2D05

Chitosanase From Bacillus circulans mutant K218P


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Bacillus circulans MH-K1 Chitosanase: Amino Acid Residues Responsible for Substrate Binding

Fukamizo, T.Amano, S.Yamaguchi, K.Yoshikawa, T.Katsumi, T.Saito, J.Suzuki, M.Miki, K.Nagata, Y.Ando, A.

(2005) J Biochem 138: 563-569

  • DOI: 10.1093/jb/mvi156
  • Primary Citation of Related Structures:  
    2D05

  • PubMed Abstract: 
  • To identify the amino acids responsible for the substrate binding of chitosanase from Bacillus circulans MH-K1 (MH-K1 chitosanase), Tyr148 and Lys218 of the chitosanase were mutated to serine and proline, respectively, and the mutated chitosanases were characterized ...

    To identify the amino acids responsible for the substrate binding of chitosanase from Bacillus circulans MH-K1 (MH-K1 chitosanase), Tyr148 and Lys218 of the chitosanase were mutated to serine and proline, respectively, and the mutated chitosanases were characterized. The enzymatic activities of Y148S and K218P were found to be 12.5% and 0.16% of the wild type, respectively. When the (GlcN)3 binding ability to the chitosanase was evaluated by fluorescence spectroscopy and thermal unfolding experiments, the binding abilities of both mutant enzymes were markedly reduced as compared with the wild type enzyme. The affinity of the enzyme for the trisaccharide decreased by 1.0 kcal/mol of binding free energy for Y148S, and 3.7 kcal/mol for K218P. The crystal structure of K218P revealed that Pro218 forms a cis-peptide bond and that the state of the flexible loop containing the 218th residue is considerably affected by the mutation. Thus, we conclude that the flexible loop containing Lys218 plays an important role in substrate binding, and that the role of Tyr148 is less critical, but still important, due to a stacking interaction or hydrogen bond.


    Related Citations: 
    • Crystal structure of chitosanase from Bacillus circulans MH-K1 at 1.6-A resolution and its substrate recognition mechanism
      Saito, J., Kita, A., Higuchi, Y., Nagata, Y., Ando, A., Miki, K.
      (1999) J Biol Chem 274: 30818
    • Crystallization and preliminary X-ray crystallographic analysis of chitosanase from Bacillus circulans MH-K1
      Saito, J.I., Nagata, Y., Ando, A., Kita, A., Miki, K.
      (1995) Acta Crystallogr D Biol Crystallogr 51: 856

    Organizational Affiliation

    Department of Advanced Bioscience, Kinki University, 3327-204 Nakamachi, Nara 631-8505. fukamizo@nara.kindai.ac.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ChitosanaseA259Niallia circulansMutation(s): 1 
Gene Names: csn
EC: 3.2.1.132
UniProt
Find proteins for P33673 (Niallia circulans)
Explore P33673 
Go to UniProtKB:  P33673
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33673
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.3α = 90
b = 128.1β = 90
c = 57.8γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-06
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations