8XK9

ternary complex of DNA polymerase SFM4-3 recognizing C2 methyoxy nucleotide

This is a non-PDB format compatible entry.

Summary for 8XK9

• Entry DOI: 10.2210/pdb8xk9/pdb
• Related: 8XJR 8XK7
• Descriptor: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3'), DNA (5'-D(*AP*AP*CP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-R(P*(OMG))-3'), DNA polymerase I, thermostable, ... (8 entities in total)
• Functional Keywords: dna polymerase, dna binding protein
• Biological source: Thermus aquaticus; More
• Total number of polymer chains: 6
• Total formula weight: 140391.28

Authors

Wen, C.,Liu, H.,Yang, L.,Gong, W. (deposition date: 2023-12-22, release date: 2024-11-27)

Primary citation

Wen, C.,Wang, G.,Yang, L.,Chen, T.,Liu, H.,Gong, W.
Structural Basis for C2'-methoxy Recognition by DNA Polymerases and Function Improvement.
J.Mol.Biol., 436:168744-168744, 2024

PubMed Abstract: 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.

PubMed: 39147125
DOI: 10.1016/j.jmb.2024.168744

Experimental method

X-RAY DIFFRACTION (2.4 Å)