3W6C

Crystal structure of catalytic domain of chitinase from Ralstonia sp. A-471 in complex with disaccharide

Summary for 3W6C

• Entry DOI: 10.2210/pdb3w6c/pdb
• Related: 3W6B 3W6D 3W6E 3W6F
• Descriptor: Lysozyme-like chitinolytic enzyme, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose (3 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: 84316.60

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

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: 23658014
DOI: 10.1074/jbc.M113.462135

Experimental method

X-RAY DIFFRACTION (2 Å)