3hax: Difference between revisions

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-[[Image:3hax.png|left|200px]]
-{{STRUCTURE_3hax|  PDB=3hax  |  SCENE=  }}
+==Crystal structure of a substrate-bound Gar1-minus H/ACA RNP from Pyrococcus furiosus==
+<StructureSection load='3hax' size='340' side='right'caption='[[3hax]], [[Resolution|resolution]] 2.11&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3hax]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HAX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HAX FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.11&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FHU:(5S,6R)-5-FLUORO-6-HYDROXY-PSEUDOURIDINE-5-MONOPHOSPHATE'>FHU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=3hax FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hax OCA], [https://pdbe.org/3hax PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hax RCSB], [https://www.ebi.ac.uk/pdbsum/3hax PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hax ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TRUB_PYRFU TRUB_PYRFU] Could be responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs (By similarity).
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ha/3hax_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3hax ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+H/ACA RNAs form ribonucleoprotein complex (RNP) with proteins Cbf5, Nop10, L7Ae, and Gar1 and guide site-specific conversion of uridine into pseudouridine in cellular RNAs. The crystal structures of H/ACA RNP with substrate bound at the active site cleft reveal that the substrate is recruited through sequence-specific pairing with guide RNA and essential protein contacts. Substrate binding leads to a reorganization of a preset pseudouridylation pocket and an adaptive movement of the PUA domain and the lower stem of the H/ACA RNA. Moreover, a thumb loop flips from the Gar1-bound state in the substrate-free RNP structure to tightly associate with the substrate. Mutagenesis and enzyme kinetics analysis suggest a critical role of Gar1 and the thumb in substrate turnover, particularly in product release. Comparison with tRNA Psi55 synthase TruB reveals the structural conservation and adaptation between an RNA-guided and stand-alone pseudouridine synthase and provides insight into the guide-independent activity of Cbf5.
-===Crystal structure of a substrate-bound Gar1-minus H/ACA RNP from Pyrococcus furiosus===
+Structural mechanism of substrate RNA recruitment in H/ACA RNA-guided pseudouridine synthase.,Duan J, Li L, Lu J, Wang W, Ye K Mol Cell. 2009 May 14;34(4):427-39. PMID:19481523<ref>PMID:19481523</ref>
-{{ABSTRACT_PUBMED_19481523}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3hax" style="background-color:#fffaf0;"></div>
-[[3hax]] is a 5 chain structure of [[Kink-turn motif]], [[Ribosomal protein L7]] and [[User:Wayne Decatur/kink-turn motif]] with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HAX OCA].
 ==See Also==
+*[[Guide-independent Pseudouridine synthase|Guide-independent Pseudouridine synthase]]
 *[[Kink-turn motif|Kink-turn motif]]
-*[[Ribosomal protein L7|Ribosomal protein L7]]
+*[[Pseudouridine synthase 3D structures|Pseudouridine synthase 3D structures]]
+*[[Ribosome biogenesis protein 3D structures|Ribosome biogenesis protein 3D structures]]
 *[[User:Wayne Decatur/kink-turn motif|User:Wayne Decatur/kink-turn motif]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:019481523</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Pyrococcus furiosus]]
-[[Category: Ye, K.]]
+[[Category: Ye K]]
-[[Category: Guide rna]]
-[[Category: H/aca]]
-[[Category: Isomerase]]
-[[Category: Isomerase-biosynthetic protein-rna complex]]
-[[Category: Pseudouridine synthase]]
-[[Category: Ribonucleoprotein]]
-[[Category: Ribosomal protein]]
-[[Category: Ribosome biogenesis]]
-[[Category: Rna-binding]]
-[[Category: Rna-protein complex]]
-[[Category: Rrna processing]]
-[[Category: Trna processing]]