6Y0R | pdb_00006y0r

Chitooligosaccharide oxidase

• PDB DOI: https://doi.org/10.2210/pdb6Y0R/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Fusarium graminearum PH-1
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2020-02-10 Released: 2020-06-03 
• Deposition Author(s): Savino, S., Fraaije, M.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.198 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.173 (DCC) 

Starting Model: experimental

Literature

Analysis of the structure and substrate scope of chitooligosaccharide oxidase reveals high affinity for C2-modified glucosamines.

Savino, S., Jensen, S., Terwisscha van Scheltinga, A., Fraaije, M.W.

(2020) FEBS Lett 594: 2819-2828

• PubMed: 32491191 
• DOI: https://doi.org/10.1002/1873-3468.13854
• Primary Citation Related Structures: 
  6Y0R


• PubMed Abstract: 
  

  Chitooligosaccharide oxidase (ChitO) is a fungal carbohydrate oxidase containing a bicovalently bound FAD cofactor. The enzyme is known to catalyse the oxidation of chitooligosaccharides, oligomers of N-acetylated glucosamines derived from chitin degradation. In this study, the unique substrate acceptance was explored by testing a range of N-acetyl-d-glucosamine derivatives, revealing that ChitO preferentially accepts carbohydrates with a hydrophobic group attached to C2. The enzyme also accepts streptozotocin, a natural product used to treat tumours. Elucidation of the crystal structure provides an explanation for the high affinity towards C2-decorated glucosamines: the active site has a secondary binding pocket that accommodates groups attached at C2. Docking simulations are fully in line with the observed substrate preference. This work expands the knowledge on this versatile enzyme.

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Organizational Affiliation: 
• Molecular Enzymology Group, University of Groningen, The Netherlands.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 53.45 kDa 
• Atom Count: 3,933 
• Modeled Residue Count: 468 
• Deposited Residue Count: 492 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitooligosaccharide oxidase	A [auth AAA]	492	Fusarium graminearum PH-1	Mutation(s): 0  Gene Names: chitO, FGRAMPH1_01T20975 EC: 1.1.3
UniProt
Find proteins for I1S2K2 (Gibberella zeae (strain ATCC MYA-4620 / CBS 123657 / FGSC 9075 / NRRL 31084 / PH-1)) Explore I1S2K2  Go to UniProtKB:  I1S2K2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	B [auth AAA]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.198 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.173 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.686	α = 90
b = 74.247	β = 90
c = 97.157	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-03 
Deposition Author(s): Savino, S., Fraaije, M.W.

Revision History  

• Version 1.0: 2020-06-03
  Type: Initial release
  
• Version 1.1: 2020-06-17
  Changes: Database references
• Version 1.2: 2020-12-16
  Changes: Database references
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary