› 3vmp

X-ray diffraction
1.88Å resolution

Crystal structure of dextranase from Streptococcus mutans in complex with 4,5-epoxypentyl alpha-D-glucopyranoside

Released:
DOI: 10.2210/pdb3vmp/pdb
PDB entry 3vmp coloured by chain, front view.
PDB entry 3vmp coloured by chain, side view.
PDB entry 3vmp coloured by chain, top view.
Source organism: Streptococcus mutans
Primary publication:
Structural elucidation of dextran degradation mechanism by streptococcus mutans dextranase belonging to glycoside hydrolase family 66.
Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K, Kimura A
J Biol Chem 287 19916-26 (2012)
PMID: 22337884

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176202 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dextranase Chain: A
Molecule details ›
Chain: A
Length: 643 amino acids
Theoretical weight: 72.6 KDa
Source organism: Streptococcus mutans
Expression system: Escherichia coli
UniProt:
  • Canonical: Q54443 (Residues: 100-732; Coverage: 75%)
Gene names: SMU_2042, dexA
Sequence domains: Glycosyl hydrolase family 66
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand E5G 1 x E5G
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P21
Unit cell:
a: 53.428Å b: 89.966Å c: 62.842Å
α: 90° β: 102.25° γ: 90°
R-values:
R R work R free
0.198 0.195 0.238
Expression system: Escherichia coli

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Citations

2 review citations

Multiple rewards from a treasure trove of novel glycoside hydrolase and polysaccharide lyase structures: new folds, mechanistic details, and evolutionary relationships.
Fushinobu et al. (2013)
1 more

2 mentions without citation

Structural elucidation of dextran degradation mechanism by streptococcus mutans dextranase belonging to glycoside hydrolase family 66.
Suzuki et al. (2012)
1 more