1qf6: Difference between revisions

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-[[Image:1qf6.png|left|200px]]
-<!--
+==STRUCTURE OF E. COLI THREONYL-TRNA SYNTHETASE COMPLEXED WITH ITS COGNATE TRNA==
-The line below this paragraph, containing "STRUCTURE_1qf6", creates the "Structure Box" on the page.
+<StructureSection load='1qf6' size='340' side='right'caption='[[1qf6]], [[Resolution|resolution]] 2.90&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'>[[1qf6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The April 2001 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QF6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QF6 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]] 2.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=AET:N-[N-(9-B-D-RIBOFURANOSYLPURIN-6-YL)METHYLCARBAMOYL]THREONINE-5-MONOPHOSPHATE'>AET</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_1qf6|  PDB=1qf6  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1qf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qf6 OCA], [https://pdbe.org/1qf6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qf6 RCSB], [https://www.ebi.ac.uk/pdbsum/1qf6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qf6 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SYT_ECOLI SYT_ECOLI] ThrS is also a translational repressor protein, it controls the translation of its own gene by binding to its mRNA.[HAMAP-Rule:MF_00184]
+== 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/qf/1qf6_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=1qf6 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+E. coli threonyl-tRNA synthetase (ThrRS) is a class II enzyme that represses the translation of its own mRNA. We report the crystal structure at 2.9 A resolution of the complex between tRNA(Thr) and ThrRS, whose structural features reveal novel strategies for providing specificity in tRNA selection. These include an amino-terminal domain containing a novel protein fold that makes minor groove contacts with the tRNA acceptor stem. The enzyme induces a large deformation of the anticodon loop, resulting in an interaction between two adjacent anticodon bases, which accounts for their prominent role in tRNA identity and translational regulation. A zinc ion found in the active site is implicated in amino acid recognition/discrimination.
-===STRUCTURE OF E. COLI THREONYL-TRNA SYNTHETASE COMPLEXED WITH ITS COGNATE TRNA===
+The structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site.,Sankaranarayanan R, Dock-Bregeon AC, Romby P, Caillet J, Springer M, Rees B, Ehresmann C, Ehresmann B, Moras D Cell. 1999 Apr 30;97(3):371-81. PMID:10319817<ref>PMID:10319817</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_10319817}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1qf6" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 10319817 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_10319817}}
-==About this Structure==
-[[1qf6]] is a 2 chain structure of [[Aminoacyl tRNA Synthetase]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The April 2001 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QF6 OCA].
 ==See Also==
-*[[Aminoacyl tRNA Synthetase]]
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
-==Reference==
+== References ==
-<ref group="xtra">PMID:010319817</ref><ref group="xtra">PMID:018172502</ref><references group="xtra"/>
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Aminoacyl-tRNA Synthetases]]
 [[Category: Escherichia coli]]
+[[Category: Large Structures]]
 [[Category: RCSB PDB Molecule of the Month]]
-[[Category: Threonine--tRNA ligase]]
+[[Category: Dock-Bregeon AC]]
-[[Category: Dock-Bregeon, A C.]]
+[[Category: Moras D]]
-[[Category: Moras, D.]]
+[[Category: Rees B]]
-[[Category: Rees, B.]]
+[[Category: Sankaranarayanan R]]
-[[Category: Sankaranarayanan, R.]]
-[[Category: Aminoacylation]]
-[[Category: Amp]]
-[[Category: Ligase-rna complex]]
-[[Category: Mrna]]
-[[Category: Protein/rna]]
-[[Category: Threonyl-trna synthetase]]
-[[Category: Translational regulation]]