› 4ebd

X-ray diffraction
2.57Å resolution

Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota

Released:
DOI: 10.2210/pdb4ebd/pdb
PDB entry 4ebd coloured by chain, front view.
PDB entry 4ebd coloured by chain, side view.
PDB entry 4ebd coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A nucleotide-analogue-induced gain of function corrects the error-prone nature of human DNA polymerase iota.
Ketkar A, Zafar MK, Banerjee S, Marquez VE, Egli M, Eoff RL
J Am Chem Soc 134 10698-705 (2012)
PMID: 22632140

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117399 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase iota Chain: A
Molecule details ›
Chain: A
Length: 420 amino acids
Theoretical weight: 47.03 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9UNA4 (Residues: 26-445; Coverage: 57%)
Gene names: POLI, RAD30B
Sequence domains:
Structure domains:
5'-D(P*AP*GP*GP*AP*CP*CP*(DOC))-3' Chain: P
Molecule details ›
Chain: P
Length: 7 nucleotides
Theoretical weight: 2.09 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(P*CP*TP*GP*GP*GP*TP*CP*CP*T)-3' Chain: T
Molecule details ›
Chain: T
Length: 9 nucleotides
Theoretical weight: 2.72 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand 0OJ 1 x 0OJ
Ligand CA 3 x CA
Ligand GOL 2 x GOL
1 modified residue:
Ligand DOC 1 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P6522
Unit cell:
a: 97.776Å b: 97.776Å c: 202.739Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.212 0.206 0.263
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

4 citation in other articles

Leukotriene biosynthesis inhibitor MK886 impedes DNA polymerase activity.
Ketkar et al. (2013)
3 more

5 mentions without citation

Expanding the repertoire of methanocarba nucleosides from purinergic signaling to diverse targets.
Jacobson et al. (2021)
4 more