3dky

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{{Seed}}
 
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[[Image:3dky.jpg|left|200px]]
 
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==Crystal Structure of the replication initiator protein encoded on plasmid pMV158 (RepB), tetragonal form, to 3.6 Ang resolution==
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The line below this paragraph, containing "STRUCTURE_3dky", creates the "Structure Box" on the page.
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<StructureSection load='3dky' size='340' side='right'caption='[[3dky]], [[Resolution|resolution]] 3.60&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'>[[3dky]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_agalactiae Streptococcus agalactiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DKY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DKY 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]] 3.6&#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=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
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{{STRUCTURE_3dky| PDB=3dky | 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=3dky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dky OCA], [https://pdbe.org/3dky PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dky RCSB], [https://www.ebi.ac.uk/pdbsum/3dky PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dky ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/REPB_STRAG REPB_STRAG] Is essential for plasmid replication. Nicks the positive strand at the plus origin of replication.
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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/dk/3dky_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=3dky 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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RepB initiates plasmid rolling-circle replication by binding to a triple 11-bp direct repeat (bind locus) and cleaving the DNA at a specific distant site located in a hairpin loop within the nic locus of the origin. The structure of native full-length RepB reveals a hexameric ring molecule, where each protomer has two domains. The origin-binding and catalytic domains show a three-layer alpha-beta-alpha sandwich fold. The active site is positioned at one of the faces of the beta-sheet and coordinates a Mn2+ ion at short distance from the essential nucleophilic Y99. The oligomerization domains (ODs), each consisting of four alpha-helices, together define a compact ring with a central channel, a feature found in ring helicases. The toroidal arrangement of RepB suggests that, similar to ring helicases, it encircles one of the DNA strands during replication to confer processivity to the replisome complex. The catalytic domains appear to be highly mobile with respect to ODs. This mobility may account for the adaptation of the protein to two distinct DNA recognition sites.
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===Crystal Structure of the replication initiator protein encoded on plasmid pMV158 (RepB), tetragonal form, to 3.6 Ang resolution===
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Plasmid replication initiator RepB forms a hexamer reminiscent of ring helicases and has mobile nuclease domains.,Boer DR, Ruiz-Maso JA, Lopez-Blanco JR, Blanco AG, Vives-Llacer M, Chacon P, Uson I, Gomis-Ruth FX, Espinosa M, Llorca O, del Solar G, Coll M EMBO J. 2009 Jun 3;28(11):1666-78. PMID:19440202<ref>PMID:19440202</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_19440202}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3dky" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19440202 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19440202}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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3DKY is a 6 chains structure of sequences from [http://en.wikipedia.org/wiki/Streptococcus_agalactiae Streptococcus agalactiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DKY OCA].
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==Reference==
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<ref group="xtra">PMID:19440202</ref><references group="xtra"/>
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[[Category: Streptococcus agalactiae]]
[[Category: Streptococcus agalactiae]]
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[[Category: Blanco, A G.]]
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[[Category: Blanco AG]]
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[[Category: Boer, D R.]]
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[[Category: Boer DR]]
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[[Category: Coll, M.]]
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[[Category: Coll M]]
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[[Category: Espinosa, M.]]
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[[Category: Del Solar G]]
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[[Category: Gomis-Ruth, F X.]]
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[[Category: Espinosa M]]
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[[Category: Ruiz-Maso, J A.]]
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[[Category: Gomis-Ruth FX]]
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[[Category: Solar, G Del.]]
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[[Category: Ruiz-Maso JA]]
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[[Category: Uson, I.]]
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[[Category: Uson I]]
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[[Category: Vives-Llacer, M.]]
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[[Category: Vives-Llacer M]]
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[[Category: Dna replication]]
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[[Category: Flexible nuclease domain]]
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[[Category: Hexamer]]
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[[Category: Nuclease]]
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[[Category: Plasmid]]
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[[Category: Plasmid replication]]
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[[Category: Replication initiation]]
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[[Category: Replication initiator]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 1 09:15:13 2009''
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Current revision

Crystal Structure of the replication initiator protein encoded on plasmid pMV158 (RepB), tetragonal form, to 3.6 Ang resolution

PDB ID 3dky

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OCA

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