2q2t: Difference between revisions

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{{Seed}}
[[Image:2q2t.png|left|200px]]


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==Structure of Chlorella virus DNA ligase-adenylate bound to a 5' phosphorylated nick==
The line below this paragraph, containing "STRUCTURE_2q2t", creates the "Structure Box" on the page.
<StructureSection load='2q2t' size='340' side='right'caption='[[2q2t]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2q2t]] is a 4 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=2Q2T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q2T FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#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=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene></td></tr>
{{STRUCTURE_2q2t|  PDB=2q2t  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2q2t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q2t OCA], [https://pdbe.org/2q2t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q2t RCSB], [https://www.ebi.ac.uk/pdbsum/2q2t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q2t ProSAT]</span></td></tr>
</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/q2/2q2t_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2q2t 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.


===Structure of Chlorella virus DNA ligase-adenylate bound to a 5' phosphorylated nick===
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>
<div class="pdbe-citations 2q2t" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_17618295}}, adds the Publication Abstract to the page
*[[DNA ligase 3D structures|DNA ligase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 17618295 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_17618295}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2Q2T 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=2Q2T OCA].
[[Category: Paramecium bursaria Chlorella virus 1]]
 
[[Category: Lima CD]]
==Reference==
[[Category: Nair PA]]
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: Nandakumar J]]
[[Category: Paramecium bursaria chlorella virus 1]]
[[Category: Shuman S]]
[[Category: Single protein]]
[[Category: Smith P]]
[[Category: Lima, C D.]]
[[Category: Nair, P A.]]
[[Category: Nandakumar, J.]]
[[Category: Shuman, S.]]
[[Category: Smith, P.]]
[[Category: Ligase]]
[[Category: Ligase/dna complex]]
[[Category: Lysine adenylate]]
[[Category: Protein-dna complex]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 14:27:37 2008''

Latest revision as of 11:31, 30 October 2024

Structure of Chlorella virus DNA ligase-adenylate bound to a 5' phosphorylated nickStructure of Chlorella virus DNA ligase-adenylate bound to a 5' phosphorylated nick

Structural highlights

2q2t is a 4 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 2.3Å
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.

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[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Nair PA, Nandakumar J, Smith P, Odell M, Lima CD, Shuman S. Structural basis for nick recognition by a minimal pluripotent DNA ligase. Nat Struct Mol Biol. 2007 Aug;14(8):770-8. Epub 2007 Jul 8. PMID:17618295 doi:http://dx.doi.org/10.1038/nsmb1266

2q2t, resolution 2.30Å

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