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1r3e

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(New page: 200px<br /><applet load="1r3e" size="450" color="white" frame="true" align="right" spinBox="true" caption="1r3e, resolution 2.1&Aring;" /> '''Crystal Structure of ...)
Current revision (06:09, 17 April 2024) (edit) (undo)
 
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[[Image:1r3e.gif|left|200px]]<br /><applet load="1r3e" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1r3e, resolution 2.1&Aring;" />
 
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'''Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA-protein Recognition Through a Combination of Rigid Docking and Induced Fit'''<br />
 
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==Overview==
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==Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA-protein Recognition Through a Combination of Rigid Docking and Induced Fit==
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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.
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<StructureSection load='1r3e' size='340' side='right'caption='[[1r3e]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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== Structural highlights ==
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<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>
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</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>
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<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>
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<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>
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</table>
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== Function ==
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[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).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r3/1r3e_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1R3E is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1R3E OCA].
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*[[Guide-independent Pseudouridine synthase|Guide-independent Pseudouridine synthase]]
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*[[Pseudouridine synthase 3D structures|Pseudouridine synthase 3D structures]]
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==Reference==
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__TOC__
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14566049 14566049]
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</StructureSection>
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[[Category: Pseudouridylate synthase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Thermotoga maritima]]
[[Category: Thermotoga maritima]]
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[[Category: Agarwalla, S.]]
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[[Category: Agarwalla S]]
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[[Category: Finer-Moore, J.]]
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[[Category: Finer-Moore J]]
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[[Category: Moustakas, D.T.]]
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[[Category: Moustakas DT]]
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[[Category: Pan, H.]]
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[[Category: Pan H]]
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[[Category: Stroud, R.M.]]
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[[Category: Stroud RM]]
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[[Category: pseudouridylation]]
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[[Category: rna modification]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 01:14:32 2007''
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Current revision

Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA-protein Recognition Through a Combination of Rigid Docking and Induced Fit

PDB ID 1r3e

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