3r8f

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<StructureSection load='3r8f' size='340' side='right'caption='[[3r8f]], [[Resolution|resolution]] 3.37&Aring;' scene=''>
<StructureSection load='3r8f' size='340' side='right'caption='[[3r8f]], [[Resolution|resolution]] 3.37&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3r8f]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. The December 2013 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''DNA Helicase'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2013_12 10.2210/rcsb_pdb/mom_2013_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R8F FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3r8f]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. The December 2013 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''DNA Helicase'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2013_12 10.2210/rcsb_pdb/mom_2013_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R8F FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 3.366&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aq_322, dnaA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</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=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3r8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r8f OCA], [https://pdbe.org/3r8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r8f RCSB], [https://www.ebi.ac.uk/pdbsum/3r8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r8f ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3r8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r8f OCA], [https://pdbe.org/3r8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r8f RCSB], [https://www.ebi.ac.uk/pdbsum/3r8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r8f ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/DNAA_AQUAE DNAA_AQUAE]] Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box): 5'-TTATC[CA]A[CA]A-3'. DnaA binds to ATP and to acidic phospholipids (By similarity).
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[https://www.uniprot.org/uniprot/DNAA_AQUAE DNAA_AQUAE] Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box): 5'-TTATC[CA]A[CA]A-3'. DnaA binds to ATP and to acidic phospholipids (By similarity).
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Many replication initiators form higher-order oligomers that process host replication origins to promote replisome formation. In addition to dedicated duplex-DNA-binding domains, cellular initiators possess AAA+ (ATPases associated with various cellular activities) elements that drive functions ranging from protein assembly to origin recognition. In bacteria, the AAA+ domain of the initiator DnaA has been proposed to assist in single-stranded DNA formation during origin melting. Here we show crystallographically and in solution that the ATP-dependent assembly of Aquifex aeolicus DnaA into a spiral oligomer creates a continuous surface that allows successive AAA+ domains to bind and extend single-stranded DNA segments. The mechanism of binding is unexpectedly similar to that of RecA, a homologous recombination factor, but it differs in that DnaA promotes a nucleic acid conformation that prevents pairing of a complementary strand. These findings, combined with strand-displacement assays, indicate that DnaA opens replication origins by a direct ATP-dependent stretching mechanism. Comparative studies reveal notable commonalities between the approach used by DnaA to engage DNA substrates and other, nucleic-acid-dependent, AAA+ systems.
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DNA stretching by bacterial initiators promotes replication origin opening.,Duderstadt KE, Chuang K, Berger JM Nature. 2011 Oct 2;478(7368):209-13. doi: 10.1038/nature10455. PMID:21964332<ref>PMID:21964332</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 3r8f" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[DnaA|DnaA]]
*[[DnaA|DnaA]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Aquifex aeolicus huber and stetter 2001]]
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[[Category: Aquifex aeolicus]]
[[Category: DNA Helicase]]
[[Category: DNA Helicase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: RCSB PDB Molecule of the Month]]
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[[Category: Berger, J M]]
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[[Category: Berger JM]]
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[[Category: Chuang, K]]
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[[Category: Chuang K]]
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[[Category: Duderstadt, K E]]
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[[Category: Duderstadt KE]]
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[[Category: Aaa+ atpase]]
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[[Category: Dna binding]]
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[[Category: Replication activator-dna complex]]
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[[Category: Replication initiator]]
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Current revision

Replication initiator DnaA bound to AMPPCP and single-stranded DNA

PDB ID 3r8f

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