Crystal structure of N-acetyl-D-Glucosamine-6-Phosphate deacetylase liganded with Zn

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Structural Diversity within the Mononuclear and Binuclear Active Sites of N-Acetyl-d-glucosamine-6-phosphate Deacetylase.

Hall, R.S.Brown, S.Fedorov, A.A.Fedorov, E.V.Xu, C.Babbitt, P.C.Almo, S.C.Raushel, F.M.

(2007) Biochemistry 46: 7953-7962

  • DOI: https://doi.org/10.1021/bi700544c
  • Primary Citation of Related Structures:  
    2P50, 2P53

  • PubMed Abstract: 

    NagA catalyzes the hydrolysis of N-acetyl-d-glucosamine-6-phosphate to d-glucosamine-6-phosphate and acetate. X-ray crystal structures of NagA from Escherichia coli were determined to establish the number and ligation scheme for the binding of zinc to the active site and to elucidate the molecular interactions between the protein and substrate. The three-dimensional structures of the apo-NagA, Zn-NagA, and the D273N mutant enzyme in the presence of a tight-binding N-methylhydroxyphosphinyl-d-glucosamine-6-phosphate inhibitor were determined. The structure of the Zn-NagA confirms that this enzyme binds a single divalent cation at the beta-position in the active site via ligation to Glu-131, His-195, and His-216. A water molecule completes the ligation shell, which is also in position to be hydrogen bonded to Asp-273. In the structure of NagA bound to the tight binding inhibitor that mimics the tetrahedral intermediate, the methyl phosphonate moiety has displaced the hydrolytic water molecule and is directly coordinated to the zinc within the active site. The side chain of Asp-273 is positioned to activate the hydrolytic water molecule via general base catalysis and to deliver this proton to the amino group upon cleavage of the amide bond of the substrate. His-143 is positioned to help polarize the carbonyl group of the substrate in conjunction with Lewis acid catalysis by the bound zinc. The inhibitor is bound in the alpha-configuration at the anomeric carbon through a hydrogen bonding interaction of the hydroxyl group at C-1 with the side chain of His-251. The phosphate group of the inhibitor attached to the hydroxyl at C-6 is ion paired with Arg-227 from the adjacent subunit. NagA from Thermotoga maritima was shown to require a single divalent cation for full catalytic activity.

  • Organizational Affiliation

    Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-acetylglucosamine-6-phosphate deacetylase
A, B, C, D
382Escherichia coli K-12Mutation(s): 0 
Gene Names: nagAb0677JW0663
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
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.183α = 90
b = 117.992β = 90
c = 265.604γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description