8F69 | pdb_00008f69

Crystal structure of murine PolG2 dimer bound to DNA

PDB DOI: https://doi.org/10.2210/pdb8F69/pdb
NAKB: 8F69

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Mus musculus, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-11-16 Released: 2023-08-09
Deposition Author(s): Wojtaszek, J.L., Hoff, K.E., Williams, R.S.
Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.228 (Depositor), 0.243 (DCC)
R-Value Work:
0.194 (Depositor)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure-specific roles for PolG2-DNA complexes in maintenance and replication of mitochondrial DNA.

Wojtaszek, J.L., Hoff, K.E., Longley, M.J., Kaur, P., Andres, S.N., Wang, H., Williams, R.S., Copeland, W.C.

(2023) Nucleic Acids Res 51: 9716-9732

PubMed: 37592734 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1093/nar/gkad679
Primary Citation Related Structures:
8F69, 8F6B

PubMed Abstract:
The homodimeric PolG2 accessory subunit of the mitochondrial DNA polymerase gamma (Pol γ) enhances DNA binding and processive DNA synthesis by the PolG catalytic subunit. PolG2 also directly binds DNA, although the underlying molecular basis and functional significance are unknown. Here, data from Atomic Force Microscopy (AFM) and X-ray structures of PolG2-DNA complexes define dimeric and hexameric PolG2 DNA binding modes. Targeted disruption of PolG2 DNA-binding interfaces impairs processive DNA synthesis without diminishing Pol γ subunit affinities. In addition, a structure-specific DNA-binding role for PolG2 oligomers is supported by X-ray structures and AFM showing that oligomeric PolG2 localizes to DNA crossings and targets forked DNA structures resembling the mitochondrial D-loop. Overall, data indicate that PolG2 DNA binding has both PolG-dependent and -independent functions in mitochondrial DNA replication and maintenance, which provide new insight into molecular defects associated with PolG2 disruption in mitochondrial disease.

Organizational Affiliation

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.

Macromolecule Content

Total Structure Weight: 108.8 kDa
Atom Count: 7,352
Modeled Residue Count: 850
Deposited Residue Count: 892
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase subunit gamma-2, mitochondrial	A [auth B], B [auth A]	428	Mus musculus	Mutation(s): 0 Gene Names: Polg2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9QZM2 (Mus musculus) Explore Q9QZM2 Go to UniProtKB: Q9QZM2
IMPC: MGI:1354947
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9QZM2
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(CPTPGPGPTPAPGPGPCPGPCPCPTPAPCPCPAPG)-3')	C, D	18	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain F [auth B] MOL2 format, chain P [auth A] MOL2 format, chain F [auth B] mmCIF format, chain P [auth A] mmCIF format, chain F [auth B]	F [auth B], P [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain F [auth B] Focus chain P [auth A] Interactions & Density Focus chain F [auth B] Focus chain P [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain Q [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain E [auth B] MOL2 format, chain R [auth A] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain E [auth B] mmCIF format, chain R [auth A] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain E [auth B]	E [auth B] G [auth B] H [auth B] I [auth B] J [auth B] E [auth B], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth A], N [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Interactions & Density Focus chain E [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A]