› 5fix

X-ray diffraction
2.01Å resolution

Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with sucrose

Released:
DOI: 10.2210/pdb5fix/pdb
PDB entry 5fix coloured by chain, front view.
PDB entry 5fix coloured by chain, side view.
PDB entry 5fix coloured by chain, top view.
Source organism: Phaffia rhodozyma
Primary publication:
Structural Analysis of β-Fructofuranosidase from Xanthophyllomyces dendrorhous Reveals Unique Features and the Crucial Role of N-Glycosylation in Oligomerization and Activity.
Ramírez-Escudero M, Gimeno-Pérez M, González B, Linde D, Merdzo Z, Fernández-Lobato M, Sanz-Aparicio J
J Biol Chem 291 6843-57 (2016)
PMID: 26823463

Function and Biology Details

Reaction catalysed: 
Hydrolysis of terminal non-reducing beta-D-fructofuranoside residues in beta-D-fructofuranosides
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-125341 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (6 distinct):
Beta-fructofuranosidase Chains: A, B
Molecule details ›
Chains: A, B
Length: 665 amino acids
Theoretical weight: 72.02 KDa
Source organism: Phaffia rhodozyma
Expression system: Komagataella phaffii GS115
UniProt:
  • Canonical: J7HDY4 (Residues: 1-665; Coverage: 100%)
Gene name: INV
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: GLC, FRU
Carbohydrate polymer
1 bound ligand:
Ligand NAG 27 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALBA BEAMLINE XALOC
Spacegroup: P21212
Unit cell:
a: 74.734Å b: 205.219Å c: 146.071Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.167 0.166 0.185
Expression system: Komagataella phaffii GS115

Quick links

Citations

1 review citation

Oligomeric Structure of Yeast and Other Invertases Governs Specificity.
Jiménez-Ortega et al. (2024)
13 other articles

2 mentions without citation

Structural Analysis of β-Fructofuranosidase from Xanthophyllomyces dendrorhous Reveals Unique Features and the Crucial Role of N-Glycosylation in Oligomerization and Activity.
Ramírez-Escudero et al. (2016)
1 more