› 1n7k

X-ray diffraction
2Å resolution

Unique tetrameric structure of deoxyribose phosphate aldolase from Aeropyrum pernix

Released:
DOI: 10.2210/pdb1n7k/pdb
PDB entry 1n7k coloured by chain, front view.
PDB entry 1n7k coloured by chain, side view.
PDB entry 1n7k coloured by chain, top view.
Source organism: Aeropyrum pernix
Primary publication:
The first crystal structure of archaeal aldolase. Unique tetrameric structure of 2-deoxy-d-ribose-5-phosphate aldolase from the hyperthermophilic archaea Aeropyrum pernix.
Sakuraba H, Tsuge H, Shimoya I, Kawakami R, Goda S, Kawarabayasi Y, Katunuma N, Ago H, Miyano M, Ohshima T
J Biol Chem 278 10799-806 (2003)
PMID: 12529358

Function and Biology Details

Reaction catalysed: 
2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195423 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Deoxyribose-phosphate aldolase Chains: A, B
Molecule details ›
Chains: A, B
Length: 234 amino acids
Theoretical weight: 24.43 KDa
Source organism: Aeropyrum pernix
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q9Y948 (Residues: 2-235; Coverage: 100%)
Gene names: APE_2437.1, deoC
Sequence domains: DeoC/LacD family aldolase
Structure domains: Aldolase class I

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-6A
Spacegroup: P21212
Unit cell:
a: 75.293Å b: 84.185Å c: 87.238Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.224 0.224 0.263
Expression system: Escherichia coli BL21

Quick links

Citations

5 review citations

Implication for buried polar contacts and ion pairs in hyperthermostable enzymes.
Matsui et al. (2007)
4 more

1 mention without citation

Using catalytic atom maps to predict the catalytic functions present in enzyme active sites.
Nosrati et al. (2012)