Summary information and primary citation

PDB-id
4ecw; DSSR-derived features in text and JSON formats
Class
transferase-DNA
Method
X-ray (1.896 Å)
Summary
Human DNA polymerase eta - DNA ternary complex: reaction in the at crystal at ph 7.0 for 250 sec
Reference
Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W (2012): "Watching DNA polymerase eta make a phosphodiester bond." Nature, 487, 196-201. doi: 10.1038/nature11181.
Abstract
DNA synthesis has been extensively studied, but the chemical reaction itself has not been visualized. Here we follow the course of phosphodiester bond formation using time-resolved X-ray crystallography. Native human DNA polymerase η, DNA and dATP were co-crystallized at pH 6.0 without Mg(2+). The polymerization reaction was initiated by exposing crystals to 1 mM Mg(2+) at pH 7.0, and stopped by freezing at desired time points for structural analysis. The substrates and two Mg(2+) ions are aligned within 40 s, but the bond formation is not evident until 80 s. From 80 to 300 s structures show a mixture of decreasing substrate and increasing product of the nucleotidyl-transfer reaction. Transient electron densities indicate that deprotonation and an accompanying C2'-endo to C3'-endo conversion of the nucleophile 3'-OH are rate limiting. A third Mg(2+) ion, which arrives with the new bond and stabilizes the intermediate state, may be an unappreciated feature of the two-metal-ion mechanism.

Cartoon-block schematics in six views (download the tarball)

PyMOL session file Download PDB file View in 3Dmol.js