7VI8

Crystal structure of ChbG

• PDB DOI: https://doi.org/10.2210/pdb7VI8/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae MGH 78578
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-09-26 Released: 2022-09-07 
• Deposition Author(s): Lee, S.Y., Park, H.H.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.257 
• R-Value Work: 0.220 

Literature

Crystal structure of ChbG from Klebsiella pneumoniae reveals the molecular basis of diacetylchitobiose deacetylation.

Lee, S.Y., Pardhe, B.D., Oh, T.J., Park, H.H.

(2022) Commun Biol 5: 862-862

• PubMed: 36002585 
• DOI: https://doi.org/10.1038/s42003-022-03824-9
• Primary Citation of Related Structures:  
  7VI8


• PubMed Abstract: 
  

  The chitobiose (chb) operon is involved in the synthesis of chitooligosaccharide and is comprised of a BCARFG gene cluster. ChbG encodes a chitooligosaccharide deacetylase (CDA) which catalyzes the removal of one acetyl group from N,N'-diacetylchitobiose. It is considered a novel type of CDA due to its lack of sequence homology. Although there are various structural studies of CDAs linked to the kinetic properties of the enzyme, the structural information of ChbG is unavailable. In this study, the crystal structure of ChbG from Klebsiella pneumoniae is provided. The molecular basis of deacetylation of diacetylchitobiose by ChbG is determined based on structural analysis, mutagenesis, biophysical analysis, and in silico docking of the substrate, diacetylchitobiose. This study contributes towards a deeper understanding of chitin and chitosan biology, as well as provides a platform to engineer CDA biocatalysts.

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Organizational Affiliation: 

College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56.11 kDa 
• Atom Count: 4,285 
• Modelled Residue Count: 504 
• Deposited Residue Count: 508 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitooligosaccharide deacetylase	A, B	254	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0  Gene Names: chbG, KPN78578_12070, KPN_01235 EC: 3.5.1.105
UniProt
Find proteins for A6T7U7 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6T7U7  Go to UniProtKB:  A6T7U7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT (Subject of Investigation/LOI)	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.257 
• R-Value Work: 0.220 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.23	α = 90
b = 67.03	β = 90
c = 146.4	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-09-07 
Deposition Author(s): Lee, S.Y., Park, H.H.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2022-09-07
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description