Crystal Structures of Escherichia coli ATP-Dependent Glucokinase and Its Complex with Glucose

Ribbon model of the ecGlK dimer. The small domain is depicted in light gray, and the large domain is in dark gray for one monomer (left); the corresponding domains of the second monomer (right) are shown in dark and light gray, respectively. The two glucose molecules bound to the dimer are shown in stick representation.

Sequence alignment of representative members of group II glucokinases (PFAM PF02685) as well as human glucokinase (PDB 1V4S) (36), human brain hexokinase I (PDB 1DGK) (3), and hexokinase PII (PDB 1IG8) (38) by means of the ClustalW program (17). Identical residues are shaded. Residues associated with glucose binding (gray triangles) and the catalytic Asp (black rectangle) are indicated. The conserved β-strand-loop-β-strand motif associated with ATP-binding (Leu6-Leu19) with identical residues indicated by dark gray ovals is highlighted. The secondary structure elements (α-helices and β-strands) of ecGlK are depicted above the sequence alignment. This figure was prepared by using ESPript (22).

Structure superposition of ecGlK (red), S. cerevisiae hexokinase PII (PDB 1IG8, green) (38), and the catalytic domain (residues 475 to 917) of human brain hexokinase I (PDB 1QHA, blue) (57). The dotted line delineates the small domain (top) from the large domain (bottom).

Comparison of fold topologies of ecGlK monomer (a) and catalytic domain (residues 475 to 917) (b) of human brain hexokinase I (PDB 1IG8).

(a) F_o-F_c omit map of the ecGlK active site region, showing electron density for glucose. Glucose and water molecules were omitted prior to refinement. This map is contoured at the level of 3σ. Hydrogen bonds between glucose and ecGlK active site residues and waters are shown as dashed lines. (b) Structural superposition of the active site regions of ecGlK-glc (light gray) and human brain hexokinase I (PDB 1DGK; dark gray) depicted in stereo. The superposition was generated by using the atoms of the glucose molecule and residues corresponding to Asn99, Asp100, Glu157, and Glu187 of ecGlK.

Domain-domain movements of ecGlK. (a) Superposition of dimers of ecGlK (red) and ecGlK-glc (blue). The superposition is based on the large domains of each model, showing the large relative movement of the small domains. Glucose is shown in stick representation. (b) Superposition of the large domains of ecGlK and ecGlK-glc with both monomers within the asymmetric unit in both crystal forms, showing the intrinsic conformational flexibility of ecGlK. Shown are the two monomers of ecGlK (monomer A, blue; monomer B, yellow) and the two monomers of ecGlK-glc (monomer A, cyan; monomer B, magenta). (c) Close-up of superposition of monomer A of ecGlK (red) and ecGlK-glc (blue) showing the glucose-binding site. Glucose is shown in stick representation.