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| ==DNA ligase from the archaeon Thermococcus sibiricus== | | ==DNA ligase from the archaeon Thermococcus sibiricus== |
| <StructureSection load='4eq5' size='340' side='right' caption='[[4eq5]], [[Resolution|resolution]] 2.85Å' scene=''> | | <StructureSection load='4eq5' size='340' side='right'caption='[[4eq5]], [[Resolution|resolution]] 2.85Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[4eq5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thesm Thesm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EQ5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EQ5 FirstGlance]. <br> | | <table><tr><td colspan='2'>[[4eq5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_sibiricus_MM_739 Thermococcus sibiricus MM 739]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EQ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EQ5 FirstGlance]. <br> |
| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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]] 2.85Å</td></tr> |
| <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2cfm|2cfm]], [[3gde|3gde]], [[2hiv|2hiv]], [[3rr5|3rr5]]</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></td></tr> |
| <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">lig, Thermostable ATP-dependent DNA ligase gene Tsib_0885, TSIB_0885 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=604354 THESM])</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=4eq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eq5 OCA], [https://pdbe.org/4eq5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4eq5 RCSB], [https://www.ebi.ac.uk/pdbsum/4eq5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4eq5 ProSAT]</span></td></tr> |
| <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_ligase_(ATP) DNA ligase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.1 6.5.1.1] </span></td></tr>
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| <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4eq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eq5 OCA], [http://pdbe.org/4eq5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4eq5 RCSB], [http://www.ebi.ac.uk/pdbsum/4eq5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4eq5 ProSAT]</span></td></tr> | |
| </table> | | </table> |
| == Function == | | == Function == |
| [[http://www.uniprot.org/uniprot/C6A2U9_THESM C6A2U9_THESM]] DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair.[HAMAP-Rule:MF_00407] | | [https://www.uniprot.org/uniprot/C6A2U9_THESM C6A2U9_THESM] DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair.[HAMAP-Rule:MF_00407] |
| <div style="background-color:#fffaf0;">
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| == Publication Abstract from PubMed ==
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| 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 to maintain the integrity of the genome in DNA replication, recombination and repair. A recombinant ATP-dependent DNA ligase from the hyperthermophilic anaerobic archaeon Thermococcus sibiricus was expressed in Escherichia coli and purified. Crystals were grown by vapour diffusion using the hanging-drop method with 17%(w/v) PEG 4000 and 8.5%(v/v) 2-propanol as precipitants. A diffraction experiment was performed with a single crystal, which diffracted X-rays to 3.0 A resolution. The crystal belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 58.590, b = 87.540, c = 126.300 A.
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| Expression, purification, crystallization and preliminary crystallographic analysis of a thermostable DNA ligase from the archaeon Thermococcus sibiricus.,Petrova TE, Bezsudnova EY, Dorokhov BD, Slutskaya ES, Polyakov KM, Dorovatovskiy PV, Ravin NV, Skryabin KG, Kovalchuk MV, Popov VO Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Feb 1;68(Pt 2):163-5. Epub, 2012 Jan 25. PMID:22297989<ref>PMID:22297989</ref>
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| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| <div class="pdbe-citations 4eq5" style="background-color:#fffaf0;"></div>
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| ==See Also== | | ==See Also== |
| *[[DNA ligase|DNA ligase]] | | *[[DNA ligase 3D structures|DNA ligase 3D structures]] |
| == References ==
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| <references/>
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: Thesm]] | | [[Category: Large Structures]] |
| [[Category: Bezsudnova, E Y]] | | [[Category: Thermococcus sibiricus MM 739]] |
| [[Category: Dorokhov, B D]] | | [[Category: Bezsudnova EY]] |
| [[Category: Dorovatovskiy, P V]] | | [[Category: Dorokhov BD]] |
| [[Category: Kovalchuk, M V]] | | [[Category: Dorovatovskiy PV]] |
| [[Category: Petrova, T]] | | [[Category: Kovalchuk MV]] |
| [[Category: Polyakov, K M]] | | [[Category: Petrova T]] |
| [[Category: Popov, V O]] | | [[Category: Polyakov KM]] |
| [[Category: Ravin, N V]] | | [[Category: Popov VO]] |
| [[Category: Skryabin, K G]] | | [[Category: Ravin NV]] |
| [[Category: Slutskaya, E S]] | | [[Category: Skryabin KG]] |
| [[Category: Adenylation domain]]
| | [[Category: Slutskaya ES]] |
| [[Category: Archaeon thermococcus sibiricus]]
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| [[Category: Atp-dependent thermostable dna ligase]]
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| [[Category: Dna-binding domain]]
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| [[Category: Ligase]]
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