Networked Communication between Polymerase and Exonuclease Active Sites in Human Mitochondrial DNA Polymerase

Mark L. Sowers, Andrew P.P. Anderson, James O. Wrabl, Y. Whitney Yin

Research output: Contribution to journalArticle

Abstract

High fidelity human mitochondrial DNA polymerase (Pol Γ) contains two active sites, a DNA polymerization site (pol) and a 3′-5′ exonuclease site (exo) for proofreading. Although separated by 35 Å, coordination between the pol and exo sites is crucial to high fidelity replication. The biophysical mechanisms for this coordination are not completely understood. To understand the communication between the two active sites, we used a statistical-mechanical model of the protein ensemble to calculate the energetic landscape and local stability. We compared a series of structures of Pol Γ, complexed with primer/template DNA, and either a nucleotide substrate or a series of nucleotide analogues, which are differentially incorporated and excised by pol and exo activity. Despite the nucleotide or its analogues being bound in the pol, Pol γresidue stability varied across the protein, particularly in the exo domain. This suggests that substrate presence in the pol can be "sensed" in the exo domain. Consistent with this hypothesis, in silico mutations made in one active site mutually perturbed the energetics of the other. To identify specific regions of the polymerase that contributed to this communication, we constructed an allosteric network connectivity map that further demonstrates specific pol-exo cooperativity. Thus, a cooperative network underlies energetic connectivity. We propose that Pol γand other dual-function polymerases exploit an energetic coupling network that facilitates domain-domain communication to enhance discrimination between correct and incorrect nucleotides.

Original languageEnglish (US)
Pages (from-to)10821-10829
Number of pages9
JournalJournal of the American Chemical Society
Volume141
Issue number27
DOIs
StatePublished - Jul 10 2019

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Exonucleases
DNA-Directed DNA Polymerase
Nucleotides
Mitochondrial DNA
Catalytic Domain
DNA
Communication
Proteins
DNA Primers
Statistical Models
Substrates
Polymerization
Computer Simulation
Mutation

ASJC Scopus subject areas

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

Cite this

Networked Communication between Polymerase and Exonuclease Active Sites in Human Mitochondrial DNA Polymerase. / Sowers, Mark L.; Anderson, Andrew P.P.; Wrabl, James O.; Yin, Y. Whitney.

In: Journal of the American Chemical Society, Vol. 141, No. 27, 10.07.2019, p. 10821-10829.

Research output: Contribution to journalArticle

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