› 1ud2

X-ray diffraction
2.13Å resolution

Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38)

Released:
DOI: 10.2210/pdb1ud2/pdb
PDB entry 1ud2 coloured by chain, front view.
PDB entry 1ud2 coloured by chain, side view.
PDB entry 1ud2 coloured by chain, top view.
Source organism: Bacillus sp. KSM-K38
Primary publication:
Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites.
Nonaka T, Fujihashi M, Kita A, Hagihara H, Ozaki K, Ito S, Miki K
J Biol Chem 278 24818-24 (2003)
PMID: 12719434

Function and Biology Details

Reaction catalysed: 
Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188065 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glycosyl hydrolase family 13 catalytic domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 480 amino acids
Theoretical weight: 55.15 KDa
Source organism: Bacillus sp. KSM-K38
Expression system: Bacillus subtilis
UniProt:
  • Canonical: Q93I48 (Residues: 22-501; Coverage: 100%)
Gene name: amyK38
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand NA 3 x NA
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL45PX
Spacegroup: P23
Unit cell:
a: 132.143Å b: 132.143Å c: 132.143Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.196 0.229
Expression system: Bacillus subtilis

Quick links

Citations

7 review citations

Role of Na+ and K+ in enzyme function.
Page et al. (2006)
6 more

1 mention without citation

Structural and functional adaptation in extremophilic microbial α-amylases.
Ahmad et al. (2022)