2VHL

The Three-dimensional structure of the N-Acetylglucosamine-6- phosphate deacetylase from Bacillus subtilis

Replaces:  1UN7

Summary for 2VHL

• Entry DOI: 10.2210/pdb2vhl/pdb
• Descriptor: N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE, 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose, TRIETHYLENE GLYCOL, ... (5 entities in total)
• Functional Keywords: n- acetyleglucosamine-6-phosphate, carbohydrate metabolism, hydrolase, deacetylase, bacillus subtilis
• Biological source: BACILLUS SUBTILIS
• Total number of polymer chains: 2
• Total formula weight: 86390.68

Authors

Vincent, F.,Yates, D.,Garman, E.,Davies, G.J. (deposition date: 2007-11-22, release date: 2007-12-04, Last modification date: 2023-12-13)

Primary citation

Vincent, F.,Yates, D.,Garman, E.,Davies, G.J.
The Three-Dimensional Structure of the N-Acetylglucosamine-6-Phosphate Deacetylase from Bacillus Subtilis
J.Biol.Chem., 279:2809-, 2004

PubMed Abstract: The enzyme N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of GlcNAc-6-P to yield glucosamine 6-phosphate and acetate, the first committed step in the biosynthetic pathway to amino-sugar-nucleotides. It is classified into carbohydrate esterase family CE-9 (see afmb.cnrs-mrs.fr/CAZY/). Here we report the cloning, expression, and three-dimensional structure (Protein Data Bank code 1un7) determination by x-ray crystallography of the Bacillus subtilis NagA at a resolution of 2.0 A. The structure presents two domains, a (beta/alpha)(8) barrel enclosing the active center and a small beta barrel domain. The structure is dimeric, and the substrate phosphate coordination at the active center is provided by an Arg/His pair contributed from the second molecule of the dimer. Both the overall structure and the active center bear a striking similarity to the urease superfamily with two metals involved in substrate binding and catalysis. PIXE (Proton-Induced x-ray Emission) data show that iron is the predominant metal in the purified protein. We propose a catalytic mechanism involving proton donation to the leaving group by aspartate, nucleophilic attack by an Fe-bridged hydroxide, and stabilization of the carbonyl oxygen by one of the two Fe atoms of the pair. We believe that this is the first sugar deacetylase to utilize this fold and catalytic mechanism.

PubMed: 14557261
DOI: 10.1074/JBC.M310165200

Experimental method

X-RAY DIFFRACTION (2.05 Å)