1V5D

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1016/j.jmb.2004.08.028
  • Primary Citation of Related Structures:  

  • 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, a ...

    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.


    Related Citations: 
    • Crystallization and preliminary X-ray analyses of the active and the inactive forms of family GH-8 chitosanase with subclass II specificity from Bacillus sp. strain K17
      Sakihama, Y.,Adachi, W.,Shimizu, S.,Sunami, T.,Fukazawa, T.,Suzuki, M.,Yatsunami, R.,Nakamura, S.,Takenaka, A.
      (2004) ACTA CRYSTALLOGR.,SECT.D 60: 2081


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
chitosanase
A, B
386Bacillus sp. KCTC 0377BPMutation(s): 0 
Gene Names: csn45
EC: 3.2.1.-
Find proteins for Q9ALZ1 (Bacillus sp. KCTC 0377BP)
Go to UniProtKB:  Q9ALZ1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PIN
Query on PIN

Download SDF File 
Download CCD File 
B
PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID)
PIPES; 1,4-PIPERAZINEDIETHANESULFONIC ACID
C8 H18 N2 O6 S2
IHPYMWDTONKSCO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 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 = 90.00
b = 98.144β = 90.00
c = 115.780γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance