› 1vfm

X-ray diffraction
2.9Å resolution

Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase 2/alpha-cyclodextrin complex

Released:
DOI: 10.2210/pdb1vfm/pdb
PDB entry 1vfm coloured by chain, front view.
PDB entry 1vfm coloured by chain, side view.
PDB entry 1vfm coloured by chain, top view.
Source organism: Thermoactinomyces vulgaris
Primary publication:
Complex structures of Thermoactinomyces vulgaris R-47 alpha-amylase 2 with acarbose and cyclodextrins demonstrate the multiple substrate recognition mechanism.
Ohtaki A, Mizuno M, Tonozuka T, Sakano Y, Kamitori S
J Biol Chem 279 31033-40 (2004)
PMID: 15138257

Function and Biology Details

Reaction catalysed: 
Hydrolysis of pullulan to panose (6-alpha-D-glucosylmaltose)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-170688 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (3 distinct):
Neopullulanase 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 585 amino acids
Theoretical weight: 67.55 KDa
Source organism: Thermoactinomyces vulgaris
Expression system: Escherichia coli
UniProt:
  • Canonical: Q08751 (Residues: 1-585; Coverage: 100%)
Gene name: tvaII
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: GLC, BGC
Carbohydrate polymer
1 bound ligand:
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P212121
Unit cell:
a: 115.395Å b: 118.428Å c: 113.69Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.191 0.248
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Dual substrate recognition of aminotransferases.
Hirotsu et al. (2005)
1 more

2 mentions without citation

Natural Products as Platforms To Overcome Antibiotic Resistance.
Rossiter et al. (2017)
1 more