9FMF

KlenTaq DNA polymerase in a ternary complex with primer/template and a fluorobenzofuran-modified dUTP (FBFdUTP)

This is a non-PDB format compatible entry.

Summary for 9FMF

• Entry DOI: 10.2210/pdb9fmf/pdb
• Related: 9FM3
• Descriptor: DNA polymerase I, thermostable, Primer, DNA template, ... (7 entities in total)
• Functional Keywords: dna polymerase, fluorobenzofuran, fluorescent nucleotide probe, klentaq, transferase
• Biological source: Thermus aquaticus; More
• Total number of polymer chains: 3
• Total formula weight: 70196.19

Authors

Betz, K.,Srivatsan, S.G. (deposition date: 2024-06-06, release date: 2024-11-13, Last modification date: 2025-01-22)

Primary citation

Ghosh, P.,Betz, K.,Gutfreund, C.,Pal, A.,Marx, A.,Srivatsan, S.G.
Structures of a DNA Polymerase Caught while Incorporating Responsive Dual-Functional Nucleotide Probes.
Angew.Chem.Int.Ed.Engl., 64:e202414319-e202414319, 2025

PubMed Abstract: Functionalizing nucleic acids using DNA polymerases is essential in biophysical and biotechnology applications. This study focuses on understanding how DNA polymerases recognize and incorporate nucleotides with diverse chemical modifications, aiming to develop advanced nucleotide probes. We present the crystal structures of ternary complexes of Thermus aquaticus DNA polymerase (KlenTaq) with C5-heterocycle-modified environment-sensitive 2'-deoxyuridine-5'-triphosphate (dUTP) probes. These nucleotides include SedUTP, BFdUTP and FBFdUTP, which bear selenophene, benzofuran and fluorobenzofuran, respectively, at the C5 position of uracil, and exhibit high conformational sensitivity. SedUTP and FBFdUTP serve as dual-app probes, combining a fluorophore with X-ray anomalous scattering Se or F NMR labels. Our study reveals that the size of the heterocycle influences how DNA polymerase families A and B incorporate these modified nucleotides during single nucleotide incorporation and primer extension reactions. Remarkably, the responsiveness of FBFdUTP enabled real-time monitoring of the binary complex formation and polymerase activity through fluorescence and F NMR spectroscopy. Comparative analysis of incorporation profiles, fluorescence, F NMR data, and crystal structures of ternary complexes highlights the plasticity of the enzyme. Key insight is provided into the role of gatekeeper amino acids (Arg660 and Arg587) in accommodating and processing these modified substrates, offering a structural basis for next-generation nucleotide probe development.

PubMed: 39428682
DOI: 10.1002/anie.202414319

Experimental method

X-RAY DIFFRACTION (2.1 Å)