PDBsum entry: 1jak

Hydrolase

PDB id: 1jak

Contents

Protein chain

499 a.a. *

Ligands

SO4

IFG

GOL ×3

Metals

_CL ×3

Waters ×529

* Residue conservation analysis

PDB id:

1jak

Name:

Hydrolase

Title:

Streptomyces plicatus beta-n-acetylhexosaminidase in complex 3r,4s,5r)-2-acetamido-3,4-dihydroxy-5-hydroxymethyl-piperid chloride (ifg)

Structure:

Beta-n-acetylhexosaminidase. Chain: a. Engineered: yes

Source:

Streptomyces plicatus. Organism_taxid: 1922. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

1.75Å R-factor: 0.176 R-free: 0.192

Authors:

B.L.Mark,D.J.Vocadlo,D.Zhao,S.Knapp,S.G.Withers,M.N.James

Key ref:

B.L.Mark et al. (2001). 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. PubMed id: 11522797 DOI: 10.1074/jbc.M107154200

Date:

30-May-01 Release date: 21-Nov-01

Protein chain

O85361  (O85361_STRPL) -  B-N-acetylhexosaminidase

Seq: 506 a.a.

Struc: 499 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: carbohydrate metabolic process (1 term)
• Biochemical function: catalytic activity (4 terms)

DOI no: 10.1074/jbc.M107154200

J Biol Chem 276:42131-42137 (2001)

PubMed id: 11522797

Biochemical and structural assessment of the 1-N-azasugar GalNAc-isofagomine as a potent family 20 beta-N-acetylhexosaminidase inhibitor.

B.L.Mark, D.J.Vocadlo, D.Zhao, S.Knapp, S.G.Withers, M.N.James.

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.

Selected figure(s)

Figure 3.
Fig. 3. Inhibition of SpHEX-catalyzed hydrolysis of pNPGlcNAc by GalNAc-isofagomine (3, Fig. 2). The concentrations of GalNAc-isofagomine were 0.62 ( circle ), 1.23 ( ), 3.08 ( ), 6.15 ( ), 9.23 ( ), and 18.5 ( ) µM.

Figure 5.
Fig. 5. Schematic of the hydrogen-bonding interactions occurring between SpHEX and GalNAc-isofagomine (3, Fig. 2). Hydrogen bonds are shown as dashed lines, and their respective distances are indicated in Ångstroms. GalNAc-isofagomine is shown in blue, and the SpHEX residue side chains are shown in black and numbered. No attempt has been made to locate the true positions of the amino acid side chains.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 42131-42137) copyright 2001.

Figures were selected by an automated process.