PDBsum entry: 2jke

Hydrolase

PDB-id: 2jke

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PROCHECK

Protein chains

687 a.a. *

Ligands

NOJ ×2

EDO ×8

Metal ions

_CA ×2

Waters ×1931

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

2jke

Name:

Hydrolase

Title:

Structure of a family 97 alpha-glucosidase from bacteroides thetaiotaomicron in complex with deoxynojirimycin

Structure:

Alpha-glucosidase (alpha-glucosidase susb). Chain: a, b. Fragment: residues 22-738. Engineered: yes

Source:

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

UniProt:

Chains A, B: P71094 (P71094_BACTN)

Seq:

Struc:

Seq:

Struc:

Seq:

738 a.a.

Struc:

687 a.a.

Key:

PfamA domain

Secondary structure

Resolution:

1.7Å

R-factor:

0.157

R-free:

0.187

Authors:

T.M.Gloster,J.P.Turkenburg,J.R.Potts,B.Henrissat,G.J.Davies

Key ref:

T.M.Gloster et al. (2008). Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora.. Chem Biol, 15, 1058-1067. [PubMed id: 18848471] [DOI: 10.1016/j.chembiol.2008.09.005]

Date:

28-Aug-08

Release date:

30-Sep-08

Related entries:

2jka native structure of a family 97 alpha- glucosidase from bacteroides thetaiotaomicron
2jkp structure of a family 97 alpha-glucosidase from bacteroides thetaiotaomicron in complex with castanospermine

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Clefts

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Key reference

DOI no: 10.1016/j.chembiol.2008.09.005

Chem Biol 15:1058-1067 (2008)

PubMed id: 18848471

Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora.

T.M.Gloster, J.P.Turkenburg, J.R.Potts, B.Henrissat, G.J.Davies.

ABSTRACT

Enzymatic cleavage of the glycosidic bond yields products in which the anomeric configuration is either retained or inverted. Each mechanism reflects the dispositions of the enzyme functional groups; a facet of which is essentially conserved in 113 glycoside hydrolase (GH) families. We show that family GH97 has diverged significantly, as it contains both inverting and retaining alpha-glycosidases. This reflects evolution of the active center; a glutamate acts as a general base in inverting members, exemplified by Bacteroides thetaiotaomicron alpha-glucosidase BtGH97a, whereas an aspartate likely acts as a nucleophile in retaining members. The structure of BtGH97a and its complexes with inhibitors, coupled to kinetic analysis of active-site variants, reveals an unusual calcium ion dependence. 1H NMR analysis shows an inversion mechanism for BtGH97a, whereas another GH97 enzyme from B. thetaiotaomicron, BtGH97b, functions as a retaining alpha-galactosidase.