› 2y1j

X-ray diffraction
2.15Å resolution

CRYSTAL STRUCTURE OF A R-DIASTEREOMER ANALOGUE OF THE SPORE PHOTOPRODUCT IN COMPLEX WITH FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS

Released:
DOI: 10.2210/pdb2y1j/pdb
PDB entry 2y1j coloured by chain, front view.
PDB entry 2y1j coloured by chain, side view.
PDB entry 2y1j coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structures and repair studies reveal the identity and the base-pairing properties of the UV-induced spore photoproduct DNA lesion.
Heil K, Kneuttinger AC, Schneider S, Lischke U, Carell T
Chemistry 17 9651-7 (2011)
PMID: 21780197

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-115947 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase I Chain: A
Molecule details ›
Chain: A
Length: 580 amino acids
Theoretical weight: 66.2 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: E1C9K5 (Residues: 1-580; Coverage: 100%)
Gene name: polA
Sequence domains: DNA polymerase family A
Structure domains:
5'-D(*GP*AP*CP*CP*AP*AP*CP*CP*CP*TP)-3' Chain: B
Molecule details ›
Chain: B
Length: 10 nucleotides
Theoretical weight: 2.97 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*AP*GP*GP*GP*QBTP*THM*GP*GP*TP*CP)-3' Chain: C
Molecule details ›
Chain: C
Length: 10 nucleotides
Theoretical weight: 3.04 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P212121
Unit cell:
a: 88.525Å b: 93.382Å c: 105.773Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.199 0.241
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

7 review citations

Radical S-adenosylmethionine enzymes.
Broderick et al. (2014)
6 more