6Q4T

KOD DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-hydroxyethoxy)-N-(prop-2-yn-1-yl)acetamide)-2-dATP

Summary for 6Q4T

• Entry DOI: 10.2210/pdb6q4t/pdb
• Descriptor: DNA polymerase,DNA polymerase,DNA polymerase, DNA (5'-D(P*AP*AP*CP*TP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'), DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*C)-3'), ... (10 entities in total)
• Functional Keywords: dna polymerase archaeal b-family modified nucleotide next-generation sequencing, dna binding protein
• Biological source: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1)); More
• Total number of polymer chains: 3
• Total formula weight: 99995.46

Authors

Kropp, H.M.,Diederichs, K.,Marx, A. (deposition date: 2018-12-06, release date: 2019-02-27, Last modification date: 2024-01-24)

Primary citation

Kropp, H.M.,Diederichs, K.,Marx, A.
The Structure of an Archaeal B-Family DNA Polymerase in Complex with a Chemically Modified Nucleotide.
Angew.Chem.Int.Ed.Engl., 58:5457-5461, 2019

PubMed Abstract: Archaeal B-family DNA polymerases (DNA pols) are the driving force of cutting-edge biotechnological applications like next-generation sequencing. The acceptance of chemically modified nucleotides by DNA pols is key to these technologies. Until now, no structural data have been available for these DNA pols in complex with modified substrates, which could build the basis for understanding interactions between the enzyme and the chemically modified nucleotide and for the further development of next-generation nucleotides. For the first time, we crystallized an exonuclease-deficient variant of the wild-type B-family KOD DNA pol with a modified nucleotide in a closed, ternary complex. We also crystalized the A-family DNA pol KlenTaq with the same nucleotide. The reported structural data reveal how the protein and the DNA modulate two distinct conformations of the appended moiety in the A- and B-family DNA pols and how these influence the processing of the modified nucleotide. Overall, this study provides first insight into the interplay between B-family DNA pols and relevant modified substrates.

PubMed: 30761722
DOI: 10.1002/anie.201900315

Experimental method

X-RAY DIFFRACTION (1.997 Å)