5KFN

Human DNA polymerase eta-DNA ternary complex with Sp-dATP-alpha-S: reaction with 1 mM Mg2+ for 1800s

Summary for 5KFN

• Entry DOI: 10.2210/pdb5kfn/pdb
• Related: 5KFA 5KFB 5KFC 5KFD 5KFE 5KFF 5KFG 5KFH 5KFI 5KFJ 5KFK 5KFL 5KFM 5KFO 5KFP 5KFQ 5KFR 5KFS 5KFT 5KFU 5KFV 5KFW 5KFX 5KFY 5KFZ 5KG0 5KG1 5KG2 5KG3 5KG4 5KG5 5KG6 5KG7
• 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: 55486.14

Authors

Gao, Y.,Yang, W. (deposition date: 2016-06-12, release date: 2016-06-22, 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 (1.45 Å)