3W6D
Crystal structure of catalytic domain of chitinase from Ralstonia sp. A-471 (E141Q) in complex with tetrasaccharide
Summary for 3W6D
| Entry DOI | 10.2210/pdb3w6d/pdb |
| Related | 3W6B 3W6C 3W6E 3W6F |
| Related PRD ID | PRD_900017 |
| Descriptor | Lysozyme-like chitinolytic enzyme, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (4 entities in total) |
| Functional Keywords | gh family 23, enzyme, glycoside hydrolase, chitinase, hydrolase |
| Biological source | Ralstonia |
| Total number of polymer chains | 4 |
| Total formula weight | 84461.81 |
| Authors | Arimori, T.,Kawamoto, N.,Okazaki, N.,Nakazawa, M.,Miyatake, K.,Fukamizo, T.,Ueda, M.,Tamada, T. (deposition date: 2013-02-14, release date: 2013-05-15, Last modification date: 2023-11-08) |
| Primary citation | Arimori, T.,Kawamoto, N.,Shinya, S.,Okazaki, N.,Nakazawa, M.,Miyatake, K.,Fukamizo, T.,Ueda, M.,Tamada, T. Crystal Structures of the Catalytic Domain of a Novel Glycohydrolase Family 23 Chitinase from Ralstonia sp. A-471 Reveals a Unique Arrangement of the Catalytic Residues for Inverting Chitin Hydrolysis J.Biol.Chem., 288:18696-18706, 2013 Cited by PubMed Abstract: Chitinase C from Ralstonia sp. A-471 (Ra-ChiC) has a catalytic domain sequence similar to goose-type (G-type) lysozymes and, unlike other chitinases, belongs to glycohydrolase (GH) family 23. Using NMR spectroscopy, however, Ra-ChiC was found to interact only with the chitin dimer but not with the peptidoglycan fragment. Here we report the crystal structures of wild-type, E141Q, and E162Q of the catalytic domain of Ra-ChiC with or without chitin oligosaccharides. Ra-ChiC has a substrate-binding site including a tunnel-shaped cavity, which determines the substrate specificity. Mutation analyses based on this structural information indicated that a highly conserved Glu-141 acts as a catalytic acid, and that Asp-226 located at the roof of the tunnel activates a water molecule as a catalytic base. The unique arrangement of the catalytic residues makes a clear contrast to the other GH23 members and also to inverting GH19 chitinases. PubMed: 23658014DOI: 10.1074/jbc.M113.462135 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.15 Å) |
Structure validation
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