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

Experimental Data Snapshot

  • Resolution: 1.45 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

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

Herrou, J.Crosson, S.

(2013) J Bacteriol 195: 2379-2388

  • DOI: https://doi.org/10.1128/JB.00116-13
  • Primary Citation of Related Structures:  

  • 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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sugar ABC transporter, periplasmic sugar-binding protein
A, B
296Caulobacter vibrioides CB15Mutation(s): 0 
Gene Names: CC_0859
Find proteins for A0A0H3C834 (Caulobacter vibrioides (strain NA1000 / CB15N))
Explore A0A0H3C834 
Go to UniProtKB:  A0A0H3C834
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3C834
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on INS

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C6 H12 O6
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Binding Affinity Annotations 
IDSourceBinding Affinity
INS Binding MOAD:  4IRX Kd: 760 (nM) from 1 assay(s)
PDBBind:  4IRX Kd: 760 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.45 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.121α = 90
b = 34.958β = 102.6
c = 181.83γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

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