8UZT

Mitochondrial single-stranded binding protein bound to DNA

This is a non-PDB format compatible entry.

Summary for 8UZT

• Entry DOI: 10.2210/pdb8uzt/pdb
• Descriptor: Single-stranded DNA-binding protein, mitochondrial, dTDNA, GLYCEROL, ... (5 entities in total)
• Functional Keywords: single-stranded binding protein, dna binding protein, mitochondrial ssb, ssb, mitochondrial replication protein, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 5
• Total formula weight: 76989.16

Authors

Riccio, A.A.,Pedersen, L.C.,Bouvette, J.,Borgnia, J.M.,Copeland, W.C. (deposition date: 2023-11-16, release date: 2024-08-21, Last modification date: 2024-10-02)

Primary citation

Riccio, A.A.,Bouvette, J.,Pedersen, L.C.,Somai, S.,Dutcher, R.C.,Borgnia, M.J.,Copeland, W.C.
Structures of the mitochondrial single-stranded DNA binding protein with DNA and DNA polymerase gamma.
Nucleic Acids Res., 52:10329-10340, 2024

PubMed Abstract: The mitochondrial single-stranded DNA (ssDNA) binding protein, mtSSB or SSBP1, binds to ssDNA to prevent secondary structures of DNA that could impede downstream replication or repair processes. Clinical mutations in the SSBP1 gene have been linked to a range of mitochondrial disorders affecting nearly all organs and systems. Yet, the molecular determinants governing the interaction between mtSSB and ssDNA have remained elusive. Similarly, the structural interaction between mtSSB and other replisome components, such as the mitochondrial DNA polymerase, Polγ, has been minimally explored. Here, we determined a 1.9-Å X-ray crystallography structure of the human mtSSB bound to ssDNA. This structure uncovered two distinct DNA binding sites, a low-affinity site and a high-affinity site, confirmed through site-directed mutagenesis. The high-affinity binding site encompasses a clinically relevant residue, R38, and a highly conserved DNA base stacking residue, W84. Employing cryo-electron microscopy, we confirmed the tetrameric assembly in solution and capture its interaction with Polγ. Finally, we derived a model depicting modes of ssDNA wrapping around mtSSB and a region within Polγ that mtSSB binds.

PubMed: 39106165
DOI: 10.1093/nar/gkae670

Experimental method

X-RAY DIFFRACTION (1.9 Å)