Volume 12, Issue 6, Pages 937-947 (June 2004) Chitobiose Phosphorylase from Vibrio proteolyticus, a Member of Glycosyl Transferase Family 36, Has a Clan GH-L-like (α/α)6 Barrel Fold  Masafumi Hidaka, Yuji Honda, Motomitsu Kitaoka, Satoru Nirasawa, Kiyoshi Hayashi, Takayoshi Wakagi, Hirofumi Shoun, Shinya Fushinobu  Structure  Volume 12, Issue 6, Pages 937-947 (June 2004) DOI: 10.1016/j.str.2004.03.027

Figure 1 Ribbon Diagrams of ChBP and Related Structures (A) Overall structure of the ChBP monomer (GlcNAc complex) shown as a ribbon model (N-terminal domain, blue; linker helices, green; α-helical barrel domain, yellow; C-terminal domain, red). The bound GlcNAc molecules (red), P394, and I417 (yellow) are shown as a ball-and-stick model, and the chloride (green) and calcium (black) ions are shown as a sphere. Residues between P394 and I417 are not included in the final model structure. (B) Ribbon diagram presentation of the ChBP dimer. The subunits are located around the crystallographic 2-fold axis. One subunit is colored as in (A), and the other one is colored white. (C) A ribbon diagram of bGA (1LF9; GH-15). Bacterial and archaeal glucoamylases comprise an N-terminal β sandwich domain (blue), linker helices (green), and an α-helical barrel domain (yellow), whereas fungal glucoamylases comprise only an α-helical barrel domain. The bound acarbose molecule (red) is shown as a ball-and-stick model. (D) A ribbon diagram of MalP (1H54; GH-65). The bound phosphate ion is shown as a ball-and-stick model. The domain constitution is identical with that of ChBP and each domain is colored as in (A). Structure 2004 12, 937-947DOI: (10.1016/j.str.2004.03.027)

Figure 2 Sequence Alignment of GT-36 Phosphorolytic Enzymes Names of GT-36 and GH enzymes are given in red and blue, respectively. Multiple sequence alignment was performed using program ClustalW (Thompson et al., 1994). Structure-based alignment with MalP and bGA was performed with the MATRAS (Kawabata and Nishikawa, 2000) server. The secondary structures and their designations are shown below the sequence alignment; arrows and coils represent the β strands and α helices, respectively. Conserved residues in GT-36 enzymes are shown in red. The catalytic residues are indicated by red rectangles, and crucial residues, as the “fixer” (see text), are indicated by blue rectangles. The catalytic base of bGA and the corresponding residue in GT-36 are highlighted with cyan. The residues involved in the recognition of the GlcNAc are indicated by orange rectangles. The residues involved in the recognition of sulfate in ChBP and phosphate in MalP are indicated by green rectangles. CBP was from Cellvibrio gilvus and CDP from Clostridium thermocellum YM4. Structure 2004 12, 937-947DOI: (10.1016/j.str.2004.03.027)

Figure 3 Differences between the GlcNAc-free and GlcNAc Complex Structures Observed in the α-Helical Barrel Domain (A) Partially disordered loop region comprising residues 485–499 in the GlcNAc-free structure. A 2|Fobs| − |Fcalc| electron density map contoured at 0.8σ is shown around the loop. A disulfide bond is formed between C424 and C493. (B) The 485–499 loop region in the GlcNAc complex structure. The view is from the same angle as in (A). A 2|Fobs| − |Fcalc| electron density map contoured at 1.0σ is shown. The disulfide bond is broken and the loop is reversed compared with in the GlcNAc-free structure, and the loop shows a well-ordered structure. This conformational change has occurred at the hinge comprising the G485, G497, G498, and G499 residues. Structure 2004 12, 937-947DOI: (10.1016/j.str.2004.03.027)

Figure 4 Active Site of ChBP (A) Stereoview of a wireframe model of ChBP, and the |Fobs| − |Fcalc| electron density of the bound GlcNAc molecules, chloride, and sulfate. GlcNAc(−1) and GlcNAc(+1) are shown as ball-and-stick model and labeled (−1) and (+1), respectively. The chloride ion is shown as a gray sphere. Sulfate ion is shown as a ball-and-stick model (green). A |Fobs| − |Fcalc| omit map of GlcNAc molecules and chloride in the GlcNAc complex (red), and that of sulfate in the GlcNAc-SO4 complex structure (blue) are shown with contouring at 3.0σ. The residues involved in GlcNAc recognition (D350 and W490), sulfate recognition (R333, H644, and T709), and catalysis (D492) are labeled. GlcNAc(−1) takes on the β-anomer configuration whereas GlcNAc(+1) takes on a mixture of α- and β-anomer configurations (indicated by an arrow). (B) Schematic drawing of the atoms and interactions involved in the recognition of GlcNAc molecules and sulfate in the GlcNAc-SO4 complex structure. C, N, O, and S atoms, and water molecules are colored black, blue, red, green, and cyan, respectively. Broken lines and semicircles indicate hydrogen bonds and hydrophobic interactions, respectively. The catalytic residue (D492) is colored red. Q168 of the next subunit also contributes to the active site pocket formation and substrate recognition. Structure 2004 12, 937-947DOI: (10.1016/j.str.2004.03.027)

Figure 5 Stereoview of ChBP, bGA, and MalP Superimposed at the Active Site Backbone traces of ChBP, bGA, and MalP are colored yellow, green, and red, respectively. Bound GlcNAc molecules in ChBP (yellow) and acarbose in bGA (green) are shown as a wireframe model. The structurally conserved residues are shown as a ball-and-stick model and labeled in the order corresponding to ChBP, bGA, and MalP. Sulfate in ChBP and phosphate in MalP are also shown as a ball-and-stick model, and the water molecule in bGA, which attacks the glycosidic bond, is shown as a cyan sphere. The C, N, O, P, and S atoms are colored black, blue, red, yellow, and green, respectively. The structures were superimposed using the rotation and translation vectors generated with the Dali server. Structure 2004 12, 937-947DOI: (10.1016/j.str.2004.03.027)

Figure 6 Schematic Reaction Mechanisms of ChBP and Hydrolytic Enzymes (A) ChBP; (B) inverting GHs. Structure 2004 12, 937-947DOI: (10.1016/j.str.2004.03.027)

Figure 7 Active Site Pocket Formation through the Dimeric Interaction The molecular surface of one subunit of ChBP and a ribbon diagram of the next subunit are shown. Bound GlcNAc molecules (yellow) and the residues in the active site pocket formation (red) are shown as a ball-and-stick model. Structure 2004 12, 937-947DOI: (10.1016/j.str.2004.03.027)