8XK7 image
Entry Detail
PDB ID:
8XK7
Title:
binary complex of DNA polymerase SFM4-3 recognizing C2 methyoxy nucleotide
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2023-12-22
Release Date:
2024-11-27
Method Details:
Experimental Method:
Resolution:
2.00 Å
R-Value Free:
0.23
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:DNA polymerase I, thermostable
Chain IDs:A
Chain Length:554
Number of Molecules:1
Biological Source:Thermus aquaticus
Polymer Type:polydeoxyribonucleotide
Description:DNA(5'-D(*AP*AP*AP*CP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*CP*OMG)-3')
Chain IDs:B
Chain Length:17
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Description:DNA(5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*CP*OMG)-3')
Chain IDs:C
Chain Length:13
Number of Molecules:1
Biological Source:synthetic construct
Primary Citation
Structural Basis for C2'-methoxy Recognition by DNA Polymerases and Function Improvement.
J.Mol.Biol. 436 168744 168744 (2024)
PMID: 39147125 DOI: 10.1016/j.jmb.2024.168744

Abstact

DNA modified with C2'-methoxy (C2'-OMe) greatly enhances its resistance to nucleases, which is beneficial for the half-life of aptamers and DNA nanomaterials. Although the unnatural DNA polymerases capable of incorporating C2'-OMe modified nucleoside monophosphates (C2'-OMe-NMPs) were engineered via directed evolution, the detailed molecular mechanism by which an evolved DNA polymerase recognizes C2'-OMe-NTPs remains poorly understood. Here, we present the crystal structures of the evolved Stoffel fragment of Taq DNA polymerase SFM4-3 processing the C2'-OMe-GTP in different states. Our results reveal the structural basis for recognition of C2'-methoxy by SFM4-3. Based on the analysis of other mutated residues in SFM4-3, a new Stoffel fragment variant with faster catalytic rate and stronger inhibitor-resistance was obtained. In addition, the capture of a novel pre-insertion co-existing with template 5'-overhang stacking conformation provides insight into the catalytic mechanism of Taq DNA polymerase.

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Primary Citation of related structures