SNAP output for PDB entry 6q4t [SNAP web server]

PDB-id

6q4t; SNAP-derived features in text and JSON formats; DNAproDB

Class

DNA binding protein

Method

X-ray (1.997 Å)

Summary

Kod DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-hydroxyethoxy)-n-(prop-2-yn-1-yl)acetamide)-2-datp

Reference

Kropp HM, Diederichs K, Marx A (2019): "The Structure of an Archaeal B-Family DNA Polymerase in Complex with a Chemically Modified Nucleotide." Angew.Chem.Int.Ed.Engl., 58, 5457-5461. doi: 10.1002/anie.201900315.

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 the DNA pols is key to these technologies. By now, no structural data are available for these DNA pols in complex with modified substrates which could build the basis for understanding interactions between the enzyme and the chemical modification and for further development of next generation nucleotides. For the first time we crystallized an exonuclease deficient variant of B-family KOD DNA pol wild-type 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 elucidates how the protein and the DNA modulate two distinct conformations of the modification in the A- and B-family DNA pols and how these influence the processing of the modified nucleotide. Overall, this study provides first insights on how B-family DNA pols interplay with relevant modified substrates.