4IRX

Crystal structure of Caulobacter myo-inositol binding protein bound to myo-inositol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.451 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

myo-inositol and D-ribose ligand discrimination in an ABC periplasmic binding protein.

Herrou, J.Crosson, S.

(2013) J.Bacteriol. 195: 2379-2388

  • DOI: 10.1128/JB.00116-13

  • PubMed Abstract: 
  • The periplasmic binding protein (PBP) IbpA mediates the uptake of myo-inositol by the IatP-IatA ATP-binding cassette transmembrane transporter. We report a crystal structure of Caulobacter crescentus IbpA bound to myo-inositol at 1.45 Å resolution. T ...

    The periplasmic binding protein (PBP) IbpA mediates the uptake of myo-inositol by the IatP-IatA ATP-binding cassette transmembrane transporter. We report a crystal structure of Caulobacter crescentus IbpA bound to myo-inositol at 1.45 Å resolution. This constitutes the first structure of a PBP bound to inositol. IbpA adopts a type I PBP fold consisting of two α-β lobes that surround a central hinge. A pocket positioned between the lobes contains the myo-inositol ligand, which binds with submicromolar affinity (0.76 ± 0.08 μM). IbpA is homologous to ribose-binding proteins and binds D-ribose with low affinity (50.8 ± 3.4 μM). On the basis of IbpA and ribose-binding protein structures, we have designed variants of IbpA with inverted binding specificity for myo-inositol and D-ribose. Five mutations in the ligand-binding pocket are sufficient to increase the affinity of IbpA for D-ribose by 10-fold while completely abolishing binding to myo-inositol. Replacement of ibpA with these mutant alleles unable to bind myo-inositol abolishes C. crescentus growth in medium containing myo-inositol as the sole carbon source. Neither deletion of ibpA nor replacement of ibpA with the high-affinity ribose binding allele affected C. crescentus growth on D-ribose as a carbon source, providing evidence that the IatP-IatA transporter is specific for myo-inositol. This study outlines the evolutionary relationship between ribose- and inositol-binding proteins and provides insight into the molecular basis upon which these two related, but functionally distinct, classes of periplasmic proteins specifically bind carbohydrate ligands.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sugar ABC transporter, periplasmic sugar-binding protein
A, B
296Caulobacter vibrioides (strain NA1000 / CB15N)Mutation(s): 0 
Gene Names: ibpA
Find proteins for A0A0H3C834 (Caulobacter vibrioides (strain NA1000 / CB15N))
Go to UniProtKB:  A0A0H3C834
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
INS
Query on INS

Download SDF File 
Download CCD File 
A, B
1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE
MYO-INOSITOL
C6 H12 O6
CDAISMWEOUEBRE-GPIVLXJGSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
INSKd: 760 nM BINDINGMOAD
INSKd: 760 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.451 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.165 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 83.121α = 90.00
b = 34.958β = 102.60
c = 181.830γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
PHENIXphasing
PHENIXmodel building
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2013-12-18
    Type: Database references
  • Version 1.2: 2016-03-30
    Type: Other