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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 

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:  

  • 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 li ...

    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
    • 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
    • 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 145: 3353


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
chitinase C
A, B
265Streptomyces griseusMutation(s): 0 
Gene Names: chiC
EC: 3.2.1.14
Find proteins for O50152 (Streptomyces griseus)
Go to UniProtKB:  O50152
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.172 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 127.850α = 90.00
b = 127.850β = 90.00
c = 127.850γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MLPHAREphasing
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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