1bs2: Difference between revisions

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 ==YEAST ARGINYL-TRNA SYNTHETASE==
-<StructureSection load='1bs2' size='340' side='right' caption='[[1bs2]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
+<StructureSection load='1bs2' size='340' side='right'caption='[[1bs2]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1bs2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BS2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BS2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1bs2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BS2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BS2 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARG:ARGININE'>ARG</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]] 2.75&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arginine--tRNA_ligase Arginine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.19 6.1.1.19] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ARG:ARGININE'>ARG</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=1bs2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bs2 OCA], [http://pdbe.org/1bs2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bs2 RCSB], [http://www.ebi.ac.uk/pdbsum/1bs2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1bs2 ProSAT]</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=1bs2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bs2 OCA], [https://pdbe.org/1bs2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bs2 RCSB], [https://www.ebi.ac.uk/pdbsum/1bs2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bs2 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SYRC_YEAST SYRC_YEAST]] Forms part of a macromolecular complex that catalyzes the attachment of specific amino acids to cognate tRNAs during protein synthesis (By similarity).[HAMAP-Rule:MF_00123]
+[https://www.uniprot.org/uniprot/SYRC_YEAST SYRC_YEAST] Forms part of a macromolecular complex that catalyzes the attachment of specific amino acids to cognate tRNAs during protein synthesis (By similarity).[HAMAP-Rule:MF_00123]
 == 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/bs/1bs2_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bs/1bs2_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 20: / Line 20: @@
 </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=1bs2 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The crystal structure of arginyl-tRNA synthetase (ArgRS) from Saccharomyces cerevisiae, a class I aminoacyl-tRNA synthetase (aaRS), with L-arginine bound to the active site has been solved at 2.75 A resolution and refined to a crystallographic R-factor of 19.7%. ArgRS is composed predominantly of alpha-helices and can be divided into five domains, including the class I-specific active site. The N-terminal domain shows striking similarity to some completely unrelated proteins and defines a module which should participate in specific tRNA recognition. The C-terminal domain, which is the putative anticodon-binding module, displays an all-alpha-helix fold highly similar to that of Escherichia coli methionyl-tRNA synthetase. While ArgRS requires tRNAArg for the first step of the aminoacylation reaction, the results show that its presence is not a prerequisite for L-arginine binding. All H-bond-forming capability of L-arginine is used by the protein for the specific recognition. The guanidinium group forms two salt bridge interactions with two acidic residues, and one H-bond with a tyrosine residue; these three residues are strictly conserved in all ArgRS sequences. This tyrosine is also conserved in other class I aaRS active sites but plays several functional roles. The ArgRS structure allows the definition of a new framework for sequence alignments and subclass definition in class I aaRSs.
-L-arginine recognition by yeast arginyl-tRNA synthetase.,Cavarelli J, Delagoutte B, Eriani G, Gangloff J, Moras D EMBO J. 1998 Sep 15;17(18):5438-48. PMID:9736621<ref>PMID:9736621</ref>
+==See Also==
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1bs2" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Arginine--tRNA ligase]]
+[[Category: Large Structures]]
-[[Category: Atcc 18824]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Cavarelli, J]]
+[[Category: Cavarelli J]]
-[[Category: Delagouute, B]]
+[[Category: Delagouute B]]
-[[Category: Eriani, G]]
+[[Category: Eriani G]]
-[[Category: Gangloff, J]]
+[[Category: Gangloff J]]
-[[Category: Moras, D]]
+[[Category: Moras D]]
-[[Category: Aminoacyl-trna synthetase]]
-[[Category: Ligase]]
-[[Category: Protein biosynthesis]]