› 5fkb

X-ray diffraction
1.78Å resolution

Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with 1-Kestose

Released:
DOI: 10.2210/pdb5fkb/pdb
PDB entry 5fkb coloured by chain, front view.
PDB entry 5fkb coloured by chain, side view.
PDB entry 5fkb 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: 663 amino acids
Theoretical weight: 71.78 KDa
Source organism: Phaffia rhodozyma
Expression system: Komagataella phaffii GS115
UniProt:
  • Canonical: J7HDY4 (Residues: 3-665; 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: PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
Spacegroup: P21212
Unit cell:
a: 74.526Å b: 205.019Å c: 145.988Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.171 0.17 0.184
Expression system: Komagataella phaffii GS115

Quick links

Citations

10 citation in other articles

Characterization of fructooligosaccharide metabolism and fructooligosaccharide-degrading enzymes in human commensal butyrate producers.
Tanno et al. (2021)
9 more

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