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3ty5

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==Crystal Structure of C. thermocellum PNKP Ligase domain in complex with ATP==
==Crystal Structure of C. thermocellum PNKP Ligase domain in complex with ATP==
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<StructureSection load='3ty5' size='340' side='right' caption='[[3ty5]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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<StructureSection load='3ty5' size='340' side='right'caption='[[3ty5]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3ty5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_thermocellum Clostridium thermocellum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TY5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TY5 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3ty5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetivibrio_thermocellus_ATCC_27405 Acetivibrio thermocellus ATCC 27405]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TY5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TY5 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Cthe_2768 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1515 Clostridium thermocellum])</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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_ligase_(ATP) RNA ligase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.3 6.5.1.3] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ty5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ty5 OCA], [https://pdbe.org/3ty5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ty5 RCSB], [https://www.ebi.ac.uk/pdbsum/3ty5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ty5 ProSAT]</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=3ty5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ty5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ty5 RCSB], [http://www.ebi.ac.uk/pdbsum/3ty5 PDBsum]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/A3DJ38_ACET2 A3DJ38_ACET2]
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Pnkp is the end-healing and end-sealing component of an RNA repair system present in diverse bacteria from ten different phyla. To gain insight to the mechanism and evolution of this repair system, we determined the crystal structures of the ligase domain of Clostridium thermocellum Pnkp in three functional states along the reaction pathway: apoenzyme, ligase*ATP substrate complex, and covalent ligase-AMP intermediate. The tertiary structure is composed of a classical ligase nucleotidyltransferase module that is embellished by a unique alpha-helical insert module and a unique C-terminal alpha-helical module. Structure-guided mutational analysis identified active site residues essential for ligase adenylylation. Pnkp defines a new RNA ligase family with signature structural and functional properties.
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The adenylyltransferase domain of bacterial Pnkp defines a unique RNA ligase family.,Smith P, Wang LK, Nair PA, Shuman S Proc Natl Acad Sci U S A. 2012 Feb 14;109(7):2296-301. Epub 2012 Jan 27. PMID:22308407<ref>PMID:22308407</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Clostridium thermocellum]]
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[[Category: Acetivibrio thermocellus ATCC 27405]]
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[[Category: Shuman, S]]
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[[Category: Large Structures]]
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[[Category: Smith, P]]
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[[Category: Shuman S]]
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[[Category: Wang, L]]
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[[Category: Smith P]]
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[[Category: Adenylyltransferase]]
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[[Category: Wang L]]
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[[Category: Dna ligase/mrna capping enzyme]]
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[[Category: Hen1]]
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[[Category: Rna ligase]]
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[[Category: Transferase]]
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Current revision

Crystal Structure of C. thermocellum PNKP Ligase domain in complex with ATP

PDB ID 3ty5

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