1x8x: Difference between revisions

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 ==Tyrosyl t-RNA Synthetase from E.coli Complexed with Tyrosine==
-<StructureSection load='1x8x' size='340' side='right' caption='[[1x8x]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='1x8x' size='340' side='right'caption='[[1x8x]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1x8x]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X8X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1X8X FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1x8x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X8X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X8X FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TYR:TYROSINE'>TYR</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&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TYR:TYROSINE'>TYR</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1x8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x8x OCA], [http://pdbe.org/1x8x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1x8x RCSB], [http://www.ebi.ac.uk/pdbsum/1x8x PDBsum], [http://www.topsan.org/Proteins/RSGI/1x8x TOPSAN]</span></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=1x8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x8x OCA], [https://pdbe.org/1x8x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x8x RCSB], [https://www.ebi.ac.uk/pdbsum/1x8x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x8x ProSAT], [https://www.topsan.org/Proteins/RSGI/1x8x TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SYY_ECOLI SYY_ECOLI]] Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).[HAMAP-Rule:MF_02006]
+[https://www.uniprot.org/uniprot/SYY_ECOLI SYY_ECOLI] Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).[HAMAP-Rule:MF_02006]
 == 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/x8/1x8x_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/x8/1x8x_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1x8x ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Tyrosyl-tRNA synthetase (TyrRS) has been studied extensively by mutational and structural analyses to elucidate its catalytic mechanism. TyrRS has the HIGH and KMSKS motifs that catalyze the amino acid activation with ATP. In the present study, the crystal structures of the Escherichia coli TyrRS catalytic domain, in complexes with l-tyrosine and a l-tyrosyladenylate analogue, Tyr-AMS, were solved at 2.0A and 2.7A resolution, respectively. In the Tyr-AMS-bound structure, the 2'-OH group and adenine ring of the Tyr-AMS are strictly recognized by hydrogen bonds. This manner of hydrogen-bond recognition is conserved among the class I synthetases. Moreover, a comparison between the two structures revealed that the KMSKS loop is rearranged in response to adenine moiety binding and hydrogen-bond formation, and the KMSKS loop adopts the more compact ("semi-open") form, rather than the flexible, open form. The HIGH motif initially recognizes the gamma-phosphate, and then the alpha and gamma-phosphates of ATP, with a slight rearrangement of the residues. The other residues around the substrate also accommodate the Tyr-AMS. This induced-fit form presents a novel "snapshot" of the amino acid activation step in the aminoacylation reaction by TyrRS. The present structures and the T.thermophilus TyrRS ATP-free and bound structures revealed that the extensive induced-fit conformational changes of the KMSKS loop and the local conformational changes within the substrate binding site form the basis for driving the amino acid activation step: the KMSKS loop adopts the open form, transiently shifts to the semi-open conformation according to the adenosyl moiety binding, and finally assumes the rigid ATP-bound, closed form. After the amino acid activation, the KMSKS loop adopts the semi-open form again to accept the CCA end of tRNA for the aminoacyl transfer reaction.
-Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase.,Kobayashi T, Takimura T, Sekine R, Kelly VP, Kamata K, Sakamoto K, Nishimura S, Yokoyama S J Mol Biol. 2005 Feb 11;346(1):105-17. Epub 2004 Dec 15. PMID:15663931<ref>PMID:15663931</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1x8x" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Aminoacyl tRNA Synthetase|Aminoacyl tRNA Synthetase]]
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Tyrosine--tRNA ligase]]
+[[Category: Large Structures]]
-[[Category: Kamata, K]]
+[[Category: Kamata K]]
-[[Category: Kelly, V P]]
+[[Category: Kelly VP]]
-[[Category: Kobayashi, T]]
+[[Category: Kobayashi T]]
-[[Category: Nishimura, S]]
+[[Category: Nishimura S]]
-[[Category: Structural genomic]]
+[[Category: Sakamoto K]]
-[[Category: Sakamoto, K]]
+[[Category: Sekine R]]
-[[Category: Sekine, R]]
+[[Category: Takimura T]]
-[[Category: Takimura, T]]
+[[Category: Yokoyama S]]
-[[Category: Yokoyama, S]]
-[[Category: Ligase]]
-[[Category: Rsgi]]