2DBT

Crystal structure of chitinase C from Streptomyces griseus HUT6037


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

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:  
    2DBT, 1WVV, 1WVU

  • 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 (Pt 12): 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 CA, B, C265Streptomyces griseusMutation(s): 0 
Gene Names: chiCNCTC13033_02762
EC: 3.2.1.14
UniProt
Find proteins for O50152 (Streptomyces griseus)
Explore O50152 
Go to UniProtKB:  O50152
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
D [auth A], E [auth B], F [auth C]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.116α = 90
b = 153.116β = 90
c = 90.031γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance