› 6juq

X-ray diffraction
2.74Å resolution

mutant PolIV-DNA incoming nucleotide complex 2

Released:
DOI: 10.2210/pdb6juq/pdb
PDB entry 6juq coloured by chain, front view.
PDB entry 6juq coloured by chain, side view.
PDB entry 6juq 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-120099 (preferred)
Entry contents:
2 distinct polypeptide molecules
3 distinct DNA molecules
Macromolecules (5 distinct):
DNA polymerase IV Chain: F
Molecule details ›
Chain: 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 polymerase IV Chain: A
Molecule details ›
Chain: A
Length: 341 amino acids
Theoretical weight: 38.29 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*C)-3') Chains: B, G
Molecule details ›
Chains: B, G
Length: 17 nucleotides
Theoretical weight: 5.2 KDa
DNA (5'-D(P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') Chain: H
Molecule details ›
Chain: H
Length: 14 nucleotides
Theoretical weight: 4.28 KDa
DNA (5'-D(P*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 15 nucleotides
Theoretical weight: 4.61 KDa

Ligands and Environments

2 bound ligands:
Ligand 2TM 2 x 2TM
Ligand MN 4 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P21
Unit cell:
a: 86.151Å b: 57.244Å c: 110.793Å
α: 90° β: 92.26° γ: 90°
R-values:
R R work R free
0.228 0.226 0.271
Expression system: Escherichia coli

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)