3fmt

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{{Seed}}
 
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[[Image:3fmt.png|left|200px]]
 
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==Crystal structure of SeqA bound to DNA==
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The line below this paragraph, containing "STRUCTURE_3fmt", creates the "Structure Box" on the page.
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<StructureSection load='3fmt' size='340' side='right'caption='[[3fmt]], [[Resolution|resolution]] 2.98&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3fmt]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FMT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FMT FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.983&#8491;</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=6MA:N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE'>6MA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
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{{STRUCTURE_3fmt| PDB=3fmt | SCENE= }}
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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=3fmt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fmt OCA], [https://pdbe.org/3fmt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fmt RCSB], [https://www.ebi.ac.uk/pdbsum/3fmt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fmt ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SEQA_ECOLI SEQA_ECOLI] Negative regulator of replication initiation, which contributes to regulation of DNA replication and ensures that replication initiation occurs exactly once per chromosome per cell cycle. Binds to pairs of hemimethylated GATC sequences in the oriC region, thus preventing assembly of replication proteins and re-initiation at newly replicated origins. Repression is relieved when the region becomes fully methylated. Can also bind to hemimethylated GATC sequences outside of oriC region. Binds, with less affinity, to fully methylated GATC sites and affects timing of replication. May play a role in chromosome organization and gene regulation.<ref>PMID:8011018</ref> <ref>PMID:7891562</ref> <ref>PMID:7553853</ref> <ref>PMID:11080170</ref> <ref>PMID:10931282</ref> <ref>PMID:20689753</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fm/3fmt_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3fmt ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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SeqA is a negative regulator of DNA replication in Escherichia coli and related bacteria that functions by sequestering the origin of replication and facilitating its resetting after every initiation event. Inactivation of the seqA gene leads to unsynchronized rounds of replication, abnormal localization of nucleoids and increased negative superhelicity. Excess SeqA also disrupts replication synchrony and affects cell division. SeqA exerts its functions by binding clusters of transiently hemimethylated GATC sequences generated during replication. However, the molecular mechanisms that trigger formation and disassembly of such complex are unclear. We present here the crystal structure of a dimeric mutant of SeqA [SeqADelta(41-59)-A25R] bound to tandem hemimethylated GATC sites. The structure delineates how SeqA forms a high-affinity complex with DNA and it suggests why SeqA only recognizes GATC sites at certain spacings. The SeqA-DNA complex also unveils additional protein-protein interaction surfaces that mediate the formation of higher ordered complexes upon binding to newly replicated DNA. Based on this data, we propose a model describing how SeqA interacts with newly replicated DNA within the origin of replication and at the replication forks.
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===Crystal structure of SeqA bound to DNA===
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Structural insights into the cooperative binding of SeqA to a tandem GATC repeat.,Chung YS, Brendler T, Austin S, Guarne A Nucleic Acids Res. 2009 Jun;37(10):3143-52. Epub 2009 Mar 20. PMID:19304745<ref>PMID:19304745</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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The line below this paragraph, {{ABSTRACT_PUBMED_19304745}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3fmt" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19304745 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19304745}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Escherichia coli K-12]]
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3FMT is a 8 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FMT OCA].
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[[Category: Large Structures]]
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[[Category: Austin S]]
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==Reference==
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[[Category: Brendler T]]
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<ref group="xtra">PMID:19304745</ref><references group="xtra"/>
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[[Category: Chung YS]]
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[[Category: Escherichia coli]]
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[[Category: Guarne A]]
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[[Category: Austin, S.]]
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[[Category: Brendler, T.]]
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[[Category: Chung, Y S.]]
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[[Category: Guarne, A.]]
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[[Category: Dna replication]]
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[[Category: Dna replication inhibitor]]
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[[Category: Dna-binding]]
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[[Category: Hemimethylated gatc]]
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[[Category: Protein-dna complex]]
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[[Category: Replication inhibitor/dna complex]]
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[[Category: Sequestration]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 6 10:31:12 2009''
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Current revision

Crystal structure of SeqA bound to DNA

PDB ID 3fmt

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OCA

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