› 6jup

X-ray diffraction
2.44Å resolution

Mutant PolIV-DNA incoming nucleotide complex

Released:
DOI: 10.2210/pdb6jup/pdb
PDB entry 6jup coloured by chain, front view.
PDB entry 6jup coloured by chain, side view.
PDB entry 6jup coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
A polar filter in DNA polymerases prevents ribonucleotide incorporation.
Johnson MK, Kottur J, Nair DT
Nucleic Acids Res 47 10693-10705 (2019)
PMID: 31544946

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120097 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chains: A, F
Molecule details ›
Chains: A, F
Length: 342 amino acids
Theoretical weight: 38.35 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: Q47155 (Residues: 2-341; Coverage: 97%)
Gene names: JW0221, b0231, dinB, dinP
Sequence domains:
DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*CP*C)-3') Chain: G
Molecule details ›
Chain: G
Length: 18 nucleotides
Theoretical weight: 5.49 KDa
Source organism: Escherichia coli
Expression system: Not provided
DNA (5'-D(P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') Chains: B, C, H
Molecule details ›
Chains: B, C, H
Length: 18 nucleotides
Theoretical weight: 5.51 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand 0KX 2 x 0KX
Ligand MG 4 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P21
Unit cell:
a: 86.184Å b: 56.974Å c: 111.136Å
α: 90° β: 92.9° γ: 90°
R-values:
R R work R free
0.222 0.221 0.245
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

One, No One, and One Hundred Thousand: The Many Forms of Ribonucleotides in DNA.
Nava et al. (2020)
2 more

1 mention without citation

A polar filter in DNA polymerases prevents ribonucleotide incorporation.
Johnson et al. (2019)