› 4h7u

X-ray diffraction
1.6Å resolution

Crystal structure of pyranose dehydrogenase from Agaricus meleagris, wildtype

Released:
DOI: 10.2210/pdb4h7u/pdb
PDB entry 4h7u coloured by chain, front view.
PDB entry 4h7u coloured by chain, side view.
PDB entry 4h7u coloured by chain, top view.
Source organism: Leucoagaricus meleagris
Primary publication:
The 1.6 Å crystal structure of pyranose dehydrogenase from Agaricus meleagris rationalizes substrate specificity and reveals a flavin intermediate.
Tan TC, Spadiut O, Wongnate T, Sucharitakul J, Krondorfer I, Sygmund C, Haltrich D, Chaiyen P, Peterbauer CK, Divne C
PLoS One 8 e53567 (2013)
PMID: 23326459

Function and Biology Details

Reaction catalysed: 
A pyranoside + acceptor = a pyranosid-3,4-diulose + reduced acceptor
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-174723 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Pyranose dehydrogenase 1 Chain: A
Molecule details ›
Chain: A
Length: 602 amino acids
Theoretical weight: 64.75 KDa
Source organism: Leucoagaricus meleagris
Expression system: Komagataella pastoris
UniProt:
  • Canonical: Q3L245 (Residues: 1-602; Coverage: 100%)
Gene name: pdh1
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand FED 1 x FED
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand NAG 1 x NAG
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MAX II BEAMLINE I911-5
Spacegroup: P212121
Unit cell:
a: 51.938Å b: 74.64Å c: 139.286Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.172 0.171 0.201
Expression system: Komagataella pastoris

Quick links

Citations

1 review citation

Alteration of Electron Acceptor Preferences in the Oxidative Half-Reaction of Flavin-Dependent Oxidases and Dehydrogenases.
Hiraka et al. (2020)
22 other articles

10 mentions without citation

Multiplicity of enzymatic functions in the CAZy AA3 family.
Sützl et al. (2018)
9 more