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5jgh

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==Crystal structure of the mitochondrial DNA packaging protein Abf2p in complex with DNA at 2.6 Angstrom resolution==
==Crystal structure of the mitochondrial DNA packaging protein Abf2p in complex with DNA at 2.6 Angstrom resolution==
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<StructureSection load='5jgh' size='340' side='right' caption='[[5jgh]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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<StructureSection load='5jgh' size='340' side='right'caption='[[5jgh]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5jgh]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JGH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JGH FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5jgh]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JGH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JGH FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5jgh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jgh OCA], [http://pdbe.org/5jgh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jgh RCSB], [http://www.ebi.ac.uk/pdbsum/5jgh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jgh ProSAT]</span></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5jgh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jgh OCA], [https://pdbe.org/5jgh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jgh RCSB], [https://www.ebi.ac.uk/pdbsum/5jgh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jgh ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/ABF2_YEAST ABF2_YEAST]] Specific binding to the autonomously replicating sequence 1 (ARS1). Interaction with regulatory regions: probably involved in compacting the mitochondrial genome. It might play a positive role in gene expression and replication.
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[https://www.uniprot.org/uniprot/ABF2_YEAST ABF2_YEAST] Specific binding to the autonomously replicating sequence 1 (ARS1). Interaction with regulatory regions: probably involved in compacting the mitochondrial genome. It might play a positive role in gene expression and replication.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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 approximately 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 degrees 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.
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DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p.,Chakraborty A, Lyonnais S, Battistini F, Hospital A, Medici G, Prohens R, Orozco M, Vilardell J, Sola M Nucleic Acids Res. 2017 Jan 25;45(2):951-967. doi: 10.1093/nar/gkw1147. Epub 2016, Nov 29. PMID:27899643<ref>PMID:27899643</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5jgh" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Chakraborty, A]]
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[[Category: Large Structures]]
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[[Category: Lyonnais, S]]
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[[Category: Saccharomyces cerevisiae]]
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[[Category: Sola, M]]
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[[Category: Saccharomyces cerevisiae S288C]]
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[[Category: Dna binding protein]]
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[[Category: Chakraborty A]]
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[[Category: Dna binding protein dna packaging]]
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[[Category: Lyonnais S]]
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[[Category: Sola M]]

Current revision

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

PDB ID 5jgh

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