and D-galactose, that bound water molecules, coupled with localized conformational changes, can govern substrate specificity and affinity. The atoms common to the three sugars are identically positioned in the binding site and the same nine strong hydrogen bonds are formed in all three complexes. Two hydrogen-bonded water molecules in the site contribute further to tight binding of L-arabinose but create an unfavourable interaction with the methyl group of D-fucose. Equally tight binding of D-galactose is attained by the replacement of one of the hydrogen-bonded water molecules by its--CH2OH group, coordinated with localized structural changes which include a shift and redirection of the hydrogen-bonding interactions of the other water molecule. These observations illustrate how ordered water molecules can contribute directly to the properties of proteins by influencing their interaction with ligands.


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

    Organizational Affiliation

    Howard Hughes Medical Institute, Houston, Texas, 77030.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-ARABINOSE-BINDING PROTEINA306Escherichia coliMutation(s): 0 
Find proteins for P02924 (Escherichia coli (strain K12))
Explore P02924 
Go to UniProtKB:  P02924
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FCA
Query on FCA

Download CCD File 
A
alpha-D-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-PHYPRBDBSA-N
 Ligand Interaction
FCB
Query on FCB

Download CCD File 
A
beta-D-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-FPRJBGLDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FCBKd:  3800   nM  Binding MOAD
FCAKd:  3800   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.134 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.92α = 90
b = 72.02β = 90
c = 78.02γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-10
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary