7UZ1

Structure of beta-glycosidase from Sulfolobus solfataricus in complex with C5a-bromo-valienide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.189 

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This is version 1.2 of the entry. See complete history


Literature

Vinyl Halide-Modified Unsaturated Cyclitols are Mechanism-Based Glycosidase Inhibitors.

Danby, P.M.Jeong, A.Sim, L.Sweeney, R.P.Wardman, J.F.Karimi, R.Geissner, A.Worrall, L.J.Reid, J.P.Strynadka, N.C.J.Withers, S.G.

(2023) Angew Chem Int Ed Engl 62: e202301258-e202301258

  • DOI: https://doi.org/10.1002/anie.202301258
  • Primary Citation of Related Structures:  
    7UZ1, 7UZ2

  • PubMed Abstract: 

    Suitably configured allyl ethers of unsaturated cyclitols act as substrates of β-glycosidases, reacting via allylic cation transition states. Incorporation of halogens at the vinylic position of these carbasugars, along with an activated leaving group, generates potent inactivators of β-glycosidases. Enzymatic turnover of these halogenated cyclitols (F, Cl, Br) displayed a counter-intuitive trend wherein the most electronegative substituents yielded the most labile pseudo-glycosidic linkages. Structures of complexes with the Sulfolobus β-glucosidase revealed similar enzyme-ligand interactions to those seen in complexes with a 2-fluorosugar inhibitor, the lone exception being displacement of tyrosine 322 from the active site by the halogen. Mutation of Y322 to Y322F largely abolished glycosidase activity, consistent with lost interactions at O5, but minimally affected (7-fold) rates of carbasugar hydrolysis, yielding a more selective enzyme for unsaturated cyclitol ether hydrolysis.


  • Organizational Affiliation

    Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-galactosidase
A, B
489Saccharolobus solfataricusMutation(s): 1 
Gene Names: HFC64_10340SSOP1_3114SULA_0798SULB_0800SULC_0798SULZ_04135
UniProt
Find proteins for P22498 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore P22498 
Go to UniProtKB:  P22498
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22498
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.189 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.088α = 90
b = 168.088β = 90
c = 95.548γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release
  • Version 1.1: 2023-05-17
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description