5B4S

Crystal Structure of GH80 chitosanase from Mitsuaria chitosanitabida

• PDB DOI: https://doi.org/10.2210/pdb5B4S/pdb

• Classification: HYDROLASE
• Organism(s): Roseateles chitosanitabidus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-04-19 Released: 2017-02-01 
• Deposition Author(s): Kumasaka, T., Yorinaga, Y., Yamamoto, M., Hamada, K., Kawamukai, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.192 
• R-Value Work: 0.160 
• R-Value Observed: 0.161 

Literature

Crystal structure of a family 80 chitosanase from Mitsuaria chitosanitabida

Yorinaga, Y., Kumasaka, T., Yamamoto, M., Hamada, K., Kawamukai, M.

(2017) FEBS Lett 591: 540-547

• PubMed: 28084023 
• DOI: https://doi.org/10.1002/1873-3468.12557
• Primary Citation of Related Structures:  
  5B4S


• PubMed Abstract: 
  

  Chitosanases belong to glycoside hydrolase families 5, 7, 8, 46, 75 and 80 and hydrolyse glucosamine polymers produced by partial or full deacetylation of chitin. Herein, we determined the crystal structure of chitosanase from the β-proteobacterium, Mitsuaria chitosanitabida, (McChoA) at 1.75 Å resolution; the first structure of a family 80 chitosanase. McChoA is a 34 kDa extracellular protein of 301 amino acids that fold into two (upper and lower) globular domains with an active site cleft between them. Key substrate-binding features are conserved with family 24 lysozymes and family 46 chitosanases. The distance between catalytic residues E41 and E61 (10.8 Å) indicates an inverting type mechanism. Uniquely, three disulphide bridges and the C terminus might contribute to enzyme activity.

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Organizational Affiliation: 

Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, Matsue, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 71.37 kDa 
• Atom Count: 5,424 
• Modelled Residue Count: 619 
• Deposited Residue Count: 650 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitosanase	A, B	325	Roseateles chitosanitabidus	Mutation(s): 0  Gene Names: choA
UniProt
Find proteins for O82856 (Roseateles chitosanitabidus) Explore O82856  Go to UniProtKB:  O82856

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.192 
• R-Value Work: 0.160 
• R-Value Observed: 0.161 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.879	α = 90
b = 56.366	β = 90
c = 207.081	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-01 
Deposition Author(s): Kumasaka, T., Yorinaga, Y., Yamamoto, M., Hamada, K., Kawamukai, M.

Revision History  

• Version 1.0: 2017-02-01
  Type: Initial release
  
• Version 1.1: 2017-03-08
  Changes: Database references
• Version 1.2: 2020-02-26
  Changes: Data collection