5YTC image
Deposition Date 2017-11-17
Release Date 2018-11-21
Last Version Date 2023-11-22
Entry Detail
PDB ID:
5YTC
Keywords:
TRANSFERASE/DNA
Title:
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
Biological Source:
Source Organism:
Thermus aquaticus (Taxon ID: 271)
synthetic construct (Taxon ID: 32630)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.28 Å
R-Value Free:
0.25
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 31 2 1
5YTC validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA polymerase I, thermostable
Gene (Uniprot):polA
Chain IDs:A
Chain Length:539
Number of Molecules:1
Biological Source:Thermus aquaticus
UniProt ID:P19821 Pfam ID:PF09281, PF00476 EC:2.7.7.7
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC)P*(DOC))-3')
Chain IDs:B
Chain Length:13
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*AP*AP*AP*(92F)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
Chain IDs:C
Chain Length:16
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
DTP
MG
Primary Citation
Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry.
Angew. Chem. Int. Ed. Engl. 58 130 133 (2019)
PMID: 30407705 DOI: 10.1002/anie.201807845

Abstact

The emergence of unnatural DNA bases provides opportunities to demystify the mechanisms by which DNA polymerases faithfully decode chemical information on the template. It was previously shown that two unnatural cytosine bases (termed "M-fC" and "I-fC"), which are chemical labeling adducts of the epigenetic base 5-formylcytosine, can induce C-to-T transition during DNA amplification. However, how DNA polymerases recognize such unnatural cytosine bases remains enigmatic. Herein, crystal structures of unnatural cytosine bases pairing to dA/dG in the KlenTaq polymerase-host-guest complex system and pairing to dATP in the KlenTaq polymerase active site were determined. Both M-fC and I-fC base pair with dA/dATP, but not with dG, in a Watson-Crick geometry. This study reveals that the formation of the Watson-Crick geometry, which may be enabled by the A-rule, is important for the recognition of unnatural cytosines.

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Primary Citation of related structures
5YTC