1r3e: Difference between revisions

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 <StructureSection load='1r3e' size='340' side='right'caption='[[1r3e]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1r3e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R3E OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1R3E FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1r3e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R3E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R3E FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FHU:(5S,6R)-5-FLUORO-6-HYDROXY-PSEUDOURIDINE-5-MONOPHOSPHATE'>FHU</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]] 2.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1r3f|1r3f]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FHU:(5S,6R)-5-FLUORO-6-HYDROXY-PSEUDOURIDINE-5-MONOPHOSPHATE'>FHU</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TRUB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</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=1r3e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r3e OCA], [https://pdbe.org/1r3e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r3e RCSB], [https://www.ebi.ac.uk/pdbsum/1r3e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r3e ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pseudouridylate_synthase Pseudouridylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.70 4.2.1.70] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1r3e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r3e OCA], [http://pdbe.org/1r3e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1r3e RCSB], [http://www.ebi.ac.uk/pdbsum/1r3e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1r3e ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TRUB_THEMA TRUB_THEMA]] Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs (By similarity).
+[https://www.uniprot.org/uniprot/TRUB_THEMA TRUB_THEMA] 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]]
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 </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=1r3e ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-RNA pseudouridine synthase, TruB, catalyzes pseudouridine formation at U55 in tRNA. This posttranscriptional modification is almost universally conserved and occurs in the T arm of most tRNAs. We determined the crystal structure of Escherichia coli TruB apo enzyme, as well as the structure of Thermotoga maritima TruB in complex with RNA. Comparison of the RNA-free and -bound forms of TruB reveals that this enzyme undergoes significant conformational changes on binding to its substrate. These conformational changes include the ordering of the "thumb loop," which binds right into the RNA hairpin loop, and a 10 degree hinge movement of the C-terminal domain. Along with the result of docking experiments performed on apo TruB, we conclude that TruB recognizes its RNA substrate through a combination of rigid docking and induced fit, with TruB first rigidly binding to its target and then maximizing the interaction by induced fit.
-Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit.,Pan H, Agarwalla S, Moustakas DT, Finer-Moore J, Stroud RM Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12648-53. Epub 2003 Oct 17. PMID:14566049<ref>PMID:14566049</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1r3e" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Guide-independent Pseudouridine synthase|Guide-independent Pseudouridine synthase]]
 *[[Pseudouridine synthase 3D structures|Pseudouridine synthase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 43589]]
 [[Category: Large Structures]]
-[[Category: Pseudouridylate synthase]]
+[[Category: Thermotoga maritima]]
-[[Category: Agarwalla, S]]
+[[Category: Agarwalla S]]
-[[Category: Finer-Moore, J]]
+[[Category: Finer-Moore J]]
-[[Category: Moustakas, D T]]
+[[Category: Moustakas DT]]
-[[Category: Pan, H]]
+[[Category: Pan H]]
-[[Category: Stroud, R M]]
+[[Category: Stroud RM]]
-[[Category: Lyase-rna complex]]
-[[Category: Pseudouridylation]]
-[[Category: Rna modification]]