SNAP output for PDB entry 1skw [SNAP web server]

PDB-id

1skw; SNAP-derived features in text and JSON formats; DNAproDB

Class

transferase-electron transport-DNA

Method

X-ray (2.3 Å)

Summary

Binary 3' complex of t7 DNA polymerase with a DNA primer-template containing a disordered cis-syn thymine dimer on the template

Reference

Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS, Ellenberger T (2004): "Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7." Nat.Struct.Mol.Biol., 11, 784-790. doi: 10.1038/nsmb792.

Abstract

Ultraviolet-induced DNA damage poses a lethal block to replication. To understand the structural basis for this, we determined crystal structures of a replicative DNA polymerase from bacteriophage T7 in complex with nucleotide substrates and a DNA template containing a cis-syn cyclobutane pyrimidine dimer (CPD). When the 3' thymine is the templating base, the CPD is rotated out of the polymerase active site and the fingers subdomain adopts an open orientation. When the 5' thymine is the templating base, the CPD lies within the polymerase active site where it base-pairs with the incoming nucleotide and the 3' base of the primer, while the fingers are in a closed conformation. These structures reveal the basis for the strong block of DNA replication that is caused by this photolesion.