6FV4

The structure of N-acetyl-D-glucosamine-6-phosphate deacetylase D267A mutant from Mycobacterium smegmatis in complex with N-acetyl-D-glucosamine-6-phosphate

Summary for 6FV4

• Entry DOI: 10.2210/pdb6fv4/pdb
• Related: 6FV3
• Descriptor: N-acetylglucosamine-6-phosphate deacetylase, ZINC ION, 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose, ... (7 entities in total)
• Functional Keywords: n-acetyl-d-glucosamine-6-phosphate, mycobacteria carbohydrate metabolism, hydrolase
• Biological source: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
• Total number of polymer chains: 2
• Total formula weight: 83652.28

Authors

Ahangar, M.S.,Furze, C.M.,Guy, C.S.,Cooper, C.,Maskew, K.S.,Graham, B.,Cameron, A.D.,Fullam, E. (deposition date: 2018-03-01, release date: 2018-05-16, Last modification date: 2024-01-17)

Primary citation

Ahangar, M.S.,Furze, C.M.,Guy, C.S.,Cooper, C.,Maskew, K.S.,Graham, B.,Cameron, A.D.,Fullam, E.
Structural and functional determination of homologs of theMycobacterium tuberculosis N-acetylglucosamine-6-phosphate deacetylase (NagA).
J. Biol. Chem., 293:9770-9783, 2018

PubMed Abstract: The () pathogen encodes a GlcNAc-6-phosphate deacetylase enzyme, NagA (Rv3332), that belongs to the amidohydrolase superfamily. NagA enzymes catalyze the deacetylation of GlcNAc-6-phosphate (GlcNAc6P) to glucosamine-6-phosphate (GlcN6P). NagA is a potential antitubercular drug target because it represents the key enzymatic step in the generation of essential amino-sugar precursors required for cell wall biosynthesis and also influences recycling of cell wall peptidoglycan fragments. Here, we report the structural and functional characterization of NagA from (MSNagA) and (MMNagA), close relatives of Using a combination of X-ray crystallography, site-directed mutagenesis, and biochemical and biophysical assays, we show that these mycobacterial NagA enzymes are selective for GlcNAc6P. Site-directed mutagenesis studies revealed crucial roles of conserved residues in the active site that underpin stereoselective recognition, binding, and catalysis of substrates. Moreover, we report the crystal structure of MSNagA in both ligand-free form and in complex with the GlcNAc6P substrate at 2.6 and 2.0 Å resolutions, respectively. The GlcNAc6P complex structure disclosed the precise mode of GlcNAc6P binding and the structural framework of the active site, including two divalent metals located in the α/β binuclear site. Furthermore, we observed a cysteine residue located on a flexible loop region that occludes the active site. This cysteine is unique to mycobacteria and may represent a unique subsite for targeting mycobacterial NagA enzymes. Our results provide critical insights into the structural and mechanistic properties of mycobacterial NagA enzymes having an essential role in amino-sugar and nucleotide metabolism in mycobacteria.

PubMed: 29728457
DOI: 10.1074/jbc.RA118.002597

Experimental method

X-RAY DIFFRACTION (1.974 Å)