› 2iq7

X-ray diffraction
1.94Å resolution

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

Released:
DOI: 10.2210/pdb2iq7/pdb
PDB entry 2iq7 coloured by chain, front view.
PDB entry 2iq7 coloured by chain, side view.
PDB entry 2iq7 coloured by chain, top view.
Source organism: Colletotrichum lupini
Primary publication:
Crystal structure of the endopolygalacturonase from the phytopathogenic fungus Colletotrichum lupini and its interaction with polygalacturonase-inhibiting proteins.
Bonivento D, Pontiggia D, Matteo AD, Fernandez-Recio J, Salvi G, Tsernoglou D, Cervone F, Lorenzo GD, Federici L
Proteins 70 294-9 (2008)
PMID: 17876815

Function and Biology Details

Reaction catalysed: 
(1,4-alpha-D-galacturonosyl)(n+m) + H(2)O = (1,4-alpha-D-galacturonosyl)(n) + (1,4-alpha-D-galacturonosyl)(m)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-106590 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (3 distinct):
endo-polygalacturonase Chains: A, B, C, D, E, F, G
Molecule details ›
Chains: A, B, C, D, E, F, G
Length: 339 amino acids
Theoretical weight: 34.21 KDa
Source organism: Colletotrichum lupini
UniProt:
  • Canonical: A1E266 (Residues: 24-362; Coverage: 98%)
Gene name: Pg1
Sequence domains: Glycosyl hydrolases family 28
Structure domains: Single-stranded right-handed beta-helix, Pectin lyase-like

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
3 bound ligands:
Ligand PG4 6 x PG4
Ligand PEG 3 x PEG
Ligand ACY 1 x ACY
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ELETTRA BEAMLINE 5.2R
Spacegroup: P212121
Unit cell:
a: 85.64Å b: 127.266Å c: 205.828Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.154 0.152 0.196

Quick links

Citations

3 review citations

Homogalacturonan-modifying enzymes: structure, expression, and roles in plants.
Sénéchal et al. (2014)
2 more

9 mentions without citation

Characterization of a newly isolated phage infecting pathogenic Escherichia coli and analysis of its mosaic structural genes.
Peng et al. (2018)
8 more