PDBsum entry 1ib4

Hydrolase

PDB id: 1ib4

Contents

Protein chains

339 a.a. *

Ligands

NAG-NAG-MAN ×2

MAN ×20

Metals

_CD ×3

Waters ×425

* Residue conservation analysis

References listed in PDB file

Key reference

Title

The X-Ray structure of aspergillus aculeatus polygalacturonase and a modeled structure of the polygalacturonase-Octagalacturonate complex.

Authors

S.W.Cho, S.Lee, W.Shin.

Ref.

J Mol Biol, 2001, 311, 863-878. [DOI no: 10.1006/jmbi.2001.4919]

PubMed id

11518536

Abstract

Polygalacturonases hydrolyze the alpha-(1-4) glycosidic bonds of de-esterified pectate in the smooth region of the plant cell wall. Crystal structures of polygalacturonase from Aspergillus aculeatus were determined at pH 4.5 and 8.5 both to 2.0 A resolution. A. aculeatus polygalacturonase is a glycoprotein with one N and ten O-glycosylation sites and folds into a right-handed parallel beta-helix. The structures of the three independent molecules are essentially the same, showing no dependency on pH or crystal packing, and are very similar to that of Aspergillus niger polygalacturonase. However, the structures of the long T1 loop containing a catalytic tyrosine residue are significantly different in the two proteins. A three-dimensional model showing the substrate binding mode for a family 28 hydrolase was obtained by a combined approach of flexible docking, molecular dynamics simulations, and energy minimization. The octagalacturonate substrate was modeled as an unbent irregular helix with the -1 ring in a half-chair ((4)H(3)) form that approaches the transition state conformation. A comparative modeling of the three polygalacturonases with known structure shows that six subsites ranging from -4 to +2 are clearly defined but subsites -5 and +3 may or may not be shaped depending on the nearby amino acid residues. Both distal subsites are mostly exposed to the solvent region and have weak binding affinity even if they exist. The complex model provides a clear explanation for the functions, either in catalysis or in substrate binding, of all conserved amino acid residues in the polygalacturonase family of proteins. Modeling suggests that the role of the conserved Asn157 and Tyr270, which had previously been unidentified, may be in transition state stabilization. In A. niger polygalacturonase, the long T1 loop may have to undergo conformational change upon binding of the substrate to bring the tyrosine residue close to subsite -1.

Figure 1.
Figure 1. (a) A ribbon diagram of the Aspergillus aculeatus polygalacturonase structure viewed onto b-sheet PB1. (b) Stereo view showing the cross-section of the b-helix and the aligned residues viewed from the N-terminal side. Four complete turns in the middle of the b-helix are shown with the labels of b-sheets and turns.

Figure 3.
Figure 3. Stereo view of a modeled structure of the PGA-octagalacturonate complex. The electrostatic potential is drawn at the solvent accessible surface of polygalacturonase from -9kT/e^ - (red) to +9kT/e^ - (blue) and the substrate is represented with a space-filling model. The N terminus is on the top and the C terminus on the bottom. The unbent substrate spans the binding cleft that is formed by the protruding loop regions T1 (left side) and T4 (right side). The Figure was produced with GRASP.[57]

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 311, 863-878) copyright 2001.