› 4hno

X-ray diffraction
0.92Å resolution

High resolution crystal structure of DNA Apurinic/apyrimidinic (AP) endonuclease IV Nfo from Thermatoga maritima

Released:
DOI: 10.2210/pdb4hno/pdb
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PDB entry 4hno coloured by chain, front view.
PDB entry 4hno coloured by chain, side view.
PDB entry 4hno coloured by chain, top view.
Source organism: Thermotoga maritima MSB8
Primary publication:
Conserved structural chemistry for incision activity in structurally non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes.
Tsutakawa SE, Shin DS, Mol CD, Izumi T, Arvai AS, Mantha AK, Szczesny B, Ivanov IN, Hosfield DJ, Maiti B, Pique ME, Frankel KA, Hitomi K, Cunningham RP, Mitra S, Tainer JA
J Biol Chem 288 8445-8455 (2013)
PMID: 23355472

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-194516 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Probable endonuclease 4 Chain: A
Molecule details ›
Chain: A
Length: 288 amino acids
Theoretical weight: 32.55 KDa
Source organism: Thermotoga maritima MSB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9WYJ7 (Residues: 2-285; Coverage: 99%)
Gene names: TM_0362, nfo
Sequence domains: Xylose isomerase-like TIM barrel
Structure domains: Divalent-metal-dependent TIM barrel enzymes

Ligands and Environments

6 bound ligands:
Ligand ZN 3 x ZN
Ligand MN 2 x MN
Ligand MG 1 x MG
Ligand TRS 1 x TRS
Ligand EDO 2 x EDO
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRL BEAMLINE BL9-1
Spacegroup: P61
Unit cell:
a: 123.37Å b: 123.37Å c: 35.395Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.126 0.125 0.139
Expression system: Escherichia coli

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Citations

12 review citations

Human apurinic/apyrimidinic endonuclease 1.
Li et al. (2014)
11 more

2 mentions without citation

Conserved structural chemistry for incision activity in structurally non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes.
Tsutakawa et al. (2013)
1 more

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