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5cou

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==Structure and mechanism of a eukaryal nick-sealing RNA ligase K170M+ATP==
==Structure and mechanism of a eukaryal nick-sealing RNA ligase K170M+ATP==
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<StructureSection load='5cou' size='340' side='right' caption='[[5cou]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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<StructureSection load='5cou' size='340' side='right'caption='[[5cou]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5cou]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5COU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5COU FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5cou]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Naegleria_gruberi Naegleria gruberi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5COU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5COU 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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 1.9&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5cot|5cot]], [[5cov|5cov]]</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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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=5cou FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cou OCA], [http://pdbe.org/5cou PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cou RCSB], [http://www.ebi.ac.uk/pdbsum/5cou PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cou ProSAT]</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=5cou FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cou OCA], [https://pdbe.org/5cou PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cou RCSB], [https://www.ebi.ac.uk/pdbsum/5cou PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cou ProSAT]</span></td></tr>
</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/D2W2Z5_NAEGR D2W2Z5_NAEGR]
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ATP-dependent RNA ligases are agents of RNA repair that join 3'-OH and 5'-PO4 RNA ends. Naegleria gruberi RNA ligase (NgrRnl) exemplifies a family of RNA nick-sealing enzymes found in bacteria, viruses, and eukarya. Crystal structures of NgrRnl at three discrete steps along the reaction pathway-covalent ligase-(lysyl-Nzeta)-AMP*Mn(2+) intermediate; ligase*ATP*(Mn(2+))2 Michaelis complex; and ligase*Mn(2+) complex-highlight a two-metal mechanism of nucleotidyl transfer, whereby (i) an enzyme-bound "catalytic" metal coordination complex lowers the pKa of the lysine nucleophile and stabilizes the transition state of the ATP alpha phosphate; and (ii) a second metal coordination complex bridges the beta- and gamma-phosphates. The NgrRnl N domain is a distinctively embellished oligonucleotide-binding (OB) fold that engages the gamma-phosphate and associated metal complex and orients the pyrophosphate leaving group for in-line catalysis with stereochemical inversion at the AMP phosphate. The unique domain architecture of NgrRnl fortifies the theme that RNA ligases have evolved many times, and independently, by fusions of a shared nucleotidyltransferase domain to structurally diverse flanking modules. The mechanistic insights to lysine adenylylation gained from the NgrRnl structures are likely to apply broadly to the covalent nucleotidyltransferase superfamily of RNA ligases, DNA ligases, and RNA capping enzymes.
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Structure and two-metal mechanism of a eukaryal nick-sealing RNA ligase.,Unciuleac MC, Goldgur Y, Shuman S Proc Natl Acad Sci U S A. 2015 Nov 10;112(45):13868-73. doi:, 10.1073/pnas.1516536112. Epub 2015 Oct 28. PMID:26512110<ref>PMID:26512110</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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<div class="pdbe-citations 5cou" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[RNA ligase|RNA ligase]]
*[[RNA ligase|RNA ligase]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Goldgur, Y]]
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[[Category: Large Structures]]
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[[Category: Shuman, S]]
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[[Category: Naegleria gruberi]]
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[[Category: Unciuleac, M C]]
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[[Category: Goldgur Y]]
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[[Category: Adenylyltransferase]]
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[[Category: Shuman S]]
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[[Category: Ligase]]
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[[Category: Unciuleac MC]]
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[[Category: Rna repair]]
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Current revision

Structure and mechanism of a eukaryal nick-sealing RNA ligase K170M+ATP

PDB ID 5cou

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