2q2u: Difference between revisions

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 ==Structure of Chlorella virus DNA ligase-product DNA complex==
-<StructureSection load='2q2u' size='340' side='right' caption='[[2q2u]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+<StructureSection load='2q2u' size='340' side='right'caption='[[2q2u]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2q2u]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Paramecium_bursaria_chlorella_virus_1 Paramecium bursaria chlorella virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q2U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q2U FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2q2u]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Paramecium_bursaria_Chlorella_virus_1 Paramecium bursaria Chlorella virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q2U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q2U FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</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]] 3&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1fvi|1fvi]], [[2q2t|2q2t]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">A544R ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10506 Paramecium bursaria Chlorella virus 1])</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=2q2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q2u OCA], [https://pdbe.org/2q2u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q2u RCSB], [https://www.ebi.ac.uk/pdbsum/2q2u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q2u ProSAT]</span></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q2u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q2u RCSB], [http://www.ebi.ac.uk/pdbsum/2q2u PDBsum]</span></td></tr>
+</table>
-<table>
+== Function ==
+[https://www.uniprot.org/uniprot/O41026_PBCV1 O41026_PBCV1]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q2/2q2u_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q2/2q2u_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
-</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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2q2u ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Chlorella virus DNA ligase, the smallest eukaryotic ligase known, has pluripotent biological activity and an intrinsic nick-sensing function, despite having none of the accessory domains found in cellular ligases. A 2.3-A crystal structure of the Chlorella virus ligase-AMP intermediate bound to duplex DNA containing a 3'-OH-5'-PO4 nick reveals a new mode of DNA envelopment, in which a short surface loop emanating from the OB domain forms a beta-hairpin 'latch' that inserts into the DNA major groove flanking the nick. A network of interactions with the 3'-OH and 5'-PO4 termini in the active site illuminates the DNA adenylylation mechanism and the crucial roles of AMP in nick sensing and catalysis. Addition of a divalent cation triggered nick sealing in crystallo, establishing that the nick complex is a bona fide intermediate in the DNA repair pathway.
-Structural basis for nick recognition by a minimal pluripotent DNA ligase.,Nair PA, Nandakumar J, Smith P, Odell M, Lima CD, Shuman S Nat Struct Mol Biol. 2007 Aug;14(8):770-8. Epub 2007 Jul 8. PMID:17618295<ref>PMID:17618295</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[DNA ligase|DNA ligase]]
+*[[DNA ligase 3D structures|DNA ligase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Paramecium bursaria chlorella virus 1]]
+[[Category: Large Structures]]
-[[Category: Lima, C D.]]
+[[Category: Paramecium bursaria Chlorella virus 1]]
-[[Category: Nair, P A.]]
+[[Category: Lima CD]]
-[[Category: Nandakumar, J.]]
+[[Category: Nair PA]]
-[[Category: Shuman, S.]]
+[[Category: Nandakumar J]]
-[[Category: Smith, P.]]
+[[Category: Shuman S]]
-[[Category: Ligase]]
+[[Category: Smith P]]
-[[Category: Ligase-dna complex]]
-[[Category: Product-complex]]
-[[Category: Protein-dna complex]]