6O1A

Alpha-L-fucosidase AlfC from Lactobacillus casei in complex with alpha-L-fucose product


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure and dynamics of an alpha-fucosidase reveal a mechanism for highly efficient IgG transfucosylation.

Klontz, E.H.Li, C.Kihn, K.Fields, J.K.Beckett, D.Snyder, G.A.Wintrode, P.L.Deredge, D.Wang, L.X.Sundberg, E.J.

(2020) Nat Commun 11: 6204-6204

  • DOI: https://doi.org/10.1038/s41467-020-20044-z
  • Primary Citation of Related Structures:  
    6O18, 6O1A, 6O1C, 6O1I, 6O1J, 6OHE

  • PubMed Abstract: 

    Fucosylation is important for the function of many proteins with biotechnical and medical applications. Alpha-fucosidases comprise a large enzyme family that recognizes fucosylated substrates with diverse α-linkages on these proteins. Lactobacillus casei produces an α-fucosidase, called AlfC, with specificity towards α(1,6)-fucose, the only linkage found in human N-glycan core fucosylation. AlfC and certain point mutants thereof have been used to add and remove fucose from monoclonal antibody N-glycans, with significant impacts on their effector functions. Despite the potential uses for AlfC, little is known about its mechanism. Here, we present crystal structures of AlfC, combined with mutational and kinetic analyses, hydrogen-deuterium exchange mass spectrometry, molecular dynamic simulations, and transfucosylation experiments to define the molecular mechanisms of the activities of AlfC and its transfucosidase mutants. Our results indicate that AlfC creates an aromatic subsite adjacent to the active site that specifically accommodates GlcNAc in α(1,6)-linkages, suggest that enzymatic activity is controlled by distinct open and closed conformations of an active-site loop, with certain mutations shifting the equilibrium towards open conformations to promote transfucosylation over hydrolysis, and provide a potentially generalizable framework for the rational creation of AlfC transfucosidase mutants.


  • Organizational Affiliation

    Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AlfC
A, B, C, D
345Lacticaseibacillus caseiMutation(s): 0 
UniProt
Find proteins for A0A422MHI3 (Lacticaseibacillus paracasei)
Explore A0A422MHI3 
Go to UniProtKB:  A0A422MHI3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A422MHI3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.983α = 90
b = 138.236β = 90
c = 264.44γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2020-12-16
    Changes: Database references, Structure summary
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description