DSSR-PyMOL cartoon-block schematics: PDB entry 5kfx

PDB-id

5kfx; DSSR-derived features in text and JSON formats

Class

replication, transferase-DNA

Method

X-ray (1.52 Å)

Summary

Human DNA polymerase eta r61a-DNA ternary complex: reaction with 1 mm mg2+ for 300s

Reference

Gao Y, Yang W (2016): "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633.

Abstract

It is generally assumed that an enzyme-substrate (ES) complex contains all components necessary for catalysis and that conversion to products occurs by rearrangement of atoms, protons, and electrons. However, we find that DNA synthesis does not occur in a fully assembled DNA polymerase-DNA-deoxynucleoside triphosphate complex with two canonical metal ions bound. Using time-resolved x-ray crystallography, we show that the phosphoryltransfer reaction takes place only after the ES complex captures a third divalent cation that is not coordinated by the enzyme. Binding of the third cation is incompatible with the basal ES complex and requires thermal activation of the ES for entry. It is likely that the third cation provides the ultimate boost over the energy barrier to catalysis of DNA synthesis.