› 7byt

X-ray diffraction
1.5Å resolution

Crystal structure of exo-beta-1,3-galactanase from Phanerochaete chrysosporium Pc1,3Gal43A with galactose

Released:
DOI: 10.2210/pdb7byt/pdb
PDB entry 7byt coloured by chain, front view.
PDB entry 7byt coloured by chain, side view.
PDB entry 7byt coloured by chain, top view.
Source organism: Phanerodontia chrysosporium
Primary publication:
Unique active-site and subsite features in the arabinogalactan-degrading GH43 exo-β-1,3-galactanase from Phanerochaete chrysosporium.
Matsuyama K, Kishine N, Fujimoto Z, Sunagawa N, Kotake T, Tsumuraya Y, Samejima M, Igarashi K, Kaneko S
J Biol Chem 295 18539-18552 (2020)
PMID: 33093171

Function and Biology Details

Reaction catalysed: 
Hydrolysis of terminal, non-reducing beta-D-galactose residues in (1->3)-beta-D-galactopyranans
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-175900 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
CBM6 domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 427 amino acids
Theoretical weight: 45.54 KDa
Source organism: Phanerodontia chrysosporium
Expression system: Komagataella pastoris
UniProt:
  • Canonical: Q50KB2 (Residues: 22-448; Coverage: 100%)
Sequence domains: Glycosyl hydrolases family 43

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
7 bound ligands:
Ligand NAG 2 x NAG
Ligand CA 1 x CA
Ligand GLA 1 x GLA
Ligand GAL 1 x GAL
Ligand ACY 2 x ACY
Ligand ACT 2 x ACT
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P212121
Unit cell:
a: 50.818Å b: 66.565Å c: 106.39Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.134 0.134 0.16
Expression system: Komagataella pastoris

Quick links

Citations

1 review citation

The Role of Arabinogalactan Type II Degradation in Plant-Microbe Interactions.
Villa-Rivera et al. (2021)
1 other article

1 mention without citation

Unique active-site and subsite features in the arabinogalactan-degrading GH43 exo-β-1,3-galactanase from Phanerochaete chrysosporium.
Matsuyama et al. (2020)