PDBsum entry: 2chn

Hydrolase

PDB id: 2chn

Contents

Protein chains

642 a.a. *

12 a.a. *

Ligands

NGT ×2

GOL ×4

Metals

_CA ×2

Waters ×1103

* Residue conservation analysis

PDB id:

2chn

Name:

Hydrolase

Title:

Bacteroides thetaiotaomicron hexosaminidase with o- glcnacase activity - NAG-thiazoline complex

Structure:

Glucosaminidase. Chain: a, b. Fragment: residues 22-737. Synonym: hexosaminiase. Engineered: yes. Other_details: thiazoline inhibitor present. Glucosaminidase. Chain: c, d. Fragment: c terminus, residues 650-653,660-668.

Source:

Bacteroides thetaiotaomicron. Organism_taxid: 226186. Strain: vpi-5482. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

1.95Å R-factor: 0.187 R-free: 0.226

Authors:

R.J.Dennis,E.J.Taylor,M.S.Macauley,K.A.Stubbs, J.P.Turkenburg,S.J.Hart,G.N.Black,D.J.Vocadlo,G.J.Davies

Key ref:

R.J.Dennis et al. (2006). Structure and mechanism of a bacterial beta-glucosaminidase having O-GlcNAcase activity. Nat Struct Mol Biol, 13, 365-371. PubMed id: 16565725 DOI: 10.1038/nsmb1079

Date:

15-Mar-06 Release date: 08-May-06

Protein chains

Q89ZI2  (OGA_BACTN) -  O-GlcNAcase BT_4395

Seq: 737 a.a.

Struc: 642 a.a.

Protein chain

No UniProt id for this chain

Enzyme reactions

• Enzyme class: Chains A, B: E.C.3.2.1.169 - Protein O-GlcNAcase.
• Reaction:
  1. [Protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine + H₂O = [protein]- L-serine + N-acetyl-D-glucosamine
  2. [Protein]-3-O-(N-acetyl-D-glucosaminyl)-L-threonine + H₂O = [protein]-L-threonine + N-acetyl-D-glucosamine

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

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (2 terms)
• Biochemical function: hydrolase activity (3 terms)

reference

DOI no: 10.1038/nsmb1079

Nat Struct Mol Biol 13:365-371 (2006)

PubMed id: 16565725

Structure and mechanism of a bacterial beta-glucosaminidase having O-GlcNAcase activity.

R.J.Dennis, E.J.Taylor, M.S.Macauley, K.A.Stubbs, J.P.Turkenburg, S.J.Hart, G.N.Black, D.J.Vocadlo, G.J.Davies.

ABSTRACT

O-GlcNAc is an abundant post-translational modification of serine and threonine residues of nucleocytoplasmic proteins. This modification, found only within higher eukaryotes, is a dynamic modification that is often reciprocal to phosphorylation. In a manner analogous to phosphatases, a glycoside hydrolase termed O-GlcNAcase cleaves O-GlcNAc from modified proteins. Enzymes with high sequence similarity to human O-GlcNAcase are also found in human pathogens and symbionts. We report the three-dimensional structure of O-GlcNAcase from the human gut symbiont Bacteroides thetaiotaomicron both in its native form and in complex with a mimic of the reaction intermediate. Mutagenesis and kinetics studies show that the bacterial enzyme, very similarly to its human counterpart, operates via an unusual 'substrate-assisted' catalytic mechanism, which will inform the rational design of enzyme inhibitors.

Selected figure(s)

Figure 1.
Figure 1. Schematic diagram of the O-GlcNAc modification. (a) Dynamic interplay of phosphorylation and O-GlcNAc modification of intracellular proteins.(b) Mechanism of action of O-GlcNAc hydrolases using substrate-assisted catalysis (residue numbers are for the the BtGH84 enzyme). (c) Transition state of the O-GlcNAcase–catalyzed hydrolysis of N-acetylglucosaminides. (d) Structure of the mechanism-derived inhibitor NAG-thiazoline, which mimics the intermediate of the substrate-assisted mechanism.

Figure 2.
Figure 2. Three-dimensional structure of B. thetaiotaomicron GH84. (a) Divergent (wall-eyed) stereo cartoon, color-ramped from, N-terminus (blue) to C-terminus (red), with NAG-thiazoline and the acid/base Asp243 in ball-and-stick representation. (b) Overlay of BtGH84 (green) with the human hexosaminidase B from family GH20 (yellow). (c) Electron density (F[obs] – F[calc], omit map at 3 ) for the NAG-thiazoline inhibitor and its environment; kinetic parameters of mutants of these residues are given in Table 1. (d) Overlay of the experimentally determined BtGH84 (green) with a homology model of the human enzyme (gray) showing only a single Trp-Phe change near the active center. (e) Overlay of the acetamide pocket of BtGH84 (green) with human GH20 hexosaminidase B (yellow, black labels), revealing a smaller pocket in the latter by virtue of the steric blockage of Trp405. This difference in pocket volume has been exploited in the design of GH84-specific inhibitors, such as the N-butyl compounds used here. These figures were drawn with MolScript^45 and BobScript^46.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2006, 13, 365-371) copyright 2006.

Figures were selected by the author.