SNAP output for PDB entry 4m3r [SNAP web server]

PDB-id

4m3r; SNAP-derived features in text and JSON formats; DNAproDB

Class

hydrolase-DNA

Method

X-ray (2.07 Å)

Summary

Rb69 DNA polymerase ternary complex with dt-dg at position n-1 of primer-template duplex

Reference

Xia S, Konigsberg WH (2014): "Mispairs with Watson-Crick base-pair geometry observed in ternary complexes of an RB69 DNA polymerase variant." Protein Sci., 23, 508-513. doi: 10.1002/pro.2434.

Abstract

Recent structures of DNA polymerase complexes with dGMPCPP/dT and dCTP/dA mispairs at the insertion site have shown that they adopt Watson-Crick geometry in the presence of Mn(2+) indicating that the tautomeric or ionization state of the base has changed. To see whether the tautomeric or ionization state of base-pair could be affected by its microenvironment, we determined 10 structures of an RB69 DNA polymerase quadruple mutant with dG/dT or dT/dG mispairs at position n-1 to n-5 of the Primer/Template duplex. Different shapes of the mispairs, including Watson-Crick geometry, have been observed, strongly suggesting that the local environment of base-pairs plays an important role in their tautomeric or ionization states.