1BAP

A PRO TO GLY MUTATION IN THE HINGE OF THE ARABINOSE-BINDING PROTEIN ENHANCES BINDING AND ALTERS SPECIFICITY: SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

A Pro to Gly mutation in the hinge of the arabinose-binding protein enhances binding and alters specificity. Sugar-binding and crystallographic studies.

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

(1990) J Biol Chem 265: 16592-16603

  • Primary Citation of Related Structures:  
    1APB, 1BAP, 9ABP

  • PubMed Abstract: 
  • The L-arabinose-binding protein (ABP) of Escherichia coli consists structurally of two distinct globular domains connected by a hinge of three separate peptide segments. Arabinose is bound and completely sequestered within the deep cleft between the two domains ...

    The L-arabinose-binding protein (ABP) of Escherichia coli consists structurally of two distinct globular domains connected by a hinge of three separate peptide segments. Arabinose is bound and completely sequestered within the deep cleft between the two domains. With reduced affinity, ABP also binds D-galactose (approximately 2-fold reduction) and D-fucose (approximately 40-fold reduction). Experiments have been conducted to explore the role in sugar binding of the hinge connecting the two domains of ABP. To increase the flexibility of the hinge region, a glycine was substituted for a proline at position 254 by site-directed mutagenesis. Unexpectedly, this mutation resulted in the dramatic enhancement of galactose binding over that of arabinose. The affinity of the mutant ABP for galactose increased by over 20-fold, while that for arabinose and fucose remained relatively unchanged. We have measured association and dissociation rates of the Gly-254 ABP with L-arabinose, D-galactose, and D-fucose and have determined the crystallographic structure of the protein complexed with each of the three sugars. Both the ligand-binding kinetic measurements and structure analysis indicate that the altered specificity is due to an effective increase in the rigidity of the hinge in the closed conformation which is induced upon galactose binding. Stabilizing contacts are formed between the strands of the hinge in the Gly-254 ABP when galactose is bound which are not found in complexes with the other sugars or the liganded wild-type protein.


    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)  |  3D 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02924
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ARB
Query on ARB

Download Ideal Coordinates CCD File 
C [auth A]beta-L-arabinopyranose
C5 H10 O5
SRBFZHDQGSBBOR-KLVWXMOXSA-N
 Ligand Interaction
ARA
Query on ARA

Download Ideal Coordinates CCD File 
B [auth A]alpha-L-arabinopyranose
C5 H10 O5
SRBFZHDQGSBBOR-QMKXCQHVSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ARB Binding MOAD:  1BAP Kd: 140 (nM) from 1 assay(s)
ARA Binding MOAD:  1BAP Kd: 140 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.46α = 90
b = 71.82β = 90
c = 77.84γ = 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: 1992-01-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    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