› 4nlg

X-ray diffraction
2.4Å resolution

Y-family DNA polymerase chimera Dbh-Dpo4(243-245)-Dbh

Released:
DOI: 10.2210/pdb4nlg/pdb
PDB entry 4nlg coloured by chain, front view.
PDB entry 4nlg coloured by chain, side view.
PDB entry 4nlg coloured by chain, top view.
Source organism: Sulfolobus acidocaldarius
Primary publication:
Three residues of the interdomain linker determine the conformation and single-base deletion fidelity of Y-family translesion polymerases.
Mukherjee P, Wilson RC, Lahiri I, Pata JD
J Biol Chem 289 6323-6331 (2014)
PMID: 24415763

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-117877 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chain: A
Molecule details ›
Chain: A
Length: 362 amino acids
Theoretical weight: 41.02 KDa
Source organism: Sulfolobus acidocaldarius
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q4JB80 (Residues: 1-354; Coverage: 100%)
Gene names: Saci_0554, dbh
Sequence domains:
Structure domains:
5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*G)-3' Chain: P
Molecule details ›
Chain: P
Length: 13 nucleotides
Theoretical weight: 4.03 KDa
Source organism: Sulfolobus acidocaldarius
Expression system: Not provided
5'-D(*TP*TP*AP*CP*GP*CP*CP*CP*TP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3' Chain: T
Molecule details ›
Chain: T
Length: 19 nucleotides
Theoretical weight: 5.76 KDa
Source organism: Sulfolobus acidocaldarius
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CA 2 x CA
Ligand DCP 1 x DCP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: C2
Unit cell:
a: 120.193Å b: 103.067Å c: 53.049Å
α: 90° β: 105.39° γ: 90°
R-values:
R R work R free
0.177 0.174 0.231
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 citation in other articles

A Role for Non-B DNA Forming Sequences in Mediating Microlesions Causing Human Inherited Disease.
Kamat et al. (2016)
2 more

2 mentions without citation

DNA binding strength increases the processivity and activity of a Y-Family DNA polymerase.
Wu et al. (2017)
1 more