Structural studies of a two-domain chitinase from Streptomyces griseus HUT6037.
Chitinase C (ChiC) from Streptomyces griseus HUT6037 was the first glycoside hydrolase family 19 chitinase that was found in an organism other than higher plants. An N-terminal chitin-binding domain and a C-terminal catalytic domain connected by a linker peptide constitute ChiC. We determined the crystal structure of full-length ChiC, which is the only representative of the two-domain chitinases in the family. The catalytic domain has an alpha-helix-rich fold with a deep cleft containing a catalytic site, and lacks three loops on the domain surface compared with the catalytic domain of plant chitinases. The chitin-binding domain is an all-beta protein with two tryptophan residues (Trp59 and Trp60) aligned on the surface. We suggest the binding mechanism of tri-N-acetylchitotriose onto the chitin-binding domain on the basis of molecular dynamics (MD) simulations. In this mechanism, the ligand molecule binds well on the surface-exposed binding site through two stacking interactions and two hydrogen bonds and only Trp59 and Trp60 are involved in the binding. Furthermore, the flexibility of the Trp60 side-chain, which may be involved in adjusting the binding surface to fit the surface of crystalline chitin by the rotation of chi2 angle, is shown.
Kezuka
Yuichiro
Y
Department of BioEngineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan.
Ohishi
Manabu
M
Itoh
Yoshikane
Y
Watanabe
Jun
J
Mitsutomi
Masaru
M
Watanabe
Takeshi
T
Nonaka
Takamasa
T
D000595:Amino Acid Sequence; D020134:Catalytic Domain; D002686:Chitin / Q000378:metabolism; D002688:Chitinases / Q000737:chemistry* / Q000378:metabolism; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D008024:Ligands; D008969:Molecular Sequence Data; D010940:Plant Proteins; D017386:Sequence Homology, Amino Acid; D013305:Streptomyces griseus / Q000201:enzymology*; D014312:Trisaccharides / Q000378:metabolism; D014364:Tryptophan / Q000737:chemistry
D008024:Ligands; D010940:Plant Proteins; D014312:Trisaccharides; D002686:Chitin; C019117:N,N',N''-triacetylchitotriose; D014364:Tryptophan; D002688:Chitinases; C119825:chitinase C