2amc: Difference between revisions

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-[[Image:2amc.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2amc", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_2amc|  PDB=2amc  |  SCENE=  }}
-'''Crystal structure of Phenylalanyl-tRNA synthetase complexed with L-tyrosine'''
+==Crystal structure of Phenylalanyl-tRNA synthetase complexed with L-tyrosine==
+<StructureSection load='2amc' size='340' side='right'caption='[[2amc]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2amc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AMC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AMC 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]] 2.7&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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'>[https://proteopedia.org/fgij/fg.htm?mol=2amc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2amc OCA], [https://pdbe.org/2amc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2amc RCSB], [https://www.ebi.ac.uk/pdbsum/2amc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2amc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SYFA_THETH SYFA_THETH]
+== 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/am/2amc_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=2amc ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Aminoacyl-tRNA synthetases (aaRSs) exert control over the faithful transfer of amino acids onto cognate tRNAs. Since chemical structures of various amino acids closely resemble each other, it is difficult to discriminate between them. Editing activity has been evolved by certain aaRSs to resolve the problem. In this study, we determined the crystal structures of complexes of T. thermophilus phenylalanyl-tRNA synthetase (PheRS) with L-tyrosine, p-chloro-phenylalanine, and a nonhydrolyzable tyrosyl-adenylate analog. The structures demonstrate plasticity of the synthetic site capable of binding substrates larger than phenylalanine and provide a structural basis for the proofreading mechanism. The editing site is localized at the B3/B4 interface, 35 A from the synthetic site. Glubeta334 plays a crucial role in the specific recognition of the Tyr moiety in the editing site. The tyrosyl-adenylate analog binds exclusively in the synthetic site. Both structural data and tyrosine-dependent ATP hydrolysis enhanced by tRNA(Phe) provide evidence for a preferential posttransfer editing pathway in the phenylalanine-specific system.
-==Overview==
+Structural basis for discrimination of L-phenylalanine from L-tyrosine by phenylalanyl-tRNA synthetase.,Kotik-Kogan O, Moor N, Tworowski D, Safro M Structure. 2005 Dec;13(12):1799-807. PMID:16338408<ref>PMID:16338408</ref>
-Aminoacyl-tRNA synthetases (aaRSs) exert control over the faithful transfer of amino acids onto cognate tRNAs. Since chemical structures of various amino acids closely resemble each other, it is difficult to discriminate between them. Editing activity has been evolved by certain aaRSs to resolve the problem. In this study, we determined the crystal structures of complexes of T. thermophilus phenylalanyl-tRNA synthetase (PheRS) with L-tyrosine, p-chloro-phenylalanine, and a nonhydrolyzable tyrosyl-adenylate analog. The structures demonstrate plasticity of the synthetic site capable of binding substrates larger than phenylalanine and provide a structural basis for the proofreading mechanism. The editing site is localized at the B3/B4 interface, 35 A from the synthetic site. Glubeta334 plays a crucial role in the specific recognition of the Tyr moiety in the editing site. The tyrosyl-adenylate analog binds exclusively in the synthetic site. Both structural data and tyrosine-dependent ATP hydrolysis enhanced by tRNA(Phe) provide evidence for a preferential posttransfer editing pathway in the phenylalanine-specific system.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-AMC is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AMC OCA].
+</div>
+<div class="pdbe-citations 2amc" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structural basis for discrimination of L-phenylalanine from L-tyrosine by phenylalanyl-tRNA synthetase., Kotik-Kogan O, Moor N, Tworowski D, Safro M, Structure. 2005 Dec;13(12):1799-807. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16338408 16338408]
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
-[[Category: Phenylalanine--tRNA ligase]]
+== References ==
-[[Category: Protein complex]]
+<references/>
-[[Category: Thermus thermophilus]]
+__TOC__
-[[Category: Kotik-Kogan, O.]]
+</StructureSection>
-[[Category: Moor, N.]]
+[[Category: Large Structures]]
-[[Category: Safro, M.]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Tworowski, D.]]
+[[Category: Kotik-Kogan O]]
-[[Category: Protein-amino acid complex]]
+[[Category: Moor N]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 19:12:49 2008''
+[[Category: Safro M]]
+[[Category: Tworowski D]]