This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
2q2u
From Proteopedia
(Difference between revisions)
| Line 3: | Line 3: | ||
<StructureSection load='2q2u' size='340' side='right'caption='[[2q2u]], [[Resolution|resolution]] 3.00Å' scene=''> | <StructureSection load='2q2u' size='340' side='right'caption='[[2q2u]], [[Resolution|resolution]] 3.00Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[2q2u]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/ | + | <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 id=' | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3Å</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 id=' | + | |
<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 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> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/O41026_PBCV1 O41026_PBCV1] | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
| Line 19: | Line 20: | ||
</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]. | </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="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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 2q2u" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
*[[DNA ligase 3D structures|DNA ligase 3D structures]] | *[[DNA ligase 3D structures|DNA ligase 3D structures]] | ||
| - | == References == | ||
| - | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: Chlorella pbcv-1 virus]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Lima | + | [[Category: Paramecium bursaria Chlorella virus 1]] |
| - | [[Category: Nair | + | [[Category: Lima CD]] |
| - | [[Category: Nandakumar | + | [[Category: Nair PA]] |
| - | [[Category: Shuman | + | [[Category: Nandakumar J]] |
| - | [[Category: Smith | + | [[Category: Shuman S]] |
| - | + | [[Category: Smith P]] | |
| - | + | ||
| - | + | ||
| - | + | ||
Current revision
Structure of Chlorella virus DNA ligase-product DNA complex
| |||||||||||
