1YRR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural analysis of N-acetylglucosamine-6-phosphate deacetylase apoenzyme from Escherichia coli.

Ferreira, F.M.Mendoza-Hernandez, G.Aparicio, R.Fischer, H.Calcagno, M.L.Oliva, G.

(2006) J Mol Biol 359: 308-321

  • DOI: 10.1016/j.jmb.2006.03.024
  • Primary Citation of Related Structures:  
    1YRR

  • 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) ...

    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.


    Related Citations: 
    • Crystallization and preliminary crystallographic analysis of N-acetylglucosamine 6-phosphate deacetylase from Escherichia coli
      Ferreira, F.M., Mendoza-Hernandez, G., Calcagno, M.L., Minauro, F., Delboni, L.F., Oliva, G.
      (2000) Acta Crystallogr D Biol Crystallogr 56: 670

    Organizational Affiliation

    Instituto de Física de São Carlos, Universidade de São Paulo, C.P. 369, 13560-970 São Carlos, SP, Brazil.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-acetylglucosamine-6-phosphate deacetylaseA, B382Escherichia coliMutation(s): 0 
Gene Names: nagA
EC: 3.5.1.25
UniProt
Find proteins for P0AF18 (Escherichia coli (strain K12))
Explore P0AF18 
Go to UniProtKB:  P0AF18
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AF18
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.157α = 90
b = 114.554β = 90
c = 80.208γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SOLVEphasing
RESOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance