PDBsum entry: 1wvu

Hydrolase

PDB id: 1wvu

Contents

Protein chains

209 a.a. *

253 a.a. *

Metals

_CL ×13

Waters ×181

* Residue conservation analysis

PDB id:

1wvu

Name:

Hydrolase

Title:

Crystal structure of chitinasE C from streptomyces griseus h

Structure:

ChitinasE C. Chain: a, b. Fragment: residues 30-294. Synonym: glycosyl hydrolase. Engineered: yes

Source:

Streptomyces griseus. Organism_taxid: 1911. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Hexamer (from PQS)

Resolution:

2.45Å R-factor: 0.175 R-free: 0.223

Authors:

Y.Kezuka,T.Watanabe,T.Nonaka

Key ref:

Y.Kezuka et al. (2006). Structural studies of a two-domain chitinase from Streptomyces griseus HUT6037. J Mol Biol, 358, 472-484. PubMed id: 16516924 DOI: 10.1016/j.jmb.2006.02.013

Date:

27-Dec-04 Release date: 27-Dec-05

Protein chain

O50152  (O50152_STRGR) -  Chitinase C

Seq: 294 a.a.

Struc: 209 a.a.

Protein chain

O50152  (O50152_STRGR) -  Chitinase C

Seq: 294 a.a.

Struc: 253 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (1 term)
• Biological process: carbohydrate metabolic process (3 terms)
• Biochemical function: carbohydrate binding (3 terms)

DOI no: 10.1016/j.jmb.2006.02.013

J Mol Biol 358:472-484 (2006)

PubMed id: 16516924

Structural studies of a two-domain chitinase from Streptomyces griseus HUT6037.

Y.Kezuka, M.Ohishi, Y.Itoh, J.Watanabe, M.Mitsutomi, T.Watanabe, T.Nonaka.

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.

Selected figure(s)

Figure 1.
Figure 1. Overall structure of ChiC (chain B of form I crystal). Two catalytic residues, two surface-exposed aromatic residues, and all cysteine residues are indicated by ball-and-stick drawings. No electron density can be seen in the region corresponding to Thr80 to Asn89 (TGGEGPGGNN) of chain B of the form I crystal (shown by a dotted line). The distance between the C^a atoms of Gly79 and Gly90 is 28.3 Å, and the approximate maximum dimension of the molecule is 80 Å. CatD[ChiC] has four cysteine residues that form two disulfide bonds (Cys166-Cys174 and Cys262 -Cys294) that correspond to those of barley chitinase (Cys97-Cys105 and Cys204-Cys236).

Figure 4.
Figure 4. Interactions between ChBD[ChiC] and tri-N-acetylchitotriose. The ligand molecule is well bound on the binding site by two stacking interactions (Trp59-NAG1 and Trp60-NAG3) and two hydrogen bonds (between Trp60-N and NAG2-O7 (carbonyl moiety of N-acetyl group of NAG2) and Trp59-NE1 and NAG2-O6). Hydrogen bonds are indicated by broken lines. Only Trp59 and Trp60 are responsible for the interactions.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 358, 472-484) copyright 2006.

Figures were selected by the author.