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==Crystal Structure Of Nad+-Dependent DNA Ligase== | ==Crystal Structure Of Nad+-Dependent DNA Ligase== | ||
<StructureSection load='1v9p' size='340' side='right' caption='[[1v9p]], [[Resolution|resolution]] 2.90Å' scene=''> | <StructureSection load='1v9p' size='340' side='right'caption='[[1v9p]], [[Resolution|resolution]] 2.90Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1v9p]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[1v9p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_filiformis Thermus filiformis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dgt 1dgt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V9P FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[ | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9Å</td></tr> | ||
<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=ZN:ZINC+ION'>ZN</scene></td></tr> | |||
<tr><td class="sblockLbl"><b>[[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9p OCA], [https://pdbe.org/1v9p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v9p RCSB], [https://www.ebi.ac.uk/pdbsum/1v9p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v9p ProSAT]</span></td></tr> | ||
</table> | |||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | == Function == | ||
<table> | [https://www.uniprot.org/uniprot/DNLJ_THEFI DNLJ_THEFI] DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA.<ref>PMID:15268945</ref> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v9/1v9p_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v9/1v9p_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=1v9p ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 1v9p" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[DNA ligase|DNA ligase]] | *[[DNA ligase 3D structures|DNA ligase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Thermus filiformis]] | [[Category: Thermus filiformis]] | ||
[[Category: Chang | [[Category: Chang C]] | ||
[[Category: Kim | [[Category: Kim HK]] | ||
[[Category: Kwon | [[Category: Kwon SK]] | ||
[[Category: Lee | [[Category: Lee JY]] | ||
[[Category: Moon | [[Category: Moon J]] | ||
[[Category: Song | [[Category: Song HK]] | ||
[[Category: Suh | [[Category: Suh SW]] | ||
[[Category: Yang | [[Category: Yang JK]] | ||
Latest revision as of 03:00, 28 December 2023
Crystal Structure Of Nad+-Dependent DNA LigaseCrystal Structure Of Nad+-Dependent DNA Ligase
Structural highlights
FunctionDNLJ_THEFI DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA.[1] 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 PubMedDNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor. Despite the difference in cofactor specificity and limited overall sequence similarity, the two classes of DNA ligase share basically the same catalytic mechanism. In this study, the crystal structure of an NAD(+)-dependent DNA ligase from Thermus filiformis, a 667 residue multidomain protein, has been determined by the multiwavelength anomalous diffraction (MAD) method. It reveals highly modular architecture and a unique circular arrangement of its four distinct domains. It also provides clues for protein flexibility and DNA-binding sites. A model for the multidomain ligase action involving large conformational changes is proposed. Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications.,Lee JY, Chang C, Song HK, Moon J, Yang JK, Kim HK, Kwon ST, Suh SW EMBO J. 2000 Mar 1;19(5):1119-29. PMID:10698952[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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