1jik: Difference between revisions

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-[[Image:1jik.jpg|left|200px]]
- {{Structure
+==Crystal structure of S. aureus TyrRS in complex with SB-243545==
-|PDB= 1jik |SIZE=350|CAPTION= <scene name='initialview01'>1jik</scene>, resolution 2.80&Aring;
+<StructureSection load='1jik' size='340' side='right'caption='[[1jik]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=545:[2-AMINO-3-(4-HYDROXY-PHENYL)-PROPIONYLAMINO]-(1,3,4,5-TETRAHYDROXY-4-HYDROXYMETHYL-PIPERIDIN-2-YL)-+ACETIC+ACID+BUTYL+ESTER'>545</scene>
+<table><tr><td colspan='2'>[[1jik]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JIK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JIK FirstGlance]. <br>
-|ACTIVITY= <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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=545:[2-AMINO-3-(4-HYDROXY-PHENYL)-PROPIONYLAMINO]-(1,3,4,5-TETRAHYDROXY-4-HYDROXYMETHYL-PIPERIDIN-2-YL)-+ACETIC+ACID+BUTYL+ESTER'>545</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1jik FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jik OCA], [https://pdbe.org/1jik PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jik RCSB], [https://www.ebi.ac.uk/pdbsum/1jik PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jik ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1jii|1JII]], [[1jij|1JIJ]], [[1jil|1JIL]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jik FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jik OCA], [http://www.ebi.ac.uk/pdbsum/1jik PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1jik RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/SYY_STAAE SYY_STAAE] 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/ji/1jik_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/main_output.php?pdb_ID=1jik ConSurf].
+<div style="clear:both"></div>
-'''Crystal structure of S. aureus TyrRS in complex with SB-243545'''
+==See Also==
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-SB-219383 and its analogues are a class of potent and specific inhibitors of bacterial tyrosyl-tRNA synthetases. Crystal structures of these inhibitors have been solved in complex with the tyrosyl-tRNA synthetase from Staphylococcus aureus, the bacterium that is largely responsible for hospital-acquired infections. The full-length enzyme yielded crystals that diffracted to 2.8 A resolution, but a truncated version of the enzyme allowed the resolution to be extended to 2.2 A. These inhibitors not only occupy the known substrate binding sites in unique ways, but also reveal a butyl binding pocket. It was reported that the Bacillus stearothermophilus TyrRS T51P mutant has much increased catalytic activity. The S. aureus enzyme happens to have a proline at position 51. Therefore, our structures may contribute to the understanding of the catalytic mechanism and provide the structural basis for designing novel antimicrobial agents.
+[[Category: Large Structures]]
-==About this Structure==
-JIK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JIK OCA].
-==Reference==
-Crystal structure of Staphylococcus aureus tyrosyl-tRNA synthetase in complex with a class of potent and specific inhibitors., Qiu X, Janson CA, Smith WW, Green SM, McDevitt P, Johanson K, Carter P, Hibbs M, Lewis C, Chalker A, Fosberry A, Lalonde J, Berge J, Brown P, Houge-Frydrych CS, Jarvest RL, Protein Sci. 2001 Oct;10(10):2008-16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11567092 11567092]
-[[Category: Single protein]]
 [[Category: Staphylococcus aureus]]
-[[Category: Tyrosine--tRNA ligase]]
+[[Category: Janson CA]]
-[[Category: Janson, C A.]]
+[[Category: Jarvest RL]]
-[[Category: Jarvest, R L.]]
+[[Category: Qiu X]]
-[[Category: Qiu, X.]]
+[[Category: Smith WW]]
-[[Category: Smith, W W.]]
-[[Category: staphylococcus aureus]]
-[[Category: structure based inhibitor design]]
-[[Category: truncation]]
-[[Category: tyrosyl-trna synthetase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:34:11 2008''