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4oi1

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==Structure of a RNA-processing protein==
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<StructureSection load='4oi1' size='340' side='right' caption='[[4oi1]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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==Clp1 bound to ssRNA dinucleotide GC, ADP, AlF4-, and Mg2+(transition state, data set II)==
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<StructureSection load='4oi1' size='340' side='right'caption='[[4oi1]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4oi1]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OI1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OI1 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4oi1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OI1 FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
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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]] 2.3&#8491;</td></tr>
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<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ohv|4ohv]], [[4ohw|4ohw]], [[4ohx|4ohx]], [[4ohy|4ohy]], [[4ohz|4ohz]], [[4oi0|4oi0]], [[4oi2|4oi2]]</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=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4oi1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oi1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4oi1 RCSB], [http://www.ebi.ac.uk/pdbsum/4oi1 PDBsum]</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=4oi1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oi1 OCA], [https://pdbe.org/4oi1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oi1 RCSB], [https://www.ebi.ac.uk/pdbsum/4oi1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oi1 ProSAT]</span></td></tr>
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<table>
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</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/CLP1_CAEEL CLP1_CAEEL] Required for endonucleolytic cleavage during polyadenylation-dependent pre-mRNA 3'-end formation (By similarity).
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RNA-specific polynucleotide kinases of the Clp1 subfamily are key components of various RNA maturation pathways. However, the structural basis explaining their substrate specificity and the enzymatic mechanism is elusive. Here, we report crystal structures of Clp1 from Caenorhabditis elegans (ceClp1) in a number of nucleotide- and RNA-bound states along the reaction pathway. The combined structural and biochemical analysis of ceClp1 elucidates the RNA specificity and lets us derive a general model for enzyme catalysis of RNA-specific polynucleotide kinases. We identified an RNA binding motif referred to as "clasp" as well as a conformational switch that involves the essential Walker A lysine (Lys127) and regulates the enzymatic activity of ceClp1. Structural comparison with other P loop proteins, such as kinases, adenosine triphosphatases (ATPases), and guanosine triphosphatases (GTPases), suggests that the observed conformational switch of the Walker A lysine is a broadly relevant mechanistic feature.
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RNA specificity and regulation of catalysis in the eukaryotic polynucleotide kinase clp1.,Dikfidan A, Loll B, Zeymer C, Magler I, Clausen T, Meinhart A Mol Cell. 2014 Jun 19;54(6):975-86. doi: 10.1016/j.molcel.2014.04.005. Epub 2014 , May 8. PMID:24813946<ref>PMID:24813946</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: Clausen, T.]]
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[[Category: Caenorhabditis elegans]]
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[[Category: Dikfidan, A.]]
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[[Category: Large Structures]]
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[[Category: Loll, B.]]
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[[Category: Clausen T]]
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[[Category: Meinhart, A.]]
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[[Category: Dikfidan A]]
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[[Category: Zeymer, C.]]
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[[Category: Loll B]]
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[[Category: Polynucleotide kinase]]
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[[Category: Meinhart A]]
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[[Category: Rna binding protein-rna complex]]
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[[Category: Zeymer C]]

Current revision

Clp1 bound to ssRNA dinucleotide GC, ADP, AlF4-, and Mg2+(transition state, data set II)

PDB ID 4oi1

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