4ED1

Human DNA polymerase eta - DNA ternary complex: AT crystal at pH 7.0 (Na+ MES) with 1 Ca2+ ion

Summary for 4ED1

• Entry DOI: 10.2210/pdb4ed1/pdb
• Related: 4ECQ 4ECR 4ECS 4ECT 4ECU 4ECV 4ECW 4ECX 4ECY 4ECZ 4ED0 4ED2 4ED3 4ED6 4ED7 4ED8
• Descriptor: DNA polymerase eta, DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3'), DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3'), ... (8 entities in total)
• Functional Keywords: transferase-dna complex, transferase/dna
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus: Q9Y253
• Total number of polymer chains: 3
• Total formula weight: 55512.25

Authors

Nakamura, T.,Zhao, Y.,Yang, W. (deposition date: 2012-03-26, release date: 2012-07-11, Last modification date: 2024-03-20)

Primary citation

Nakamura, T.,Zhao, Y.,Yamagata, Y.,Hua, Y.J.,Yang, W.
Watching DNA polymerase eta make a phosphodiester bond
Nature, 487:196-201, 2012

PubMed 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.

PubMed: 22785315
DOI: 10.1038/nature11181

Experimental method

X-RAY DIFFRACTION (1.806 Å)