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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3rr5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_sp._1519 Thermococcus sp. 1519]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RR5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RR5 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3rr5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_sp._1519 Thermococcus sp. 1519]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RR5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RR5 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.018&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2cfm|2cfm]], [[3gde|3gde]], [[2hiv|2hiv]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">lig ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=619742 Thermococcus sp. 1519])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA_ligase_(ATP) DNA ligase (ATP)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.1 6.5.1.1] </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=3rr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rr5 OCA], [https://pdbe.org/3rr5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rr5 RCSB], [https://www.ebi.ac.uk/pdbsum/3rr5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rr5 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=3rr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rr5 OCA], [https://pdbe.org/3rr5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rr5 RCSB], [https://www.ebi.ac.uk/pdbsum/3rr5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rr5 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/C0LJI8_9EURY C0LJI8_9EURY]] DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair (By similarity).[HAMAP-Rule:MF_00407]  
[https://www.uniprot.org/uniprot/C0LJI8_9EURY C0LJI8_9EURY] DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair (By similarity).[HAMAP-Rule:MF_00407]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
DNA ligases join single-strand breaks in double-stranded DNA by catalyzing the formation of a phosphodiester bond between adjacent 5'-phosphate and 3'-hydroxyl termini. Their function is essential for maintaining genome integrity in the replication, recombination and repair of DNA. High flexibility is important for the function of DNA ligase molecules. Two types of overall conformations of archaeal DNA ligase that depend on the relative position of the OB-fold domain have previously been revealed: closed and open extended conformations. The structure of ATP-dependent DNA ligase from Thermococcus sp. 1519 (LigTh1519) in the crystalline state determined at a resolution of 3.02 A shows a new relative arrangement of the OB-fold domain which is intermediate between the positions of this domain in the closed and the open extended conformations of previously determined archaeal DNA ligases. However, small-angle X-ray scattering (SAXS) measurements indicate that in solution the LigTh1519 molecule adopts either an open extended conformation or both an intermediate and an open extended conformation with the open extended conformation being dominant.
 
ATP-dependent DNA ligase from Thermococcus sp. 1519 displays a new arrangement of the OB-fold domain.,Petrova T, Bezsudnova EY, Boyko KM, Mardanov AV, Polyakov KM, Volkov VV, Kozin M, Ravin NV, Shabalin IG, Skryabin KG, Stekhanova TN, Kovalchuk MV, Popov VO Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Dec 1;68(Pt 12):1440-7., doi: 10.1107/S1744309112043394. Epub 2012 Nov 14. PMID:23192021<ref>PMID:23192021</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3rr5" 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: Large Structures]]
[[Category: Large Structures]]
[[Category: Thermococcus sp. 1519]]
[[Category: Thermococcus sp. 1519]]
[[Category: Bezsudnova, E Y]]
[[Category: Bezsudnova EY]]
[[Category: Boyko, K M]]
[[Category: Boyko KM]]
[[Category: Kovalchuk, M V]]
[[Category: Kovalchuk MV]]
[[Category: Mardanov, A V]]
[[Category: Mardanov AV]]
[[Category: Petrova, T]]
[[Category: Petrova T]]
[[Category: Polyakov, K M]]
[[Category: Polyakov KM]]
[[Category: Popov, V O]]
[[Category: Popov VO]]
[[Category: Ravin, N V]]
[[Category: Ravin NV]]
[[Category: Shabalin, I G]]
[[Category: Shabalin IG]]
[[Category: Skryabin, K G]]
[[Category: Skryabin KG]]
[[Category: Stekhanova, T N]]
[[Category: Stekhanova TN]]
[[Category: Archaeon]]
[[Category: Atp-dependent thermostable dna ligase]]
[[Category: Ligase]]

Latest revision as of 12:34, 14 March 2024

DNA ligase from the archaeon Thermococcus sp. 1519

3rr5, resolution 3.02Å

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