PDBsum entry 2iq7

Hydrolase

PDB id: 2iq7

Contents

Protein chains

(+ 1 more) 339 a.a. *

Ligands

NAG-NAG-MAN-MAN-MAN-MAN

NAG-NAG ×6

PG4 ×6

PEG ×3

ACY

Waters ×2438

* Residue conservation analysis

PDB id:

2iq7

Name:

Hydrolase

Title:

Crystal structure of the polygalacturonase from colletotrichum lupini and its implications for the interaction with polygalacturonase- inhibiting proteins

Structure:

Endopolygalacturonase. Chain: a, b, c, d, e, f, g. Ec: 3.2.1.15

Source:

Colletotrichum lupini. Organism_taxid: 145971

Resolution:

1.94Å R-factor: 0.154 R-free: 0.196

Authors:

D.Bonivento,L.Federici,A.D.Matteo

Key ref:

D.Bonivento et al. (2008). Crystal structure of the endopolygalacturonase from the phytopathogenic fungus Colletotrichum lupini and its interaction with polygalacturonase-inhibiting proteins. Proteins, 70, 294-299. PubMed id: 17876815 DOI: 10.1002/prot.21610

Date:

13-Oct-06 Release date: 23-Oct-07

Protein chains

A1E266  (A1E266_9PEZI) -  endo-polygalacturonase from Colletotrichum lupini var. setosum

Seq: 362 a.a.

Struc: 339 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.15 - endo-polygalacturonase.
• Reaction: (1,4-alpha-D-galacturonosyl)n+m + H2O = (1,4-alpha-D-galacturonosyl)n + (1,4-alpha-D-galacturonosyl)m

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

Key reference

DOI no: 10.1002/prot.21610

Proteins 70:294-299 (2008)

PubMed id: 17876815

Crystal structure of the endopolygalacturonase from the phytopathogenic fungus Colletotrichum lupini and its interaction with polygalacturonase-inhibiting proteins.

D.Bonivento, D.Pontiggia, A.D.Matteo, J.Fernandez-Recio, G.Salvi, D.Tsernoglou, F.Cervone, G.D.Lorenzo, L.Federici.

ABSTRACT

No abstract given.

Selected figure(s)

Figure 1.
Figure 1. (A) Ribbon representation of CluPG1. A cross section of the -helix is shown on the right panel; the color code indicates the secondary structure elements in a representative coil. (B) Structural superposition of CluPG1 with AnPGII and FmPG. The red circle indicates an eight residues insertion in the structure of FmPG that likely plays a role in the interaction of this enzyme with PGIPs.

Figure 2.
Figure 2. (A) CluPG1 enzyme kinetics and inhibition played by PvPGIP2. The uninhibited enzyme is represented in squares; triangles and circles represent the data obtained in the presence of 4 and 8 nM PvPGIP2, respectively. Curves represent the fits of experimental data with non-linear regression analysis using the Michaelis-Menten equation. K[m] and V[max] values are reported in the inset. A decrease in V[max] while K[m] remains constant is indicative of noncompetitive inhibition. (B) Optimal docking areas of CluPG1, AnPGII, and FmPG. Surface residues with an ODA value lower than -2 kcal/mol are colored in red, otherwise in blue. Black arrows mark the position of the active sites. The putative interaction areas of CluPG1 and AnPGII, located below the binding cleft, are almost superimposable. Differently, FmPG shows two distinct patches on opposite sides of the active site. A different PG-PGIP interaction area for the latter enzyme with respect to CluPG1 and AnPGII is suggested, which accounts for the different modes of inhibition observed. The view is 90° anticlockwise rotated over the z-axis with respect to Figure 1.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 70, 294-299) copyright 2008.