D-maltodextrin binding protein belongs to a large family of periplasmic binding proteins of gram-negative bacteria. Other members of the family include: L-arabinose binding protein (ABP), sulphate binding protein (SBP), D-galactose/D-glucose binding protein (GGBP), phosphate binding protein (PBP), leucine/isoleucine/valine binding protein (LIVBP) and leu-specific binding protein (LBP). All of these proteins are high-affinity active transporter, and a few also serve as receptors for bacterial chemotaxis.
All periplasmic binding proteins are monomeric with two globular domains separated by a deep cleft. Each domain has a central beta-pleated sheet flanked on both sides by 2 to 3 parallet alpha-helices. These proteins exists in two forms. In the open form with ligand bound, the cleft is wide open separating the two domains further apart. Ligands sit in the interdomain cleft, held by hydrogen bond and van der Waals forces. Ligand-bound proteinsis are the closed form.
1OMP cleft edgeview looking along the long axis of the cleft, with segment 3(purple) at the end nearer to the viewer. N-domain is coloured cyan for helix and blue for sheet; C-domain is coloured green for helix and greenblue for sheet. The other colours show turns and loops. The cleft is facing downward.
1OMP cleft topview looking at the bottom of the cleft. Segment 1(residues 110-113) is violet; segment 2(residues 259-263) is magenta.
MBP consists of 370 residues with molecular weight Mr = 40600. MBP is similar to many two-domain single polypeptide, like hexokinase and phosphofructokinase, whose domains are linked by 2 to 3 segments. The N-domain (residues 1-109, 264-309) is joined to the C-domain (residues 114-258, 316-370) by three segments: first segment (residues 110-113), second segment (259-263), third segment (310-315). Segments 1 and 2 form a short sheet-like structure at the base of the cleft. The third segment forms a short loop along the side of the cleft and is almost perpendicular to the first two segments.
1OMP segments are shown asthick wireframes, with the rest of the molecule as ribbon.
beta-cyclic-dextran-bound 1DMB endview with ligand in CPK colours.
beta-cyclic-dextran-bound 1DMB bottom view from the top.
The maltodextrin site is located at the base of the cleft between the domains. When bound the sugar is buried in the cleft and almost completely inaccessible to the bulk solvent. There is an extensive network of hydrogen bonds and van der Waals interactions. Hydrogen bonds are formed between the saccharide hydroxyls and 6 chaged side chains, 1 trp side chain, 1 main chain amide and five via water molecules. Van der Waals interactions include stacking of aromatic rings against the faces of the pyranose rings. Maltose first binds to one domain. The central residue of interdomain segment 1, E111 forms hydrogen bond through its side chain carboxyl oxygen and the C2 hydroxyl of the reducing glucosyl unit of maltose. The side chain of E111 subsequently moves up the cleft. This may initiate the domain motion to close the cleft
1OMP, aromatic residues and water molecules in cleft (red and redorange respectively).
beta-cyclic-dextran-bound 1DMP, aromatic residues in cleft with cyclic dextran in wireframe.
There is a large conformational change between the bound and free forms of MBP, as a result of large bending and twisting motions between the two domains. The large conformational change is crucial for the differential binding of bound and free binding proteins to membrane receptors. The transition occurs virtually without any conformational change within each individual domain. Perturbations occur mostly at the aromatic residues lining the binding cleft, including those making hydrophobic stacking interactions with the bound sugar. These are W62, Y155, W230 and W340, which become somewhat pressed onto the sides of the binding cleft on binding sugar. The polar residues within the cleft undergo little conformational change except for E111.
The main conformational changes are the result of bending of the main chain of the hinge segments. The largest motion is the hinge opening of 350 about an axis through the centres of the hinge segments 1(E 111) and 2(V 261). The following table shows the changes in the main chain angles that combine to make the hinge open.
In addition to the predominant hinge-opening motion, the domain motion also involves an 80 anti-clockwise rotation of the N-domain relative to the C-domain. As a result of hinge-opening, the third interdomain segment is strained. Because helix XI of the N-domain and helix XII of the C-domain that it connects are packed tightly against their respective beta sheet, the strained segment pulls the N-domain towards itself. The strain on the segment is localised at the central residue A312, which shows marked changes in its (phi, psi) angles from (-630, -20) to (-1620, 1030), ie changes of (-990, 1050).