› 5axh

X-ray diffraction
2.2Å resolution

Crystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus, D312G mutant in complex with isomaltohexaose

Released:
DOI: 10.2210/pdb5axh/pdb
Model geometry
Fit model/data
PDB entry 5axh coloured by chain, front view.
PDB entry 5axh coloured by chain, side view.
PDB entry 5axh coloured by chain, top view.
Source organism: Thermoanaerobacter pseudethanolicus ATCC 33223
Primary publication:
Crystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus.
Suzuki N, Kishine N, Fujimoto Z, Sakurai M, Momma M, Ko JA, Nam SH, Kimura A, Kim YM
J Biochem 159 331-9 (2016)
PMID: 26494689

Function and Biology Details

Reaction catalysed: 
Endohydrolysis of (1->6)-alpha-D-glucosidic linkages in dextran
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-109168 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (3 distinct):
Dextranase Chains: A, B
Molecule details ›
Chains: A, B
Length: 618 amino acids
Theoretical weight: 71.33 KDa
Source organism: Thermoanaerobacter pseudethanolicus ATCC 33223
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B0KBZ7 (Residues: 3-610; Coverage: 100%)
Gene name: Teth39_0264
Sequence domains: Glycosyl hydrolase family 66
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: GLC, BGC
Carbohydrate polymer
2 bound ligands:
Ligand PO4 4 x PO4
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P212121
Unit cell:
a: 78.334Å b: 99.179Å c: 169.254Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.162 0.16 0.205
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Marine Bacterial Dextranases: Fundamentals and Applications.
Barzkar et al. (2022)
1 more

1 mention without citation

Bacteroidota polysaccharide utilization system for branched dextran exopolysaccharides from lactic acid bacteria.
Nakamura et al. (2023)