4IRX

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

Summary for 4IRX

• Entry DOI: 10.2210/pdb4irx/pdb
• Descriptor: Sugar ABC transporter, periplasmic sugar-binding protein, 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE (3 entities in total)
• Functional Keywords: abc transporter, periplasmic binding protein, nutrient uptake, myo-inositol, selenomethionine, transport protein
• Biological source: Caulobacter crescentus
• Total number of polymer chains: 2
• Total formula weight: 62592.89

Authors

Herrou, J.,Crosson, S. (deposition date: 2013-01-15, release date: 2013-03-20, Last modification date: 2024-10-16)

Primary citation

Herrou, J.,Crosson, S.
myo-inositol and D-ribose ligand discrimination in an ABC periplasmic binding protein.
J.Bacteriol., 195:2379-2388, 2013

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.

PubMed: 23504019
DOI: 10.1128/JB.00116-13

Experimental method

X-RAY DIFFRACTION (1.451 Å)