PDBsum entry: 2p50

Hydrolase

PDB id: 2p50

Contents

Protein chains

382 a.a. *

356 a.a. *

Metals

_ZN ×4

Waters ×349

* Residue conservation analysis

PDB id:

2p50

Name:

Hydrolase

Title:

Crystal structure of n-acetyl-d-glucosamine-6-phosphate deac liganded with zn

Structure:

N-acetylglucosamine-6-phosphate deacetylase. Chain: a, b, c, d. Synonym: glcnac 6-p deacetylase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: naga, b0677, jw0663. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.20Å R-factor: 0.212 R-free: 0.257

Authors:

A.A.Fedorov,E.V.Fedorov,R.S.Hall,F.M.Raushel,S.C.Almo

Key ref:

R.S.Hall et al. (2007). Structural diversity within the mononuclear and binuclear active sites of N-acetyl-D-glucosamine-6-phosphate deacetylase. Biochemistry, 46, 7953-7962. PubMed id: 17567048 DOI: 10.1021/bi700544c

Date:

14-Mar-07 Release date: 24-Jul-07

Protein chain

P0AF18  (NAGA_ECOLI) -  N-acetylglucosamine-6-phosphate deacetylase

Seq: 382 a.a.

Struc: 382 a.a.

Protein chains

P0AF18  (NAGA_ECOLI) -  N-acetylglucosamine-6-phosphate deacetylase

Seq: 382 a.a.

Struc: 356 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.3.5.1.25 - N-acetylglucosamine-6-phosphate deacetylase.
• Pathway: UDP-N-acetylglucosamine Biosynthesis
• Reaction: N-acetyl-D-glucosamine 6-phosphate + H₂O = D-glucosamine 6-phosphate + acetate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: carbohydrate metabolic process (3 terms)
• Biochemical function: hydrolase activity (4 terms)

reference

DOI no: 10.1021/bi700544c

Biochemistry 46:7953-7962 (2007)

PubMed id: 17567048

Structural diversity within the mononuclear and binuclear active sites of N-acetyl-D-glucosamine-6-phosphate deacetylase.

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

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.