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TitlePol γ possesses separate metal binding sites for polymerase and strand displacement functions.
Journal, issue, pagesbioRxiv, Year 2026
Publish dateJan 25, 2026
PubMed AbstractAccurate replication of mitochondrial genome (mtDNA) integrity, which is essential for cellular metabolism and energy supply, relies primarily on DNA polymerase gamma (Pol γ), Twinkle helicase, and ...Accurate replication of mitochondrial genome (mtDNA) integrity, which is essential for cellular metabolism and energy supply, relies primarily on DNA polymerase gamma (Pol γ), Twinkle helicase, and mitochondrial single-stranded DNA binding protein (mtSSB). Twinkle alone exhibits little helicase activity while reports indicate that Pol γ displays from modest to limited unwinding activity. This led us to dissect Pol γ strand displacement activity using structural, biochemical and in silico approaches. Here, we show that human Pol γ carries out robust strand displacement synthesis at physiological concentrations of divalent metal ions which reveals that distinct metal-binding sites can independently regulate DNA synthesis and unwinding activities. We further showed that Pol γ can displace RNA/DNA hybrid with comparable efficiency as DNA/DNA duplex, representing a key implication on RNA primer removal to preserve mtDNA integrity. Our cryo-electron microscopy structures of Pol γ complexed with a template containing downstream dsDNA and an incoming nucleotide revealed the structural mechanism for the strand displacement activity. We identified four conformational states that represent successive stages of DNA unwinding, accompanied by coordinated rearrangement of the downstream DNA and Pol γ elements that mediate strand displacement. This work establishes biochemical and structural mechanisms of Pol γ strand displacement activity, providing fundamental insight into human mitochondrial DNA replication and integrity.
External linksbioRxiv / PubMed:41648309 / PubMed Central
MethodsEM (single particle)
Resolution2.62 - 3.23 Å
Structure data

72478

9y4c

EMDB-72478, PDB-9y4c:
Strand displacement state I of Human mitochondrial DNA polymerase gamma ternary complex
Method: EM (single particle) / Resolution: 3.23 Å

72479

9y4d

EMDB-72479, PDB-9y4d:
Strand displacement state II of Human mitochondrial DNA polymerase gamma ternary complex
Method: EM (single particle) / Resolution: 2.94 Å

72480

9y4e

EMDB-72480, PDB-9y4e:
Strand displacement state III of Human mitochondrial DNA polymerase gamma ternary complex
Method: EM (single particle) / Resolution: 3.05 Å

72481

9y4f

EMDB-72481, PDB-9y4f:
Strand displacement state IV of Human mitochondrial DNA polymerase gamma ternary complex
Method: EM (single particle) / Resolution: 2.62 Å

Chemicals

ChemComp-CA:
Unknown entry

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

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsTRANSFERASE/DNA / DNA polymerase gamma / strand displacement / mitochondria / TRANSFERASE-DNA complex

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