1lrr: Difference between revisions

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 <StructureSection load='1lrr' size='340' side='right'caption='[[1lrr]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1lrr]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LRR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1LRR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1lrr]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LRR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LRR FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6MA:N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE'>6MA</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.65&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">seqA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
+<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></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1lrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lrr OCA], [http://pdbe.org/1lrr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lrr RCSB], [http://www.ebi.ac.uk/pdbsum/1lrr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lrr 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=1lrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lrr OCA], [https://pdbe.org/1lrr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lrr RCSB], [https://www.ebi.ac.uk/pdbsum/1lrr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lrr ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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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=1lrr ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The SeqA protein binds clusters of fully methylated or hemimethylated GATC sequences at oriC and negatively modulates the initiation of DNA replication. We find that SeqA can be proteolytically cleaved into an N-terminal multimerization and a C-terminal DNA-binding domain and have determined the crystal structure of the C-terminal domain in complex with a hemimethylated GATC site. SeqA makes direct hydrogen bonds and van der Waals contacts with the hemimethylated A-T base pair in addition to interactions with the surrounding bases and DNA backbone. The tetrameric protein-DNA complex found in the crystal suggests that SeqA binds multiple GATC sites on separate DNA duplexes, altering the overall DNA topology and sequestering oriC from replication initiation.
-Insights into negative modulation of E. coli replication initiation from the structure of SeqA-hemimethylated DNA complex.,Guarne A, Zhao Q, Ghirlando R, Yang W Nat Struct Biol. 2002 Nov;9(11):839-43. PMID:12379844<ref>PMID:12379844</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1lrr" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Guarne, A]]
+[[Category: Guarne A]]
-[[Category: Guirlando, R]]
+[[Category: Guirlando R]]
-[[Category: Yang, W]]
+[[Category: Yang W]]
-[[Category: Zhao, Q]]
+[[Category: Zhao Q]]
-[[Category: Methylated gatc]]
-[[Category: Protein-dna complex]]
-[[Category: Replication]]
-[[Category: Replication inhibitor-dna complex]]