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Structure paper

TitleMolecular and structural basis for replication initiation and strand separation by human mitochondrial DNA polymerase γ.
Journal, issue, pagesNucleic Acids Res, Vol. 54, Issue 18, Year 2026
Publish dateSep 22, 2026
AuthorsViktoriia Sokolova / Gina Buchel / Sarah Strock / Ashok R Nayak / Dmitry Temiakov /
PubMed AbstractDefects in human mitochondrial DNA (mtDNA) replication can lead to somatic mutations associated with a range of devastating mitochondrial diseases. However, the molecular mechanisms governing the ...Defects in human mitochondrial DNA (mtDNA) replication can lead to somatic mutations associated with a range of devastating mitochondrial diseases. However, the molecular mechanisms governing the earliest steps of mtDNA replication and their fidelity remain poorly understood. Here, we found that DNA polymerase gamma (Polγ) forms stable complexes with RNA-DNA primer-template substrates, exhibiting greater stability and lower misincorporation than on DNA-primed substrates. Structural analysis revealed that Polγ interacts with the 2'-OH groups of ribose within the first four nucleotides of the primer, explaining the stability of complexes that utilize RNA primers. Although Polγ requires TWINKLE to extend RNA primers, its intrinsic strand-displacement activity allows it to extend DNA primers independently. Structural data further show that the strand-separation mechanism in human Polγ is distinct from that of its yeast paralog, Mip1, and involves previously unresolved elements-the catcher and a GP loop in the exonuclease domain-that support intrinsic strand-displacement synthesis by Polγ. Structure-guided mutagenesis of elements involved in strand separation supports these structural observations. Together, our study provides mechanistic insight into mtDNA replication initiation and strand separation and has implications for understanding the molecular basis of mitochondrial disease.
External linksNucleic Acids Res / PubMed:42788360 / PubMed Central
MethodsEM (single particle)
Resolution2.6 - 2.93 Å
Structure data

71503

9pck

EMDB-71503, PDB-9pck:
Human DNA Polymerase Gamma-RNA-DNA Primer-Template Complex with Incoming ATP
Method: EM (single particle) / Resolution: 2.6 Å

76732

12sl

EMDB-76732, PDB-12sl:
Structure of a Strand-Displacement Complex of Human Mitochondrial DNA Polymerase Gamma
Method: EM (single particle) / Resolution: 2.93 Å

EMDB-77233: Raw Consensus map of the Strand-Displacement Complex of Human Mitochondrial DNA Polymerase Gamma
Method: EM (single particle) / Resolution: 2.93 Å

EMDB-77234: Focused map (Catalytic Subunit) of the Strand-Displacement Complex of Human Mitochondrial DNA Polymerase Gamma
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-77235: Focused map (Accessory Subunit) of the Strand-Displacement Complex of Human Mitochondrial DNA Polymerase Gamma
Method: EM (single particle) / Resolution: 2.81 Å

Chemicals

ChemComp-DTP:
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

ChemComp-MG:
Unknown entry

ChemComp-2DT:
3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE

ChemComp-TTP:
THYMIDINE-5'-TRIPHOSPHATE

ChemComp-2DA:
2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE

ChemComp-HOH:
WATER

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsREPLICATION / Mitochondrial DNA Polymerase Gamma / PolG / DNA strand displacement / Mitochondrial DNA Polymerase / Transferase-RNA complex

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