1JAK

Streptomyces plicatus beta-N-acetylhexosaminidase in Complex with (2R,3R,4S,5R)-2-acetamido-3,4-dihydroxy-5-hydroxymethyl-piperidinium chloride (IFG)

Summary for 1JAK

• Entry DOI: 10.2210/pdb1jak/pdb
• Related: 1HP4 1HP5
• Descriptor: Beta-N-acetylhexosaminidase, SULFATE ION, CHLORIDE ION, ... (6 entities in total)
• Functional Keywords: glycoside hydrolase, family 20, beta-n-acetylhexosaminidase, substrate-assisted catalysis, alpha/beta barrel, isofagomine inhibitor complex, hydrolase
• Biological source: Streptomyces plicatus
• Cellular location: Membrane; Multi-pass membrane protein: Q9Y691
• Total number of polymer chains: 1
• Total formula weight: 56809.71

Authors

Mark, B.L.,Vocadlo, D.J.,Zhao, D.,Knapp, S.,Withers, S.G.,James, M.N. (deposition date: 2001-05-30, release date: 2001-11-21, Last modification date: 2024-10-30)

Primary citation

Mark, B.L.,Vocadlo, D.J.,Zhao, D.,Knapp, S.,Withers, S.G.,James, M.N.
Biochemical and structural assessment of the 1-N-azasugar GalNAc-isofagomine as a potent family 20 beta-N-acetylhexosaminidase inhibitor.
J.Biol.Chem., 276:42131-42137, 2001

PubMed Abstract: Azasugar inhibitors of the isofagomine class are potent competitive inhibitors of configuration-retaining beta-glycosidases. This potency results from the formation of a strong electrostatic interaction between a protonated endocyclic nitrogen at the "anomeric" center of the inhibitor and the catalytic nucleophile of the enzyme. Although the majority of retaining beta-glycosidases use a mechanism involving a carboxylate residue as a nucleophile, Streptomyces plicatus beta-N-acetylhexos-aminidase (SpHEX) and related family 20 glycosidases lack such a catalytic residue and use instead the carbonyl oxygen of the 2-acetamido group of the substrate as a nucleophile to "attack" the anomeric center. Thus, a strong electrostatic interaction between the inhibitor and enzyme is not expected to occur; nonetheless, the 1-N-azasugar (2R,3R,4S,5R)-2-acetamido-3,4-dihydroxy-5-hydroxymethyl-piperidinium hydrochloride (GalNAc-isofagomine.HCl), which was synthesized and assayed for its ability to inhibit SpHEX, was found to be a potent competitive inhibitor of the enzyme (K(i) = 2.7 microm). A crystallographic complex of GalNAc-isofagomine bound to SpHEX was solved and refined to 1.75 A and revealed that the lack of a strong electrostatic interaction between the "anomeric" center of GalNAc-isofagomine and SpHEX is compensated for by a novel 2.8-A hydrogen bond formed between the equatorial proton of the endocyclic nitrogen of the azasugar ring and the carboxylate of the general acid-base residue Glu-314 of SpHEX. This interaction appears to contribute to the unexpected potency of GalNAc-isofagomine toward SpHEX.

PubMed: 11522797
DOI: 10.1074/jbc.M107154200

Experimental method

X-RAY DIFFRACTION (1.75 Å)