1r6u: Difference between revisions

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-[[Image:1r6u.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1r6u", creates the "Structure Box" on the page.
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-{{STRUCTURE_1r6u|  PDB=1r6u  |  SCENE=  }}
-'''Crystal structure of an active fragment of human tryptophanyl-tRNA synthetase with cytokine activity'''
+==Crystal structure of an active fragment of human tryptophanyl-tRNA synthetase with cytokine activity==
+<StructureSection load='1r6u' size='340' side='right'caption='[[1r6u]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1r6u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R6U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R6U 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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=TYM:TRYPTOPHANYL-5AMP'>TYM</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=1r6u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r6u OCA], [https://pdbe.org/1r6u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r6u RCSB], [https://www.ebi.ac.uk/pdbsum/1r6u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r6u ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SYWC_HUMAN SYWC_HUMAN] Isoform 1, isoform 2 and T1-TrpRS have aminoacylation activity while T2-TrpRS lacks it. Isoform 2, T1-TrpRS and T2-TrpRS possess angiostatic activity whereas isoform 1 lacks it. T2-TrpRS inhibits fluid shear stress-activated responses of endothelial cells. Regulates ERK, Akt, and eNOS activation pathways that are associated with angiogenesis, cytoskeletal reorganization and shear stress-responsive gene expression.<ref>PMID:11773626</ref> <ref>PMID:1373391</ref> <ref>PMID:11773625</ref> <ref>PMID:14630953</ref>
+== 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/r6/1r6u_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=1r6u ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Higher eukaryote tRNA synthetases have expanded functions that come from enlarged, more differentiated structures that were adapted to fit aminoacylation function. How those adaptations affect catalytic mechanisms is not known. Presented here is the structure of a catalytically active natural splice variant of human tryptophanyl-tRNA synthetase (TrpRS) that is a potent angiostatic factor. This and related structures suggest that a eukaryote-specific N-terminal extension of the core enzyme changed substrate recognition by forming an active site cap. At the junction of the extension and core catalytic unit, an arginine is recruited to replace a missing landmark lysine almost 200 residues away. Mutagenesis, rapid kinetic, and substrate binding studies support the functional significance of the cap and arginine recruitment. Thus, the enzyme function of human TrpRS has switched more to the N terminus of the sequence. This switch has the effect of creating selective pressure to retain the N-terminal extension for functional expansion.
-==Overview==
+Functional and crystal structure analysis of active site adaptations of a potent anti-angiogenic human tRNA synthetase.,Yang XL, Guo M, Kapoor M, Ewalt KL, Otero FJ, Skene RJ, McRee DE, Schimmel P Structure. 2007 Jul;15(7):793-805. PMID:17637340<ref>PMID:17637340</ref>
-Higher eukaryote tRNA synthetases have expanded functions that come from enlarged, more differentiated structures that were adapted to fit aminoacylation function. How those adaptations affect catalytic mechanisms is not known. Presented here is the structure of a catalytically active natural splice variant of human tryptophanyl-tRNA synthetase (TrpRS) that is a potent angiostatic factor. This and related structures suggest that a eukaryote-specific N-terminal extension of the core enzyme changed substrate recognition by forming an active site cap. At the junction of the extension and core catalytic unit, an arginine is recruited to replace a missing landmark lysine almost 200 residues away. Mutagenesis, rapid kinetic, and substrate binding studies support the functional significance of the cap and arginine recruitment. Thus, the enzyme function of human TrpRS has switched more to the N terminus of the sequence. This switch has the effect of creating selective pressure to retain the N-terminal extension for functional expansion.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-R6U is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R6U OCA].
+</div>
+<div class="pdbe-citations 1r6u" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Functional and crystal structure analysis of active site adaptations of a potent anti-angiogenic human tRNA synthetase., Yang XL, Guo M, Kapoor M, Ewalt KL, Otero FJ, Skene RJ, McRee DE, Schimmel P, Structure. 2007 Jul;15(7):793-805. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17637340 17637340]
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Tryptophan--tRNA ligase]]
+[[Category: McRee DE]]
-[[Category: McRee, D E.]]
+[[Category: Otero FJ]]
-[[Category: Otero, F J.]]
+[[Category: Ribas de Pouplana L]]
-[[Category: Pouplana, L Ribas de.]]
+[[Category: Schimmel P]]
-[[Category: Schimmel, P.]]
+[[Category: Skene RJ]]
-[[Category: Skene, R J.]]
+[[Category: Yang X-L]]
-[[Category: Yang, X L.]]
-[[Category: Anticodon recognition domain]]
-[[Category: Bound trp-amp]]
-[[Category: Class ic trna synthetase]]
-[[Category: Rossmann fold catalytic domain]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 07:09:17 2008''