4oi0: Difference between revisions

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==bound to ssRNA dinucleotide GC, ADP, AlF4-, and Mg2+(transition state, data set I)==
==bound to ssRNA dinucleotide GC, ADP, AlF4-, and Mg2+(transition state, data set I)==
<StructureSection load='4oi0' size='340' side='right' caption='[[4oi0]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='4oi0' size='340' side='right'caption='[[4oi0]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4oi0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OI0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OI0 FirstGlance]. <br>
<table><tr><td colspan='2'>[[4oi0]] 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=4OI0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OI0 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=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SAR:SARCOSINE'>SAR</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]] 2.2&#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]], [[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=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SAR:SARCOSINE'>SAR</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=4oi0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oi0 OCA], [http://pdbe.org/4oi0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4oi0 RCSB], [http://www.ebi.ac.uk/pdbsum/4oi0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4oi0 ProSAT]</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=4oi0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oi0 OCA], [https://pdbe.org/4oi0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oi0 RCSB], [https://www.ebi.ac.uk/pdbsum/4oi0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oi0 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== 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 4oi0" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</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-rna complex]]
[[Category: Zeymer C]]

Latest revision as of 15:39, 1 March 2024

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

Structural highlights

4oi0 is a 2 chain structure with sequence from Caenorhabditis elegans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CLP1_CAEEL Required for endonucleolytic cleavage during polyadenylation-dependent pre-mRNA 3'-end formation (By similarity).

4oi0, resolution 2.20Å

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OCA
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