3GS6

Vibrio Cholerea family 3 glycoside hydrolase (NagZ)in complex with N-butyryl-PUGNAc

Summary for 3GS6

• Entry DOI: 10.2210/pdb3gs6/pdb
• Related: 1TR9 1Y65 2OXN 3GSM
• Descriptor: Beta-hexosaminidase, [[(3R,4R,5S,6R)-3-(BUTANOYLAMINO)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)OXAN-2-YLIDENE]AMINO] N-PHENYLCARBAMATE, GLYCEROL, ... (4 entities in total)
• Functional Keywords: glycoside hydrolase family 3, cell cycle, cell division, cell shape, cell wall biogenesis/degradation, glycosidase, hydrolase, peptidoglycan synthesis
• Biological source: Vibrio cholerae
• Cellular location: Cytoplasm (By similarity): Q9KU37
• Total number of polymer chains: 1
• Total formula weight: 38280.42

Authors

Balcewich, M.D.,Mark, B.L. (deposition date: 2009-03-26, release date: 2009-06-30, Last modification date: 2023-09-06)

Primary citation

Balcewich, M.D.,Stubbs, K.A.,He, Y.,James, T.W.,Davies, G.J.,Vocadlo, D.J.,Mark, B.L.
Insight into a strategy for attenuating AmpC-mediated beta-lactam resistance: structural basis for selective inhibition of the glycoside hydrolase NagZ.
Protein Sci., 18:1541-1551, 2009

PubMed Abstract: NagZ is an exo-N-acetyl-beta-glucosaminidase, found within Gram-negative bacteria, that acts in the peptidoglycan recycling pathway to cleave N-acetylglucosamine residues off peptidoglycan fragments. This activity is required for resistance to cephalosporins mediated by inducible AmpC beta-lactamase. NagZ uses a catalytic mechanism involving a covalent glycosyl enzyme intermediate, unlike that of the human exo-N-acetyl-beta-glucosaminidases: O-GlcNAcase and the beta-hexosaminidase isoenzymes. These latter enzymes, which remove GlcNAc from glycoconjugates, use a neighboring-group catalytic mechanism that proceeds through an oxazoline intermediate. Exploiting these mechanistic differences we previously developed 2-N-acyl derivatives of O-(2-acetamido-2-deoxy-D-glucopyranosylidene)amino-N-phenylcarbamate (PUGNAc), which selectively inhibits NagZ over the functionally related human enzymes and attenuate antibiotic resistance in Gram-negatives that harbor inducible AmpC. To understand the structural basis for the selectivity of these inhibitors for NagZ, we have determined its crystallographic structure in complex with N-valeryl-PUGNAc, the most selective known inhibitor of NagZ over both the human beta-hexosaminidases and O-GlcNAcase. The selectivity stems from the five-carbon acyl chain of N-valeryl-PUGNAc, which we found ordered within the enzyme active site. In contrast, a structure determination of a human O-GlcNAcase homologue bound to a related inhibitor N-butyryl-PUGNAc, which bears a four-carbon chain and is selective for both NagZ and O-GlcNAcase over the human beta-hexosamnidases, reveals that this inhibitor induces several conformational changes in the active site of this O-GlcNAcase homologue. A comparison of these complexes, and with the human beta-hexosaminidases, reveals how selectivity for NagZ can be engineered by altering the 2-N-acyl substituent of PUGNAc to develop inhibitors that repress AmpC mediated beta-lactam resistance.

PubMed: 19499593
DOI: 10.1002/pro.137

Experimental method

X-RAY DIFFRACTION (2.3 Å)