5KFS

Human DNA polymerase eta R61A-DNA ternary complex: ground state at pH7.0 (K+ MES) with 1 Ca2+ ion

Summary for 5KFS

• Entry DOI: 10.2210/pdb5kfs/pdb
• 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: in crystallo reaction, dna polymerase, metal ion dependent catalysis, replication, transferase-dna complex, transferase/dna
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 3
• Total formula weight: 55442.24

Authors

Gao, Y.,Yang, W. (deposition date: 2016-06-12, release date: 2016-06-29, Last modification date: 2023-09-27)

Primary citation

Gao, Y.,Yang, W.
Capture of a third Mg2+ is essential for catalyzing DNA synthesis.
Science, 352:1334-1337, 2016

PubMed 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.

PubMed: 27284197
DOI: 10.1126/science.aad9633

Experimental method

X-RAY DIFFRACTION (1.46 Å)