› 2d0f

X-ray diffraction
2.08Å resolution

Crystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant D356N complexed with P2, a pullulan model oligosaccharide

Released:
DOI: 10.2210/pdb2d0f/pdb
PDB entry 2d0f coloured by chain, front view.
PDB entry 2d0f coloured by chain, side view.
PDB entry 2d0f coloured by chain, top view.
Source organism: Thermoactinomyces vulgaris
Primary publication:
Complexes of Thermoactinomyces vulgaris R-47 alpha-amylase 1 and pullulan model oligossacharides provide new insight into the mechanism for recognizing substrates with alpha-(1,6) glycosidic linkages.
Abe A, Yoshida H, Tonozuka T, Sakano Y, Kamitori S
FEBS J 272 6145-53 (2005)
PMID: 16302977

Function and Biology Details

Reaction catalysed: 
Hydrolysis of pullulan to panose (6-alpha-D-glucosylmaltose)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-178752 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (3 distinct):
Neopullulanase 1 Chain: A
Molecule details ›
Chain: A
Length: 637 amino acids
Theoretical weight: 71.11 KDa
Source organism: Thermoactinomyces vulgaris
Expression system: Escherichia coli
UniProt:
  • Canonical: Q60053 (Residues: 30-666; Coverage: 100%)
Gene name: tvaI
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: BGC, GLC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: BGC, GLC
Carbohydrate polymer
2 bound ligands:
Ligand CA 3 x CA
Ligand MPD 4 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: C2
Unit cell:
a: 121.532Å b: 50.429Å c: 107.834Å
α: 90° β: 104.3° γ: 90°
R-values:
R R work R free
0.157 0.154 0.187
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Occurrence and functional significance of secondary carbohydrate binding sites in glycoside hydrolases.
Cuyvers et al. (2012)
2 more

1 mention without citation

Crystal Structure and Mutational Analysis of Isomalto-dextranase, a Member of Glycoside Hydrolase Family 27.
Okazawa et al. (2015)