PDBsum entry: 2vtf

Hydrolase

PDB id: 2vtf

Contents

Protein chains

616 a.a. *

Ligands

B3P ×4

PGE ×4

Waters ×1500

* Residue conservation analysis

PDB id:

2vtf

Name:

Hydrolase

Title:

X-ray crystal structure of the endo-beta-n- acetylglucosaminidase from arthrobacter protophormiae e173q mutant reveals a tim barrel catalytic domain and two ancillary domains

Structure:

Endo-beta-n-acetylglucosaminidase. Chain: a, b. Fragment: residues 25-645. Engineered: yes. Mutation: yes

Source:

Arthrobacter protophormiae. Organism_taxid: 37930. Strain: aku0647. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.79Å R-factor: 0.166 R-free: 0.202

Authors:

Z.Ling,R.J.Bingham,M.D.L.Suits,J.W.B.Moir,A.J.Fairbanks, E.J

Key ref:

Z.Ling et al. (2009). The X-ray crystal structure of an Arthrobacter protophormiae endo-beta-N-acetylglucosaminidase reveals a (beta/alpha)(8) catalytic domain, two ancillary domains and active site residues key for transglycosylation activity. J Mol Biol, 389, 1-9. PubMed id: 19327363 DOI: 10.1016/j.jmb.2009.03.050

Date:

14-May-08 Release date: 31-Mar-09

Protein chains

Q9ZB22  (Q9ZB22_9MICC) -  Endo-beta-N-acetylglucosaminidase

Seq: 645 a.a.

Struc: 616 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.2.1.96 - Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase.
• Reaction: Endohydrolysis of the di-N-acetylchitobiosyl unit in high-mannose glycopeptides and glycoproteins containing the -[Man(GlcNAc)2]Asn- structure. One N-acetyl-D-glucosamine residue remains attached to the protein; the rest of the oligosaccharide is released intact.

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: metabolic process (1 term)
• Biochemical function: hydrolase activity (4 terms)

DOI no: 10.1016/j.jmb.2009.03.050

J Mol Biol 389:1-9 (2009)

PubMed id: 19327363

The X-ray crystal structure of an Arthrobacter protophormiae endo-beta-N-acetylglucosaminidase reveals a (beta/alpha)(8) catalytic domain, two ancillary domains and active site residues key for transglycosylation activity.

Z.Ling, M.D.Suits, R.J.Bingham, N.C.Bruce, G.J.Davies, A.J.Fairbanks, J.W.Moir, E.J.Taylor.

ABSTRACT

Glycoside hydrolase family GH85 is a family of endo-beta-N-acetylglucosaminidases that is responsible for the hydrolysis of beta-1,4 linkage in the N,N-diacetylchitobiose core of N-linked glycans. The endo-beta-N-acetylglucosaminidase from Arthrobacter protophormiae (Endo-A) is of particular interest, given its increasing use for the chemoenzymatic synthesis of bespoke N-glycans using N-glycan oxazolines as glycosyl donors. The E173Q variant of Endo-A is especially attractive for synthesis, as it is hydrolytically impaired but still able to catalyze N-glycan synthesis by transglycosylation using activated oxazoline donors. Here we present the three-dimensional structure of the A. protophormiae Endo-A E173Q variant, solved by multiple-wavelength anomalous scattering methods and refined at 1.8 A resolution. The structure reveals that GH85 enzymes display a trimodular architecture in which a (beta/alpha)(8) catalytic domain occurs with two ancillary beta-sheet modules. The active centre is fully consistent with the known neighboring-group catalytic mechanism in which E173 acts as the catalytic acid/base for reaction via an oxazoline intermediate. Of note is the presence of an asparagine in the active centre, in a position likely to interact with the acetyl NH group that, in all other known families of glycosidase using this mechanism, is an aspartate or glutamate residue. The substrate-binding surface reveals an open topography, consistent with the ability to accept a large range of glycoprotein substrates and the ability to transglycosylate other acceptors. The three-dimensional structure of this important biocatalyst reveals that residues implicated in the enhancement of transglycosylation and synthetic capacity are proximal to the active centre, where they may act to favor binding of acceptor substrates.

Selected figure(s)

Figure 1.
Fig. 1. The reaction and roles of Endo-A. (a) The reaction catalyzed by GH85 enzymes is the hydrolysis of the chitobiosyl core of N-linked glycans. (b) Neighboring-group participation mechanism for Endo-A via an oxazoline intermediate. (c) The synthetic utility of Endo-A and its variants in harnessing N-glycan oxazoline donors for the synthesis of glycoproteins with defined glycoforms.

Figure 3.
Fig. 3. Mechanistic questions raised by asparagine at position 171. (a) Reaction via a charged oxazolinium-ion-like intermediate in which the carbonyl of N171 aids the formation of the intermediate. (b) Reaction via an uncharged oxazoline intermediate that demands N171 to act as a base, perhaps via its imine tautomer.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 389, 1-9) copyright 2009.

Figures were selected by the author.