2nqp

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[[Image:2nqp.gif|left|200px]]
 
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{{Structure
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==Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA==
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|PDB= 2nqp |SIZE=350|CAPTION= <scene name='initialview01'>2nqp</scene>, resolution 3.50&Aring;
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<StructureSection load='2nqp' size='340' side='right'caption='[[2nqp]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
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<table><tr><td colspan='2'>[[2nqp]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NQP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NQP FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA-pseudouridine_synthase_I tRNA-pseudouridine synthase I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.99.12 5.4.99.12] </span>
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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]] 3.5&#8491;</td></tr>
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|GENE= truA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
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|DOMAIN=
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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=2nqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nqp OCA], [https://pdbe.org/2nqp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nqp RCSB], [https://www.ebi.ac.uk/pdbsum/2nqp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nqp ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1dj0|1DJ0]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2nqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nqp OCA], [http://www.ebi.ac.uk/pdbsum/2nqp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2nqp RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/TRUA_ECOLI TRUA_ECOLI] Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs.<ref>PMID:17466622</ref>
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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/nq/2nqp_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=2nqp ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Translational accuracy and efficiency depend upon modification of uridines in the tRNA anticodon stem loop (ASL) by a highly conserved pseudouridine synthase TruA. TruA specifically modifies uridines at positions 38, 39, and/or 40 of tRNAs with highly divergent sequences and structures through a poorly characterized mechanism that differs from previously studied RNA-modifying enzymes. The molecular basis for the site and substrate "promiscuity" was studied by determining the crystal structures of E. coli TruA in complex with two different leucyl tRNAs in conjunction with functional assays and computer simulation. The structures capture three stages of the TruA*tRNA reaction, revealing the mechanism by which TruA selects the target site. We propose that TruA utilizes the intrinsic flexibility of the ASL for site promiscuity and also to select against intrinsically stable tRNAs to avoid their overstabilization through pseudouridylation, thereby maintaining the balance between the flexibility and stability required for its biological function.
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'''Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA'''
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How U38, 39, and 40 of many tRNAs become the targets for pseudouridylation by TruA.,Hur S, Stroud RM Mol Cell. 2007 Apr 27;26(2):189-203. PMID:17466622<ref>PMID:17466622</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2nqp" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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Translational accuracy and efficiency depend upon modification of uridines in the tRNA anticodon stem loop (ASL) by a highly conserved pseudouridine synthase TruA. TruA specifically modifies uridines at positions 38, 39, and/or 40 of tRNAs with highly divergent sequences and structures through a poorly characterized mechanism that differs from previously studied RNA-modifying enzymes. The molecular basis for the site and substrate "promiscuity" was studied by determining the crystal structures of E. coli TruA in complex with two different leucyl tRNAs in conjunction with functional assays and computer simulation. The structures capture three stages of the TruA*tRNA reaction, revealing the mechanism by which TruA selects the target site. We propose that TruA utilizes the intrinsic flexibility of the ASL for site promiscuity and also to select against intrinsically stable tRNAs to avoid their overstabilization through pseudouridylation, thereby maintaining the balance between the flexibility and stability required for its biological function.
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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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==About this Structure==
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*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
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2NQP is a [[Protein complex]] structure of sequences 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=2NQP OCA].
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== References ==
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<references/>
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==Reference==
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__TOC__
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How U38, 39, and 40 of many tRNAs become the targets for pseudouridylation by TruA., Hur S, Stroud RM, Mol Cell. 2007 Apr 27;26(2):189-203. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17466622 17466622]
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Protein complex]]
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[[Category: Escherichia coli K-12]]
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[[Category: tRNA-pseudouridine synthase I]]
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[[Category: Large Structures]]
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[[Category: Hur, S.]]
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[[Category: Hur S]]
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[[Category: Stroud, R M.]]
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[[Category: Stroud RM]]
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[[Category: anticodon stem loop]]
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[[Category: multisite specificity]]
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[[Category: pseudouridine synthase]]
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[[Category: trna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:06:57 2008''
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Current revision

Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA

PDB ID 2nqp

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