6CQM

Crystal Structure of mitochondrial single-stranded DNA binding proteins from S. cerevisiae, Rim1 (Form2)

Summary for 6CQM

• Entry DOI: 10.2210/pdb6cqm/pdb
• Descriptor: Single-stranded DNA-binding protein RIM1, mitochondrial (1 entity in total)
• Functional Keywords: mitochondrial single-stranded dna binding proteins, dna binding protein
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
• Total number of polymer chains: 8
• Total formula weight: 107486.22

Authors

Singh, S.P.,Kukshal, V.,Bona, P.D.,Lytle, A.K.,Edwin, A.,Galletto, R. (deposition date: 2018-03-15, release date: 2018-05-30, Last modification date: 2024-03-13)

Primary citation

Singh, S.P.,Kukshal, V.,De Bona, P.,Antony, E.,Galletto, R.
The mitochondrial single-stranded DNA binding protein from S. cerevisiae, Rim1, does not form stable homo-tetramers and binds DNA as a dimer of dimers.
Nucleic Acids Res., 46:7193-7205, 2018

PubMed Abstract: Rim1 is the mitochondrial single-stranded DNA binding protein in Saccharomyces cerevisiae and functions to coordinate replication and maintenance of mtDNA. Rim1 can form homo-tetramers in solution and this species has been assumed to be solely responsible for ssDNA binding. We solved structures of tetrameric Rim1 in two crystals forms which differ in the relative orientation of the dimers within the tetramer. In testing whether the different arrangement of the dimers was due to formation of unstable tetramers, we discovered that while Rim1 forms tetramers at high protein concentration, it dissociates into a smaller oligomeric species at low protein concentrations. A single point mutation at the dimer-dimer interface generates stable dimers and provides support for a dimer-tetramer oligomerization model. The presence of Rim1 dimers in solution becomes evident in DNA binding studies using short ssDNA substrates. However, binding of the first Rim1 dimer is followed by binding of a second dimer, whose affinity depends on the length of the ssDNA. We propose a model where binding of DNA to a dimer of Rim1 induces tetramerization, modulated by the ability of the second dimer to interact with ssDNA.

PubMed: 29931186
DOI: 10.1093/nar/gky530

Experimental method

X-RAY DIFFRACTION (3 Å)