Crystal structure of a bacterial fucodiase in complex with 1-((1R,2R,3R,4R,5R,6R)-2,3,4-trihydroxy-5-methyl-7-azabicyclo[4.1.0]heptan-7-yl)ethan-1-one

Experimental Data Snapshot

  • Resolution: 1.64 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

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In vitroandin vivocomparative and competitive activity-based protein profiling of GH29 alpha-l-fucosidases.

Jiang, J.Kallemeijn, W.W.Wright, D.W.van den Nieuwendijk, A.M.C.H.Rohde, V.C.Folch, E.C.van den Elst, H.Florea, B.I.Scheij, S.Donker-Koopman, W.E.Verhoek, M.Li, N.Schurmann, M.Mink, D.Boot, R.G.Codee, J.D.C.van der Marel, G.A.Davies, G.J.Aerts, J.M.F.G.Overkleeft, H.S.

(2015) Chem Sci 6: 2782-false

  • DOI: https://doi.org/10.1039/c4sc03739a
  • Primary Citation of Related Structures:  
    4WSJ, 4WSK

  • PubMed Abstract: 

    GH29 α-l-fucosidases catalyze the hydrolysis of α-l-fucosidic linkages. Deficiency in human lysosomal α-l-fucosidase (FUCA1) leads to the recessively inherited disorder, fucosidosis. Herein we describe the development of fucopyranose-configured cyclophellitol aziridines as activity-based probes (ABPs) for selective in vitro and in vivo labeling of GH29 α-l-fucosidases from bacteria, mice and man. Crystallographic analysis on bacterial α-l-fucosidase confirms that the ABPs act by covalent modification of the active site nucleophile. Competitive activity-based protein profiling identified l-fuconojirimycin as the single GH29 α-l-fucosidase inhibitor from eight configurational isomers.

  • Organizational Affiliation

    Leiden Institute of Chemistry , Leiden University , P. O. Box 9502 , 2300 RA Leiden , The Netherlands . Email: h.s.overkleeft@chem.leidenuniv.nl ; Email: j.m.aerts@amc.uva.nl.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
445Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
Gene Names: BT_2970
Find proteins for Q8A3I4 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A3I4 
Go to UniProtKB:  Q8A3I4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A3I4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.64 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.48α = 90
b = 186.98β = 94.17
c = 98.19γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomA0067812

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2015-05-27
    Changes: Database references
  • Version 2.0: 2017-08-30
    Changes: Advisory, Atomic model, Author supporting evidence, Derived calculations
  • Version 2.1: 2018-04-18
    Changes: Data collection, Database references
  • Version 2.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description