Conformational changes of glucose/galactose‐binding protein illuminated by open, unliganded, and ultra‐high‐resolution ligand‐bound structures

Abstract

D-Glucose/D-Galactose-binding protein (GGBP) mediates chemotaxis toward and active transport of glucose and galactose in a number of bacterial species. GGBP, like other periplasmic binding proteins, can exist in open (ligand-free) and closed (ligand-bound) states. We report a 0.92 Å resolution structure of GGBP from Escherichia coli in the glucose-bound state and the first structure of an open, unbound form of GGBP (at 1.55 Å resolution). These structures vary in the angle between the two structural domains; the observed difference of 31°arises from torsion angle changes in a three-segment hinge. A comparison with the closely related periplasmic receptors, ribose-and allose-binding proteins, shows that the GGBP hinge residue positions that undergo the largest conformational changes are different. Furthermore, the high-quality data collected for the atomic resolution glucose-bound structure allow for the refinement of specific hydrogen atom positions, the assignment of alternate side chain conformations, the first description of CO 2 trapped after radiation-induced decarboxylation, and insight into the role of the exo-anomeric effect in sugar binding. Together, these structures provide insight into how the hinge-bending movement of GGBP facilitates ligand binding, transport, and signaling.Keywords: hinge motion; atomic resolution; chemotaxis; exo-anomeric effect; radiation damage Supplemental material: see www.proteinscience.org Periplasmic binding proteins (PBPs) constitute a large family of bacterial receptors that recognize a variety of small molecule ligands. These soluble proteins can serve as intermediary receptors for transport (via ABC transport systems), chemotaxis, and quorum sensing (Tam and Saier 1993;Chen et al. 2002). All PBPs consist of two a/b globular domains connected by a hinge (FukamiKobayashi et al. 1999). This ''Venus flytrap'' architecture is also present in intracellular bacterial proteins, such as the Lac repressor, and in many eukaryotic receptors, including certain G-protein-coupled receptors, ion channels, and GABA receptors (Felder et al. 1999).PBPs exist in open and closed forms. As demonstrated by small-angle scattering and cross-linking studies, the open form predominates in the absence of ligands (Careaga et al. 1995;Shilton et al. 1996). Ligand binding induces a large-scale hinge-bending motion that clamps the ligand within the binding cleft and stabilizes the closed form. Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi

Structure and stability of D-galactose/D-glucose-binding protein. The role of D-glucose binding and Ca ion depletion

“…Ca 2+ ion is localized in the loop of C-terminal domain (134-142 residues), forming coordination bonds with oxygen atoms of every second residue of this loop and with Glu 205 residue. Structure of Ca-binding center resembles "EF-hand" motive, typical for intracellular Ca-binding proteins [2,15].…”

“…The comparison analysis of GGPB and GGBP/Glc complex was performed on the basis of PDB data [1]: files 2FW0.ent [2] and 2GBP.ent [15], respectively. The analysis of properties of microenvironment and localization of tryptophan and tyrosine residues in GGPB and GGBP/Glc was done as described earlier [12].…”

“…This is also proved by the linear character of the parametric dependences between fluorescence intensity recorded at 320 and 365 nm. [15] and 2FWO.ent [2] using graphical software VMD [5], Raster 3D [7].…”

High Resolution Structures of Periplasmic Glucose-binding Protein of Pseudomonas putida CSV86 Reveal Structural Basis of Its Substrate Specificity

“…Although the substrate-binding proteins have been well studied, there are very few structures reported where both the apo and sugar-bound forms are available depicting the conformational changes upon substrate binding in the protein. Among monosaccharidebinding proteins, only the Escherichia coli glucose/galactosebinding protein (ecGGBP) structure has been determined in unliganded and glucose-complexed forms (15). Because the SBPs have low sequence identity (less than 20%), phylogeny analysis based on multiple sequence alignments is not very reli-able (6).…”

Overview of Fluorescence Glucose Sensing: A Technology with a Bright Future

“…These proteins can adopt an open form in the absence of ligand and a closed form in the presence of ligand. 29 This conformational change from open to closed in the presence of glucose can be used to induce a change in FRET when such GBPs are bound to nanotubes. The reversible conformational change induces a reversible decrease in fluorescence.…”