2q2u

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(New page: 200px<br /><applet load="2q2u" size="350" color="white" frame="true" align="right" spinBox="true" caption="2q2u, resolution 3.000&Aring;" /> '''Structure of Chlore...)
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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 Wed Jan 23 12:34:16 2008''
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Current revision

Structure of Chlorella virus DNA ligase-product DNA complex

PDB ID 2q2u

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