ISDA

Entry Detail

PDB ID:

5YTC

Keywords:

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, synthetic construct

Host Organism:

Escherichia coli

PDB Version:

Deposition Date:

2017-11-17

Release Date:

2018-11-21

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

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:DNA polymerase I, thermostable
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
Description: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
Description: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

Primary Citation

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, Y.Q, Yi, C.Show

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