5JGH

Crystal structure of the mitochondrial DNA packaging protein Abf2p in complex with DNA at 2.6 Angstrom resolution

Summary for 5JGH

• Entry DOI: 10.2210/pdb5jgh/pdb
• Descriptor: ARS-binding factor 2, mitochondrial, DNA (5'-D(*TP*TP*TP*AP*TP*TP*AP*TP*TP*TP*TP*AP*TP*AP*TP*TP*AP*TP*AP*TP*AP*A)-3'), DNA (5'-D(*TP*TP*AP*TP*AP*TP*AP*AP*TP*AP*TP*AP*AP*AP*AP*TP*AP*AP*TP*AP*AP*A)-3'), ... (5 entities in total)
• Functional Keywords: dna binding protein dna packaging, dna binding protein
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast); More
• Cellular location: Mitochondrion: Q02486
• Total number of polymer chains: 12
• Total formula weight: 132034.68

Authors

Chakraborty, A.,Lyonnais, S.,Sola, M. (deposition date: 2016-04-20, release date: 2017-02-08, Last modification date: 2024-05-01)

Primary citation

Chakraborty, A.,Lyonnais, S.,Battistini, F.,Hospital, A.,Medici, G.,Prohens, R.,Orozco, M.,Vilardell, J.,Sola, M.
DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p.
Nucleic Acids Res., 45:951-967, 2017

PubMed Abstract: The mitochondrial genome (mtDNA) is assembled into nucleo-protein structures termed nucleoids and maintained differently compared to nuclear DNA, the involved molecular basis remaining poorly understood. In yeast (Saccharomyces cerevisiae), mtDNA is a ∼80 kbp linear molecule and Abf2p, a double HMG-box protein, packages and maintains it. The protein binds DNA in a non-sequence-specific manner, but displays a distinct 'phased-binding' at specific DNA sequences containing poly-adenine tracts (A-tracts). We present here two crystal structures of Abf2p in complex with mtDNA-derived fragments bearing A-tracts. Each HMG-box of Abf2p induces a 90° bend in the contacted DNA, causing an overall U-turn. Together with previous data, this suggests that U-turn formation is the universal mechanism underlying mtDNA compaction induced by HMG-box proteins. Combining this structural information with mutational, biophysical and computational analyses, we reveal a unique DNA binding mechanism for Abf2p where a characteristic N-terminal flag and helix are crucial for mtDNA maintenance. Additionally, we provide the molecular basis for A-tract mediated exclusion of Abf2p binding. Due to high prevalence of A-tracts in yeast mtDNA, this has critical relevance for nucleoid architecture. Therefore, an unprecedented A-tract mediated protein positioning mechanism regulates DNA packaging proteins in the mitochondria, and in combination with DNA-bending and U-turn formation, governs mtDNA compaction.

PubMed: 27899643
DOI: 10.1093/nar/gkw1147

Experimental method

X-RAY DIFFRACTION (2.6 Å)