2DBT

Crystal structure of chitinase C from Streptomyces griseus HUT6037

Summary for 2DBT

• Entry DOI: 10.2210/pdb2dbt/pdb
• Related: 1WVU 1WVV
• Descriptor: chitinase C, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID (3 entities in total)
• Functional Keywords: family 19 chitinase, hydrolase
• Biological source: Streptomyces griseus
• Total number of polymer chains: 3
• Total formula weight: 86206.42

Authors

Kezuka, Y.,Watanabe, T.,Nonaka, T. (deposition date: 2005-12-16, release date: 2006-03-28, Last modification date: 2024-11-13)

Primary citation

Kezuka, Y.,Ohishi, M.,Itoh, Y.,Watanabe, J.,Mitsutomi, M.,Watanabe, T.,Nonaka, T.
Structural Studies of a Two-domain Chitinase from Streptomyces griseus HUT6037
J.Mol.Biol., 358:472-484, 2006

PubMed Abstract: 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.

PubMed: 16516924
DOI: 10.1016/j.jmb.2006.02.013

Experimental method

X-RAY DIFFRACTION (3.14 Å)