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Structure paper

TitlePolγ coordinates DNA synthesis and proofreading to ensure mitochondrial genome integrity.
Journal, issue, pagesNat Struct Mol Biol, Vol. 30, Issue 6, Page 812-823, Year 2023
Publish dateMay 18, 2023
AuthorsJoon Park / Geoffrey K Herrmann / Patrick G Mitchell / Michael B Sherman / Y Whitney Yin /
PubMed AbstractAccurate replication of mitochondrial DNA (mtDNA) by DNA polymerase γ (Polγ) is essential for maintaining cellular energy supplies, metabolism, and cell cycle control. To illustrate the structural ...Accurate replication of mitochondrial DNA (mtDNA) by DNA polymerase γ (Polγ) is essential for maintaining cellular energy supplies, metabolism, and cell cycle control. To illustrate the structural mechanism for Polγ coordinating polymerase (pol) and exonuclease (exo) activities to ensure rapid and accurate DNA synthesis, we determined four cryo-EM structures of Polγ captured after accurate or erroneous incorporation to a resolution of 2.4-3.0 Å. The structures show that Polγ employs a dual-checkpoint mechanism to sense nucleotide misincorporation and initiate proofreading. The transition from replication to error editing is accompanied by increased dynamics in both DNA and enzyme, in which the polymerase relaxes its processivity and the primer-template DNA unwinds, rotates, and backtracks to shuttle the mismatch-containing primer terminus 32 Å to the exo site for editing. Our structural and functional studies also provide a foundation for analyses of Polγ mutation-induced human diseases and aging.
External linksNat Struct Mol Biol / PubMed:37202477 / PubMed Central
MethodsEM (single particle)
Resolution2.46 - 3.04 Å
Structure data

27154

8d33

EMDB-27154, PDB-8d33:
Human mitochondrial DNA polymerase gamma ternary complex with GC basepair
Method: EM (single particle) / Resolution: 2.46 Å

27155

8d37

EMDB-27155, PDB-8d37:
Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in replication conformer
Method: EM (single particle) / Resolution: 2.65 Å

27163

8d3r

EMDB-27163, PDB-8d3r:
Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in intermediate conformer
Method: EM (single particle) / Resolution: 3.04 Å

EMDB-27169: Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in editing conformer (consensus)
Method: EM (single particle) / Resolution: 2.91 Å

EMDB-27170: Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in editing conformer (local refinement of subunit A and primer/template DNA)
Method: EM (single particle) / Resolution: 2.76 Å

EMDB-27171: Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in editing conformer (local refinement of subunit B)
Method: EM (single particle) / Resolution: 2.76 Å

27172

8d42

EMDB-27172, PDB-8d42:
Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in editing conformer (composite)
Method: EM (single particle) / Resolution: 2.91 Å

Chemicals

ChemComp-CA:
Unknown entry

ChemComp-DCP:
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsTRANSFERASE/DNA / DNA-binding protein / DNA polymerase / TRANSFERASE-DNA complex

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