1fyf: Difference between revisions

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-[[Image:1fyf.gif|left|200px]]
- {{Structure
+==CRYSTAL STRUCTURE OF A TRUNCATED FORM OF THREONYL-TRNA SYNTHETASE COMPLEXED WITH A SERYL ADENYLATE ANALOG==
-|PDB= 1fyf |SIZE=350|CAPTION= <scene name='initialview01'>1fyf</scene>, resolution 1.65&Aring;
+<StructureSection load='1fyf' size='340' side='right'caption='[[1fyf]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=SSA:5&#39;-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE'>SSA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
+<table><tr><td colspan='2'>[[1fyf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FYF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FYF FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Threonine--tRNA_ligase Threonine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.3 6.1.1.3] </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]] 1.65&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SSA:5-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE'>SSA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1fyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fyf OCA], [https://pdbe.org/1fyf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fyf RCSB], [https://www.ebi.ac.uk/pdbsum/1fyf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fyf ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1qf6|1QF6]], [[1evk|1EVK]], [[1evl|1EVL]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fyf OCA], [http://www.ebi.ac.uk/pdbsum/1fyf PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1fyf RCSB]</span>
+== 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/fy/1fyf_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=1fyf ConSurf].
+<div style="clear:both"></div>
-'''CRYSTAL STRUCTURE OF A TRUNCATED FORM OF THREONYL-TRNA SYNTHETASE COMPLEXED WITH A SERYL ADENYLATE ANALOG'''
+==See Also==
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-Threonyl-tRNA synthetase, a class II synthetase, uses a unique zinc ion to discriminate against the isosteric valine at the activation step. The crystal structure of the enzyme with an analog of seryl adenylate shows that the noncognate serine cannot be fully discriminated at that step. We show that hydrolysis of the incorrectly formed ser-tRNA(Thr) is performed at a specific site in the N-terminal domain of the enzyme. The present study suggests that both classes of synthetases use effectively the ability of the CCA end of tRNA to switch between a hairpin and a helical conformation for aminoacylation and editing. As a consequence, the editing mechanism of both classes of synthetases can be described as mirror images, as already seen for tRNA binding and amino acid activation.
-==About this Structure==
-FYF is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FYF OCA].
-==Reference==
-Transfer RNA-mediated editing in threonyl-tRNA synthetase. The class II solution to the double discrimination problem., Dock-Bregeon A, Sankaranarayanan R, Romby P, Caillet J, Springer M, Rees B, Francklyn CS, Ehresmann C, Moras D, Cell. 2000 Dec 8;103(6):877-84. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11136973 11136973]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Threonine--tRNA ligase]]
+[[Category: Dock-Bregeon AC]]
-[[Category: Dock-Bregeon, A C.]]
+[[Category: Moras D]]
-[[Category: Moras, D.]]
+[[Category: Sankaranarayanan R]]
-[[Category: Sankaranarayanan, R.]]
-[[Category: adenylate analog]]
-[[Category: amino acid recognition]]
-[[Category: deletion mutant]]
-[[Category: trna-synthetase]]
-[[Category: zinc ion]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:32:46 2008''