6GTA image
Deposition Date 2018-06-17
Release Date 2018-08-22
Last Version Date 2024-01-17
Entry Detail
PDB ID:
6GTA
Keywords:
Title:
Alpha-galactosidase mutant D378A from Thermotoga maritima in complex with intact cyclohexene-based carbasugar mimic of galactose with 3,5 difluorophenyl leaving group
Biological Source:
Method Details:
Experimental Method:
Resolution:
2.20 Å
R-Value Free:
0.23
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Alpha-galactosidase
Gene (Uniprot):galA
Mutations:D387A
Chain IDs:A
Chain Length:575
Number of Molecules:1
Biological Source:Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Primary Citation
Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level.
Nat Commun 9 3243 3243 (2018)
PMID: 30104598 DOI: 10.1038/s41467-018-05702-7

Abstact

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 (2H3) conformations for the cyclohexene fragment, while the covalently linked intermediate adopts a flattened half-chair (2H3) 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.

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Primary Citation of related structures