PDBsum entry 2jkp

Hydrolase

PDB id: 2jkp

Contents

Protein chains

687 a.a.

Ligands

CTS ×2

EDO ×4

Metals

_CA ×2

Waters ×1255

References listed in PDB file

Key reference

Title

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

Authors

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

Ref.

Chem Biol, 2008, 15, 1058-1067. [DOI no: 10.1016/j.chembiol.2008.09.005]

PubMed id

18848471

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.

Figure 1.
GH Mechanisms and [alpha]-Glucosidase Inhibitors (A and B) Hydrolysis with (A) inversion and (B) retention of anomeric configuration. (C) Inhibitors deoxynojirimycin (1), castanospermine (2), and acarbose (3). Chem Biol. 2008 October 20; 15(10-3): 1058–1067. doi: 10.1016/j.chembiol.2008.09.005. Copyright [copyright] 2008 Elsevier Ltd.

Figure 2.
Structural Insights into BtGH97a (A) Divergent stereo ribbon representation of BtGH97a; the N-terminal domain is in red, the core ([beta]/[alpha])[8] domain in yellow, and the C-terminal domain in blue. (B and C) Ball-and-stick representation of BtGH97a in complex with (B) 1 and (C) 2; observed electron density for the maximum likelihood weighted 2F[obs] [minus sign] F[calc] map is contoured at 1[sigma]. The purple spheres represent calcium ions. (D) Ball-and-stick representation of the active-site overlap between BtGH97a and a GH27 enzyme (PDB ID code 1UAS). Figures were drawn using BOBSCRIPT (Esnouf, 1997). (E) Interactions between BtGH97 and 1. Chem Biol. 2008 October 20; 15(10-3): 1058–1067. doi: 10.1016/j.chembiol.2008.09.005. Copyright [copyright] 2008 Elsevier Ltd.

The above figures are reprinted from an Open Access publication published by Cell Press: Chem Biol (2008, 15, 1058-1067) copyright 2008.