› 3aam

X-ray diffraction
1.58Å resolution

Crystal structure of endonuclease IV from Thermus thermophilus HB8

Released:
DOI: 10.2210/pdb3aam/pdb
Model geometry
Fit model/data
PDB entry 3aam coloured by chain, front view.
PDB entry 3aam coloured by chain, side view.
PDB entry 3aam coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
An additional C-terminal loop in endonuclease IV, an apurinic/apyrimidinic endonuclease, controls binding affinity to DNA.
Asano R, Ishikawa H, Nakane S, Nakagawa N, Kuramitsu S, Masui R
Acta Crystallogr D Biol Crystallogr 67 149-55 (2011)
PMID: 21358045

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to 5'-phosphooligonucleotide end-products
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-178057 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Xylose isomerase-like TIM barrel domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 270 amino acids
Theoretical weight: 29.13 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5SK18 (Residues: 1-270; Coverage: 100%)
Gene name: TTHA0834
Sequence domains: Xylose isomerase-like TIM barrel
Structure domains: Divalent-metal-dependent TIM barrel enzymes

Ligands and Environments

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

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SPRING-8 BEAMLINE BL26B2
Spacegroup: P21
Unit cell:
a: 36.646Å b: 85.273Å c: 36.58Å
α: 90° β: 105.37° γ: 90°
R-values:
R R work R free
0.199 0.199 0.223
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 citation in other articles

A unique DNA-binding mode of African swine fever virus AP endonuclease.
Chen et al. (2020)
5 more

2 mentions without citation

Thermococcus Eurythermalis Endonuclease IV Can Cleave Various Apurinic/Apyrimidinic Site Analogues in ssDNA and dsDNA.
Wang et al. (2018)
1 more