› 4uqg

X-ray diffraction
2Å resolution

A new bio-isosteric base pair based on reversible bonding

Released:
DOI: 10.2210/pdb4uqg/pdb
PDB entry 4uqg coloured by chain, front view.
PDB entry 4uqg coloured by chain, side view.
PDB entry 4uqg coloured by chain, top view.
Source organisms:
Primary publication:
"Post-it" type connected DNA created with a reversible covalent cross-link.
Tomás-Gamasa M, Serdjukow S, Su M, Müller M, Carell T
Angew Chem Int Ed Engl 54 796-800 (2015)
PMID: 25446281

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-509041 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase I Chain: A
Molecule details ›
Chain: A
Length: 579 amino acids
Theoretical weight: 66.15 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: E1C9K5 (Residues: 2-580; Coverage: 100%)
Gene name: polA
Sequence domains:
Structure domains:
5'-D(*GP*AP*CP*C T0TP*TP*CP*CP*CP*TP)-3' Chain: B
Molecule details ›
Chain: B
Length: 10 nucleotides
Theoretical weight: 3.03 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*AP*GP*GP*GP*A SAYP*GP*GP*TP*CP)-3' Chain: C
Molecule details ›
Chain: C
Length: 10 nucleotides
Theoretical weight: 3.12 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, FRU
Carbohydrate polymer
1 bound ligand:
Ligand SO4 4 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 87.442Å b: 93.996Å c: 105.416Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.178 0.211
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

16 citation in other articles

Characterization of Interstrand DNA-DNA Cross-Links Using the α-Hemolysin Protein Nanopore.
Zhang et al. (2015)
15 more

1 mention without citation

Mycobacterial DNA polymerase I: activities and crystal structures of the POL domain as apoenzyme and in complex with a DNA primer-template and of the full-length FEN/EXO-POL enzyme.
Ghosh et al. (2020)