1n78: Difference between revisions

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-{{Seed}}
-[[Image:1n78.png|left|200px]]
-<!--
+==Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with tRNA(Glu) and glutamol-AMP.==
-The line below this paragraph, containing "STRUCTURE_1n78", creates the "Structure Box" on the page.
+<StructureSection load='1n78' size='340' side='right'caption='[[1n78]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1n78]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N78 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N78 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOM:GLUTAMOL-AMP'>GOM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-{{STRUCTURE_1n78|  PDB=1n78  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1n78 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n78 OCA], [https://pdbe.org/1n78 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n78 RCSB], [https://www.ebi.ac.uk/pdbsum/1n78 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n78 ProSAT], [https://www.topsan.org/Proteins/RSGI/1n78 TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SYE_THET8 SYE_THET8] Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu).<ref>PMID:11224561</ref> <ref>PMID:17161369</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/n7/1n78_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=1n78 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Aminoacyl-tRNA synthetases catalyze the formation of an aminoacyl-AMP from an amino acid and ATP, prior to the aminoacyl transfer to tRNA. A subset of aminoacyl-tRNA synthetases, including glutamyl-tRNA synthetase (GluRS), have a regulation mechanism to avoid aminoacyl-AMP formation in the absence of tRNA. In this study, we determined the crystal structure of the 'non-productive' complex of Thermus thermophilus GluRS, ATP and L-glutamate, together with those of the GluRS.ATP, GluRS.tRNA.ATP and GluRS.tRNA.GoA (a glutamyl-AMP analog) complexes. In the absence of tRNA(Glu), ATP is accommodated in a 'non-productive' subsite within the ATP-binding site, so that the ATP alpha-phosphate and the glutamate alpha-carboxyl groups in GluRS. ATP.Glu are too far from each other (6.2 A) to react. In contrast, the ATP-binding mode in GluRS.tRNA. ATP is dramatically different from those in GluRS.ATP.Glu and GluRS.ATP, but corresponds to the AMP moiety binding mode in GluRS.tRNA.GoA (the 'productive' subsite). Therefore, tRNA binding to GluRS switches the ATP-binding mode. The interactions of the three tRNA(Glu) regions with GluRS cause conformational changes around the ATP-binding site, and allow ATP to bind to the 'productive' subsite.
-===Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with tRNA(Glu) and glutamol-AMP.===
+ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding.,Sekine S, Nureki O, Dubois DY, Bernier S, Chenevert R, Lapointe J, Vassylyev DG, Yokoyama S EMBO J. 2003 Feb 3;22(3):676-88. PMID:12554668<ref>PMID:12554668</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1n78" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12554668}}, adds the Publication Abstract to the page
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12554668 is the PubMed ID number.
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
--->
+== References ==
-{{ABSTRACT_PUBMED_12554668}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-N78 is a 4 chains 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=1N78 OCA].
+[[Category: Large Structures]]
-==Reference==
-ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding., Sekine S, Nureki O, Dubois DY, Bernier S, Chenevert R, Lapointe J, Vassylyev DG, Yokoyama S, EMBO J. 2003 Feb 3;22(3):676-88. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12554668 12554668]
-[[Category: Glutamate--tRNA ligase]]
 [[Category: Thermus thermophilus]]
-[[Category: Bernier, S.]]
+[[Category: Bernier S]]
-[[Category: Chenevert, R.]]
+[[Category: Chenevert R]]
-[[Category: Dubois, D Y.]]
+[[Category: Dubois DY]]
-[[Category: Lapointe, J.]]
+[[Category: Lapointe J]]
-[[Category: Nureki, O.]]
+[[Category: Nureki O]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Sekine S]]
-[[Category: Sekine, S.]]
+[[Category: Vassylyev DG]]
-[[Category: Vassylyev, D G.]]
+[[Category: Yokoyama S]]
-[[Category: Yokoyama, S.]]
-[[Category: Ers/trna/goa]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Nov 16 14:05:31 2008''