4oi2: Difference between revisions

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 ==C. Elegans Clp1 and ADP and Mg2+ (turnover state)==
-<StructureSection load='4oi2' size='340' side='right' caption='[[4oi2]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+<StructureSection load='4oi2' size='340' side='right'caption='[[4oi2]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4oi2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Caeel Caeel]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OI2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OI2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4oi2]] 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=4OI2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OI2 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]] 2.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ohv|4ohv]], [[4ohw|4ohw]], [[4ohx|4ohx]], [[4ohy|4ohy]], [[4ohz|4ohz]], [[4oi0|4oi0]], [[4oi1|4oi1]]</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">clpf-1, F59A2.4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6239 CAEEL])</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=4oi2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oi2 OCA], [https://pdbe.org/4oi2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oi2 RCSB], [https://www.ebi.ac.uk/pdbsum/4oi2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oi2 ProSAT]</span></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=4oi2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oi2 OCA], [http://pdbe.org/4oi2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4oi2 RCSB], [http://www.ebi.ac.uk/pdbsum/4oi2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4oi2 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>
-<div class="pdbe-citations 4oi2" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Caeel]]
+[[Category: Caenorhabditis elegans]]
-[[Category: Clausen, T]]
+[[Category: Large Structures]]
-[[Category: Dikfidan, A]]
+[[Category: Clausen T]]
-[[Category: Loll, B]]
+[[Category: Dikfidan A]]
-[[Category: Meinhart, A]]
+[[Category: Loll B]]
-[[Category: Zeymer, C]]
+[[Category: Meinhart A]]
-[[Category: Polynucleotide kinase]]
+[[Category: Zeymer C]]
-[[Category: Rna binding protein]]