1r3e: Difference between revisions

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-{{Seed}}
-[[Image:1r3e.png|left|200px]]
-<!--
+==Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA-protein Recognition Through a Combination of Rigid Docking and Induced Fit==
-The line below this paragraph, containing "STRUCTURE_1r3e", creates the "Structure Box" on the page.
+<StructureSection load='1r3e' size='340' side='right'caption='[[1r3e]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<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>
-or leave the SCENE parameter empty for the default display.
+</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='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>
-{{STRUCTURE_1r3e|  PDB=1r3e  |  SCENE=  }}
+<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>
+</table>
+== Function ==
+[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]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r3/1r3e_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=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.
-===Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA-protein Recognition Through a Combination of Rigid Docking and 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==
-The line below this paragraph, {{ABSTRACT_PUBMED_14566049}}, adds the Publication Abstract to the page
+*[[Guide-independent Pseudouridine synthase|Guide-independent Pseudouridine synthase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 14566049 is the PubMed ID number.
+*[[Pseudouridine synthase 3D structures|Pseudouridine synthase 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_14566049}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-R3E is a 4 chains structure of sequences from [http://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].
+[[Category: Large Structures]]
-==Reference==
-<ref group="xtra">PMID:14566049</ref><references group="xtra"/>
-[[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: Pseudouridylation]]
-[[Category: Rna modification]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 03:36:33 2009''