Alpha-galactosidase from Thermotoga maritima in complex with cyclohexene-based carbasugar mimic of galactose

Experimental Data Snapshot

  • Resolution: 1.22 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 

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Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level.

Ren, W.Pengelly, R.Farren-Dai, M.Shamsi Kazem Abadi, S.Oehler, V.Akintola, O.Draper, J.Meanwell, M.Chakladar, S.Swiderek, K.Moliner, V.Britton, R.Gloster, T.M.Bennet, A.J.

(2018) Nat Commun 9: 3243-3243

  • DOI: https://doi.org/10.1038/s41467-018-05702-7
  • Primary Citation of Related Structures:  
    6GTA, 6GVD, 6GWF, 6GWG, 6GX8

  • PubMed Abstract: 

    Mechanism-based glycoside hydrolase inhibitors are carbohydrate analogs that mimic the natural substrate's structure. Their covalent bond formation with the glycoside hydrolase makes these compounds excellent tools for chemical biology and potential drug candidates. Here we report the synthesis of cyclohexene-based α-galactopyranoside mimics and the kinetic and structural characterization of their inhibitory activity toward an α-galactosidase from Thermotoga maritima (TmGalA). By solving the structures of several enzyme-bound species during mechanism-based covalent inhibition of TmGalA, we show that the Michaelis complexes for intact inhibitor and product have half-chair ( 2 H 3 ) conformations for the cyclohexene fragment, while the covalently linked intermediate adopts a flattened half-chair ( 2 H 3 ) conformation. Hybrid QM/MM calculations confirm the structural and electronic properties of the enzyme-bound species and provide insight into key interactions in the enzyme-active site. These insights should stimulate the design of mechanism-based glycoside hydrolase inhibitors with tailored chemical properties.

  • Organizational Affiliation

    Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-galactosidase575Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: galATM_1192Tmari_1199
Find proteins for G4FEF4 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore G4FEF4 
Go to UniProtKB:  G4FEF4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG4FEF4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.22 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.957α = 90
b = 96.135β = 90
c = 97.9γ = 90
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description