› 4dqs

X-ray diffraction
1.66Å resolution

Binary complex of Bacillus DNA Polymerase I Large Fragment and duplex DNA with rC in primer terminus paired with dG of template

Released:
DOI: 10.2210/pdb4dqs/pdb
PDB entry 4dqs coloured by chain, front view.
PDB entry 4dqs coloured by chain, side view.
PDB entry 4dqs coloured by chain, top view.
Source organism: Geobacillus kaustophilus HTA426
Primary publication:
Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides.
Wang W, Wu EY, Hellinga HW, Beese LS
J Biol Chem 287 28215-26 (2012)
PMID: 22648417

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-113145 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
1 distinct DNA/RNA hybrid molecule
Macromolecules (3 distinct):
DNA polymerase I Chain: A
Molecule details ›
Chain: A
Length: 592 amino acids
Theoretical weight: 67.52 KDa
Source organism: Geobacillus kaustophilus HTA426
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5KWC1 (Residues: 287-878; Coverage: 67%)
Gene names: GK2730, polA
Sequence domains: DNA polymerase family A
Structure domains:
DNA (5'-D(*GP*A*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3') Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 4.92 KDa
Source organism: Geobacillus kaustophilus HTA426
Expression system: Not provided
DNA/RNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-R(P*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.66 KDa
Source organism: Geobacillus kaustophilus HTA426
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CTP 1 x CTP
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 12.3.1
Spacegroup: P212121
Unit cell:
a: 88.41Å b: 93.41Å c: 105.76Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.161 0.16 0.181
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

8 review citations

Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell.
Wei et al. (2016)
7 more

2 mentions without citation

Building better polymerases: Engineering the replication of expanded genetic alphabets.
Ouaray et al. (2020)
1 more