PDBsum entry: 1czf

Hydrolase

PDB id: 1czf

Contents

Protein chains

335 a.a. *

Ligands

NAG ×2

Metals

_ZN ×6

Waters ×980

* Residue conservation analysis

PDB id:

1czf

Name:

Hydrolase

Title:

Endo-polygalacturonase ii from aspergillus niger

Structure:

Polygalacturonase ii. Chain: a, b. Synonym: pg-ii, pectinase, endopolygalacturonase ii. Ec: 3.2.1.15

Source:

Aspergillus niger. Organism_taxid: 5061. Variant: nw156. Secretion: extracellular

Biol. unit:

Dimer (from PQS)

Resolution:

1.68Å R-factor: 0.166 R-free: 0.191

Authors:

Y.Van Santen,K.H.Kalk,B.W.Dijkstra

Key ref:

Y.van Santen et al. (1999). 1.68-A crystal structure of endopolygalacturonase II from Aspergillus niger and identification of active site residues by site-directed mutagenesis. J Biol Chem, 274, 30474-30480. PubMed id: 10521427 DOI: 10.1074/jbc.274.43.30474

Date:

02-Sep-99 Release date: 28-Oct-99

Protein chains

P26214  (PGLR2_ASPNG) -  Endopolygalacturonase II

Seq: 362 a.a.

Struc: 335 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.15 - Polygalacturonase.
• Reaction: Random hydrolysis of 1,4-alpha-D-galactosiduronic linkages in pectate and other galacturonans.

 Gene Ontology (GO) functional annotation 

• Biological process: carbohydrate metabolic process (1 term)
• Biochemical function: polygalacturonase activity (1 term)

DOI no: 10.1074/jbc.274.43.30474

J Biol Chem 274:30474-30480 (1999)

PubMed id: 10521427

1.68-A crystal structure of endopolygalacturonase II from Aspergillus niger and identification of active site residues by site-directed mutagenesis.

Y.van Santen, J.A.Benen, K.H.Schröter, K.H.Kalk, S.Armand, J.Visser, B.W.Dijkstra.

ABSTRACT

Polygalacturonases specifically hydrolyze polygalacturonate, a major constituent of plant cell wall pectin. To understand the catalytic mechanism and substrate and product specificity of these enzymes, we have solved the x-ray structure of endopolygalacturonase II of Aspergillus niger and we have carried out site-directed mutagenesis studies. The enzyme folds into a right-handed parallel beta-helix with 10 complete turns. The beta-helix is composed of four parallel beta-sheets, and has one very small alpha-helix near the N terminus, which shields the enzyme's hydrophobic core. Loop regions form a cleft on the exterior of the beta-helix. Site-directed mutagenesis of Asp(180), Asp(201), Asp(202), His(223), Arg(256), and Lys(258), which are located in this cleft, results in a severe reduction of activity, demonstrating that these residues are important for substrate binding and/or catalysis. The juxtaposition of the catalytic residues differs from that normally encountered in inverting glycosyl hydrolases. A comparison of the endopolygalacturonase II active site with that of the P22 tailspike rhamnosidase suggests that Asp(180) and Asp(202) activate the attacking nucleophilic water molecule, while Asp(201) protonates the glycosidic oxygen of the scissile bond.

Selected figure(s)

Figure 2.
Fig. 2. A stereo view of the active site cleft, looking onto PB1. Residues that are completely conserved among all polygalacturonases, Asn178, Asp180, Asp201, Asp202, His223, Gly224, Arg256, and Lys 258, are shown in ball-and-stick. The putative hydrolytic water molecule is indicated by W.

Figure 3.
Fig. 3. Schematic representation of the catalytic mechanism proposed for family 28 glycosyl hydrolases. The conserved Asp201 (A. niger endopolygalacturonase numbering) acts as the proton donor, while Asp180 and Asp202 activate the hydrolytic water molecule.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (1999, 274, 30474-30480) copyright 1999.

Figures were selected by the author.