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[[Image:2q2u.gif|left|200px]]


{{Structure
==Structure of Chlorella virus DNA ligase-product DNA complex==
|PDB= 2q2u |SIZE=350|CAPTION= <scene name='initialview01'>2q2u</scene>, resolution 3.000&Aring;
<StructureSection load='2q2u' size='340' side='right'caption='[[2q2u]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=OMC:O2&#39;-METHYLYCYTIDINE-5&#39;-MONOPHOSPHATE'>OMC</scene>
<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>
|ACTIVITY=  
</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>
|GENE= A544R ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10506 Paramecium bursaria Chlorella virus 1])
<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>
|DOMAIN=
<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>
|RELATEDENTRY=[[1fvi|1FVI]], [[2q2t|2Q2T]]
</table>
|RESOURCES=<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.ebi.ac.uk/pdbsum/2q2u PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2q2u RCSB]</span>
== 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>
    <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/main_output.php?pdb_ID=2q2u ConSurf].
<div style="clear:both"></div>


'''Structure of Chlorella virus DNA ligase-product DNA complex'''
==See Also==
 
*[[DNA ligase 3D structures|DNA ligase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
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.
[[Category: Large Structures]]
 
[[Category: Paramecium bursaria Chlorella virus 1]]
==About this Structure==
[[Category: Lima CD]]
2Q2U is a [[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].
[[Category: Nair PA]]
 
[[Category: Nandakumar J]]
==Reference==
[[Category: Shuman S]]
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://www.ncbi.nlm.nih.gov/pubmed/17618295 17618295]
[[Category: Smith P]]
[[Category: Paramecium bursaria chlorella virus 1]]
[[Category: Single protein]]
[[Category: Lima, C D.]]
[[Category: Nair, P A.]]
[[Category: Nandakumar, J.]]
[[Category: Shuman, S.]]
[[Category: Smith, P.]]
[[Category: ligase]]
[[Category: ligase/dna complex]]
[[Category: product-complex]]
[[Category: protein-dna complex]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:43:53 2008''

Latest revision as of 12:13, 21 February 2024

Structure of Chlorella virus DNA ligase-product DNA complexStructure of Chlorella virus DNA ligase-product DNA complex

Structural highlights

2q2u is a 12 chain structure with sequence from Paramecium bursaria Chlorella virus 1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

O41026_PBCV1

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2q2u, resolution 3.00Å

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OCA
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