2q2u

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[[Image:2q2u.gif|left|200px]]<br /><applet load="2q2u" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2q2u, resolution 3.000&Aring;" />
 
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'''Structure of Chlorella virus DNA ligase-product DNA complex'''<br />
 
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==Overview==
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==Structure of Chlorella virus DNA ligase-product DNA complex==
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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.
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<StructureSection load='2q2u' size='340' side='right'caption='[[2q2u]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
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== Structural highlights ==
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<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>
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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&#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=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene></td></tr>
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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=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>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/O41026_PBCV1 O41026_PBCV1]
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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/q2/2q2u_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=2q2u ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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2Q2U is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of 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].
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*[[DNA ligase 3D structures|DNA ligase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17618295 17618295]
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[[Category: Large Structures]]
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[[Category: Paramecium bursaria chlorella virus 1]]
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[[Category: Paramecium bursaria Chlorella virus 1]]
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[[Category: Single protein]]
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[[Category: Lima CD]]
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[[Category: Lima, C D.]]
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[[Category: Nair PA]]
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[[Category: Nair, P A.]]
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[[Category: Nandakumar J]]
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[[Category: Nandakumar, J.]]
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[[Category: Shuman S]]
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[[Category: Shuman, S.]]
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[[Category: Smith P]]
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[[Category: Smith, P.]]
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[[Category: ligase]]
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[[Category: ligase/dna complex]]
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[[Category: product-complex]]
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[[Category: protein-dna complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:35:22 2008''
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Current revision

Structure of Chlorella virus DNA ligase-product DNA complex

PDB ID 2q2u

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