4ohx: Difference between revisions

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 ==C. Elegans Clp1 bound to ADP and Mg2+ (RNA released state)==
-<StructureSection load='4ohx' size='340' side='right' caption='[[4ohx]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
+<StructureSection load='4ohx' size='340' side='right'caption='[[4ohx]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4ohx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OHX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OHX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4ohx]] is a 1 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=4OHX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OHX FirstGlance]. <br>
-</td></tr><tr id='ligand'><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=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]] 1.98&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ohv|4ohv]], [[4ohw|4ohw]], [[4ohy|4ohy]], [[4ohz|4ohz]], [[4oi0|4oi0]], [[4oi1|4oi1]], [[4oi2|4oi2]]</td></tr>
+<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=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<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=4ohx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ohx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ohx RCSB], [http://www.ebi.ac.uk/pdbsum/4ohx PDBsum]</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=4ohx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ohx OCA], [https://pdbe.org/4ohx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ohx RCSB], [https://www.ebi.ac.uk/pdbsum/4ohx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ohx ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CLP1_CAEEL CLP1_CAEEL]] Required for endonucleolytic cleavage during polyadenylation-dependent pre-mRNA 3'-end formation (By similarity).
+[https://www.uniprot.org/uniprot/CLP1_CAEEL CLP1_CAEEL] Required for endonucleolytic cleavage during polyadenylation-dependent pre-mRNA 3'-end formation (By similarity).
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-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.
-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>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Clausen, T]]
+[[Category: Caenorhabditis elegans]]
-[[Category: Dikfidan, A]]
+[[Category: Large Structures]]
-[[Category: Loll, B]]
+[[Category: Clausen T]]
-[[Category: Meinhart, A]]
+[[Category: Dikfidan A]]
-[[Category: Zeymer, C]]
+[[Category: Loll B]]
-[[Category: Polynucleotide kinase]]
+[[Category: Meinhart A]]
-[[Category: Rna binding protein]]
+[[Category: Zeymer C]]