3WH1

Crystal Structure of a Family GH19 Chitinase from Bryum coronatum in complex with (GlcNAc)4 at 1.0 A resolution

Summary for 3WH1

• Entry DOI: 10.2210/pdb3wh1/pdb
• Related: 4IJ4
• Descriptor: Chitinase A, 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, 1,2-ETHANEDIOL, ... (4 entities in total)
• Functional Keywords: chitinase, hydrolase, carbohydrate
• Biological source: Bryum coronatum
• Total number of polymer chains: 1
• Total formula weight: 23818.05

Authors

Numata, T.,Umemoto, N.,Ohnuma, T.,Fukamizo, T. (deposition date: 2013-08-21, release date: 2014-03-26, Last modification date: 2024-10-30)

Primary citation

Ohnuma, T.,Umemoto, N.,Nagata, T.,Shinya, S.,Numata, T.,Taira, T.,Fukamizo, T.
Crystal structure of a "loopless" GH19 chitinase in complex with chitin tetrasaccharide spanning the catalytic center.
Biochim.Biophys.Acta, 1844:793-802, 2014

PubMed Abstract: The structure of a GH19 chitinase from the moss Bryum coronatum (BcChi-A) in complex with the substrate was examined by X-ray crystallography and NMR spectroscopy in solution. The X-ray crystal structure of the inactive mutant of BcChi-A (BcChi-A-E61A) liganded with chitin tetramer (GlcNAc)4 revealed a clear electron density of the tetramer bound to subsites -2, -1, +1, and +2. Individual sugar residues were recognized by several amino acids at these subsites through a number of hydrogen bonds. This is the first crystal structure of GH19 chitinase liganded with oligosaccharide spanning the catalytic center. NMR titration experiments of chitin oligosaccharides into the BcChi-A-E61A solution showed that the binding mode observed in the crystal structure is similar to that in solution. The C-1 carbon of -1 GlcNAc, the Oε1 atom of the catalytic base (Glu70), and the Oγ atom of Ser102 form a "triangle" surrounding the catalytic water, and the arrangement structurally validated the proposed catalytic mechanism of GH19 chitinases. The glycosidic linkage between -1 and +1 sugars was found to be twisted and under strain. This situation may contribute to the reduction of activation energy for hydrolysis. The complex structure revealed a more refined mechanism of the chitinase catalysis.

PubMed: 24582745
DOI: 10.1016/j.bbapap.2014.02.013

Experimental method

X-RAY DIFFRACTION (1 Å)