The crystal structure of the active form chitosanase from Bacillus sp. K17 at pH6.4

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.167 

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Crystal structure of family GH-8 chitosanase with subclass II specificity from Bacillus sp. K17

Adachi, W.Sakihama, Y.Shimizu, S.Sunami, T.Fukazawa, T.Suzuki, M.Yatsunami, R.Nakamura, S.Takenaka, A.

(2004) J Mol Biol 343: 785-795

  • DOI: https://doi.org/10.1016/j.jmb.2004.08.028
  • Primary Citation of Related Structures:  
    1V5C, 1V5D

  • PubMed Abstract: 

    Crystal structures of chitosanase from Bacillus sp. K17 (ChoK) have been determined at 1.5 A resolution in the active form and at 2.0 A resolution in the inactive form. This enzyme belongs to the family GH-8, out of 93 glycoside hydrolase families, and exhibits the substrate specificity of subclass II chitosanase. The catalytic site is constructed on the scaffold of a double-alpha(6)/alpha(6)-barrel, which is formed by six repeating helix-loop-helix motifs. This structure is quite different from those of the GH-46 chitosanases and of GH-5. Structural comparison with CelA (a cellulase belonging to the same family GH-8) suggests that the proton donor Glu122 is conserved, but the proton acceptor is the inserted Glu309 residue, and that the corresponding Asp278 residue in CelA is inactivated in ChoK. The four acidic residues, Asp179, Glu309, Asp183 and Glu107, can be involved in substrate recognition through interactions with the amino groups of the glucosamine residues bound in the -3, -2, -1 and +1 sites, respectively. The hydrophobic Trp235, Trp166, Phe413 and Tyr318 residues are highly conserved for binding of the hexose rings at the -3, -2, +1 and +2 sites, respectively. These structural features indicate that enzymes in GH-8 can be further divided into three subfamilies. Different types of chitosanases are discussed in terms of convergent evolution from different structural ancestors.

  • Organizational Affiliation

    Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
386Bacillus sp. (in: firmicutes)Mutation(s): 0 
Find proteins for Q9ALZ1 (Bacillus sp. KCTC 0377BP)
Explore Q9ALZ1 
Go to UniProtKB:  Q9ALZ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ALZ1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PIN

Download Ideal Coordinates CCD File 
C8 H18 N2 O6 S2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.804α = 90
b = 98.144β = 90
c = 115.78γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations