1qyu: Difference between revisions

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-[[Image:1qyu.png|left|200px]]
-{{STRUCTURE_1qyu|  PDB=1qyu  |  SCENE=  }}
+==Structure of the catalytic domain of 23S rRNA pseudouridine synthase RluD==
+<StructureSection load='1qyu' size='340' side='right'caption='[[1qyu]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1qyu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QYU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QYU 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&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=1qyu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qyu OCA], [https://pdbe.org/1qyu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qyu RCSB], [https://www.ebi.ac.uk/pdbsum/1qyu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qyu ProSAT]</span></td></tr>
+</table>
+== 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/qy/1qyu_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1qyu ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Escherichia coli pseudouridine synthase RluD makes pseudouridines 1911, 1915, and 1917 in the loop of helix 69 in 23S RNA. These are the most highly conserved ribosomal pseudouridines known. Of 11 pseudouridine synthases in E. coli, only cells lacking RluD have severe growth defects and abnormal ribosomes. We have determined the 2.0 A structure of the catalytic domain of RluD (residues 77-326), the first structure of an RluA family member. The catalytic domain folds into a mainly antiparallel beta-sheet flanked by several loops and helices. A positively charged cleft that presumably binds RNA leads to the conserved Asp 139. The RluD N-terminal S4 domain, connected by a flexible linker, is disordered in our structure. RluD is very similar in both catalytic domain structure and active site arrangement to the pseudouridine synthases RsuA, TruB, and TruA. We identify five sequence motifs, two of which are novel, in the RluA, RsuA, TruB, and TruA families, uniting them as one superfamily. These results strongly suggest that four of the five families of pseudouridine synthases arose by divergent evolution. The RluD structure also provides insight into its multisite specificity.
-===Structure of the catalytic domain of 23S rRNA pseudouridine synthase RluD===
+Crystal structure of the catalytic domain of RluD, the only rRNA pseudouridine synthase required for normal growth of Escherichia coli.,Del Campo M, Ofengand J, Malhotra A RNA. 2004 Feb;10(2):231-9. PMID:14730022<ref>PMID:14730022</ref>
-{{ABSTRACT_PUBMED_14730022}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1qyu" style="background-color:#fffaf0;"></div>
-[[1qyu]] is a 1 chain structure of [[TRNA pseudouridine synthase]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QYU OCA].
 ==See Also==
-*[[TRNA pseudouridine synthase|TRNA pseudouridine synthase]]
+*[[Guide-independent Pseudouridine synthase|Guide-independent Pseudouridine synthase]]
+*[[Pseudouridine synthase 3D structures|Pseudouridine synthase 3D structures]]
-==Reference==
+== References ==
-<ref group="xtra">PMID:014730022</ref><references group="xtra"/>
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Pseudouridylate synthase]]
+[[Category: Large Structures]]
-[[Category: Campo, M Del.]]
+[[Category: Del Campo M]]
-[[Category: Malhotra, A.]]
+[[Category: Malhotra A]]
-[[Category: Ofengand, J.]]
+[[Category: Ofengand J]]
-[[Category: Catalytic domain]]
-[[Category: Lyase]]
-[[Category: Pseudouridine synthase]]
-[[Category: Rlud]]