5UTP

Crystal structure of Burkholderia cenocepacia family 3 glycoside hydrolase (NagZ) bound to N-ethylbutyryl-PUGNAc

Summary for 5UTP

• Entry DOI: 10.2210/pdb5utp/pdb
• Related: 4G6C 4GNV 4MSS 5UTQ
• Descriptor: Beta-hexosaminidase, N-[(2Z,3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(phenylcarbamoyl)oxy]imino}tetrahydro-2H-pyran-3-yl]-2-ethylbutanamide (3 entities in total)
• Functional Keywords: glycoside hydrolase, family 3, nagz, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Burkholderia cenocepacia
• Cellular location: Cytoplasm : A0A125HFC0
• Total number of polymer chains: 2
• Total formula weight: 77052.40

Authors

Vadlamani, G.,Mark, B.L. (deposition date: 2017-02-15, release date: 2017-04-19, Last modification date: 2023-10-04)

Primary citation

Vadlamani, G.,Stubbs, K.A.,Desire, J.,Bleriot, Y.,Vocadlo, D.J.,Mark, B.L.
Conformational flexibility of the glycosidase NagZ allows it to bind structurally diverse inhibitors to suppress beta-lactam antibiotic resistance.
Protein Sci., 26:1161-1170, 2017

PubMed Abstract: NagZ is an N-acetyl-β-d-glucosaminidase that participates in the peptidoglycan (PG) recycling pathway of Gram-negative bacteria by removing N-acetyl-glucosamine (GlcNAc) from PG fragments that have been excised from the cell wall during growth. The 1,6-anhydromuramoyl-peptide products generated by NagZ activate β-lactam resistance in many Gram-negative bacteria by inducing the expression of AmpC β-lactamase. Blocking NagZ activity can thereby suppress β-lactam antibiotic resistance in these bacteria. The NagZ active site is dynamic and it accommodates distortion of the glycan substrate during catalysis using a mobile catalytic loop that carries a histidine residue which serves as the active site general acid/base catalyst. Here, we show that flexibility of this catalytic loop also accommodates structural differences in small molecule inhibitors of NagZ, which could be exploited to improve inhibitor specificity. X-ray structures of NagZ bound to the potent yet non-selective N-acetyl-β-glucosaminidase inhibitor PUGNAc (O-(2-acetamido-2-deoxy-d-glucopyranosylidene) amino-N-phenylcarbamate), and two NagZ-selective inhibitors - EtBuPUG, a PUGNAc derivative bearing a 2-N-ethylbutyryl group, and MM-156, a 3-N-butyryl trihydroxyazepane, revealed that the phenylcarbamate moiety of PUGNAc and EtBuPUG completely displaces the catalytic loop from the NagZ active site to yield a catalytically incompetent form of the enzyme. In contrast, the catalytic loop was found positioned in the catalytically active conformation within the NagZ active site when bound to MM-156, which lacks the phenylcarbamate extension. Displacement of the catalytic loop by PUGNAc and its N-acyl derivative EtBuPUG alters the active site conformation of NagZ, which presents an additional strategy to improve the potency and specificity of NagZ inhibitors.

PubMed: 28370529
DOI: 10.1002/pro.3166

Experimental method

X-RAY DIFFRACTION (2.2 Å)