› 5ytc

X-ray diffraction
2.28Å resolution

Large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with the unnatural base M-fC pair with dATP in the active site

Released:
DOI: 10.2210/pdb5ytc/pdb
PDB entry 5ytc coloured by chain, front view.
PDB entry 5ytc coloured by chain, side view.
PDB entry 5ytc coloured by chain, top view.
Source organisms:
Primary publication:
Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry.
Zeng H, Mondal M, Song R, Zhang J, Xia B, Liu M, Zhu C, He B, Gao YQ, Yi C
Angew Chem Int Ed Engl 58 130-133 (2019)
PMID: 30407705

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-119440 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase I, thermostable Chain: A
Molecule details ›
Chain: A
Length: 539 amino acids
Theoretical weight: 60.87 KDa
Source organism: Thermus aquaticus
Expression system: Escherichia coli
UniProt:
  • Canonical: P19821 (Residues: 294-832; Coverage: 65%)
Gene names: pol1, polA
Sequence domains:
Structure domains:
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC)P*(DOC))-3') Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 3.89 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*AP*AP*AP*(92F)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 5 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DTP 1 x DTP
Ligand MG 2 x MG
1 modified residue:
Ligand DOC 2 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P3121
Unit cell:
a: 108.886Å b: 108.886Å c: 90.533Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.197 0.194 0.258
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

Non-Oxidative Enzymatic (De)Carboxylation of (Hetero)Aromatics and Acrylic Acid Derivatives.
Payer et al. (2019)
2 more