1YRR

Crystal Structure Of The N-Acetylglucosamine-6-Phosphate Deacetylase From Escherichia Coli K12 at 2.0 A Resolution

Summary for 1YRR

• Entry DOI: 10.2210/pdb1yrr/pdb
• Descriptor: N-acetylglucosamine-6-phosphate deacetylase, PHOSPHATE ION, GLYCEROL, ... (4 entities in total)
• Functional Keywords: (beta/alpha)8 barrel, beta sandwich, hydrolase
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 82450.11

Authors

Ferreira, F.M.,Aparicio, R.,Mendoza-Hernandez, G.,Calcagno, M.L.,Oliva, G. (deposition date: 2005-02-04, release date: 2006-03-21, Last modification date: 2024-04-03)

Primary citation

Ferreira, F.M.,Mendoza-Hernandez, G.,Aparicio, R.,Fischer, H.,Calcagno, M.L.,Oliva, G.
Structural analysis of N-acetylglucosamine-6-phosphate deacetylase apoenzyme from Escherichia coli.
J.Mol.Biol., 359:308-321, 2006

PubMed Abstract: We report the crystal structure of the apoenzyme of N-acetylglucosamine-6-phosphate (GlcNAc6P) deacetylase from Escherichia coli (EcNAGPase) and the spectrometric evidence of the presence of Zn2+ in the native protein. The GlcNAc6P deacetylase is an enzyme of the amino sugar catabolic pathway that catalyzes the conversion of the GlcNAc6P into glucosamine 6-phosphate (GlcN6P). The crystal structure was phased by the single isomorphous replacement with anomalous scattering (SIRAS) method using low-resolution (2.9 A) iodine anomalous scattering and it was refined against a native dataset up to 2.0 A resolution. The structure is similar to two other NAGPases whose structures are known from Thermotoga maritima (TmNAGPase) and Bacillus subtilis (BsNAGPase); however, it shows a phosphate ion bound at the metal-binding site. Compared to these previous structures, the apoenzyme shows extensive conformational changes in two loops adjacent to the active site. The E. coli enzyme is a tetramer and its dimer-dimer interface was analyzed. The tetrameric structure was confirmed in solution by small-angle X-ray scattering data. Although no metal ions were detected in the present structure, experiments of photon-induced X-ray emission (PIXE) spectra and of inductively coupled plasma emission spectroscopy (ICP-AES) with enzyme that was neither exposed to chelating agents nor metal ions during purification, revealed the presence of 1.4 atoms of Zn per polypeptide chain. Enzyme inactivation by metal-sequestering agents and subsequent reactivation by the addition of several divalent cations, demonstrate the role of metal ions in EcNAGPase structure and catalysis.

PubMed: 16630633
DOI: 10.1016/j.jmb.2006.03.024

Experimental method

X-RAY DIFFRACTION (2 Å)