1WVU

Crystal structure of chitinase C from Streptomyces griseus HUT6037

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural Studies of a Two-domain Chitinase from Streptomyces griseus HUT6037

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

(2006) J Mol Biol 358: 472-484

  • DOI: 10.1016/j.jmb.2006.02.013
  • Primary Citation of Related Structures:  
    1WVV, 1WVU, 2DBT

  • 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 ...

    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.

    Related Citations: 
    • Functional analysis of the chitin-binding domain of a family 19 chitinase from Streptomyces griseus HUT6037: substrate-binding affinity and cis-dominant increase of antifungal function
      Itoh, Y., Kawase, T., Nikaidou, N., Fukada, H., Mitsutomi, M., Watanabe, T., Itoh, Y.
      (2002) Biosci Biotechnol Biochem 66: 1084
    • Family 19 chitinases of Streptomyces species: characterization and distribution
      Watanabe, T., Kanai, R., Kawase, T., Tanabe, T., Mitsutomi, M., Sakuda, S., Miyashita, K.
      (1999) Microbiology (N Y) 145: 3353
    • A modular family 19 chitinase found in the prokaryotic organism Streptomyces griseus HUT 6037
      Ohno, T., Armand, S., Hata, T., Nikaidou, N., Henrissat, B., Mitsutomi, M., Watanabe, T.
      (1996) J Bacteriol 178: 5065
    Organizational Affiliation: 

    Department of BioEngineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
chitinase C A, B265Streptomyces griseusMutation(s): 0 
Gene Names: chiC, NCTC13033_02762
EC: 3.2.1.14
Find proteins for O50152 (Streptomyces griseus)
Explore O50152 
Go to UniProtKB:  O50152
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.85α = 90
b = 127.85β = 90
c = 127.85γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MLPHAREphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-27
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance