8JQE

Structure of CmCBDA in complex with Mn2+ and glycerol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural Insights into the Catalytic Activity of Cyclobacterium marinum N -Acetylglucosamine Deacetylase.

Hu, S.Xu, L.Xie, C.Hong, J.

(2024) J Agric Food Chem 72: 783-793

  • DOI: https://doi.org/10.1021/acs.jafc.3c06146
  • Primary Citation of Related Structures:  
    8JQE, 8JQF

  • PubMed Abstract: 

    N -Acetylglucosamine deacetylase from Cyclobacterium marinum (CmCBDA) is a highly effective and selective biocatalyst for the production of d-glucosamine (GlcN) from N -acetylglucosamine (GlcNAc). However, the underlying catalytic mechanism remains elusive. Here, we show that CmCBDA is a metalloenzyme with a preference for Ni 2+ over Mn 2+ . Crystal structures of CmCBDA in complex with Ni 2+ and Mn 2+ revealed slight remodeling of the CmCBDA active site by the metal ions. We also demonstrate that CmCBDA exists as a mixture of homodimers and monomers in solution, and dimerization is indispensable for catalytic activity. A mutagenesis analysis also indicated that the active site residues Asp22, His72, and His143 as well as the residues involved in dimerization, Pro52, Trp53, and Tyr55, are essential for catalytic activity. Furthermore, a mutation on the protein surface, Lys219Glu, resulted in a 2.3-fold improvement in the deacetylation activity toward GlcNAc. Mechanistic insights obtained here may facilitate the development of CmCBDA variants with higher activities.


  • Organizational Affiliation

    School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
YdjC family protein
A, B
305Cyclobacterium marinumMutation(s): 0 
Gene Names: Cycma_4778
UniProt
Find proteins for G0J5L4 (Cyclobacterium marinum (strain ATCC 25205 / DSM 745 / LMG 13164 / NCIMB 1802))
Explore G0J5L4 
Go to UniProtKB:  G0J5L4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0J5L4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.617α = 90
b = 60.27β = 111.11
c = 87.444γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2024-01-03 
  • Deposition Author(s): Li, X.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-03
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Database references