2dxi: Difference between revisions

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-[[Image:2dxi.gif|left|200px]]
- {{Structure
+==2.2 A crystal structure of glutamyl-tRNA synthetase from Thermus thermophilus complexed with tRNA(Glu), ATP, and L-glutamol==
-|PDB= 2dxi |SIZE=350|CAPTION= <scene name='initialview01'>2dxi</scene>, resolution 2.20&Aring;
+<StructureSection load='2dxi' size='340' side='right'caption='[[2dxi]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=ATP:ADENOSINE-5&#39;-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=GAU:(4S)-4-AMINO-5-HYDROXYPENTANOIC+ACID'>GAU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
+<table><tr><td colspan='2'>[[2dxi]] 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=2DXI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DXI FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamate--tRNA_ligase Glutamate--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.17 6.1.1.17] </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]] 2.2&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GAU:(4S)-4-AMINO-5-HYDROXYPENTANOIC+ACID'>GAU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=2dxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dxi OCA], [https://pdbe.org/2dxi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dxi RCSB], [https://www.ebi.ac.uk/pdbsum/2dxi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dxi ProSAT], [https://www.topsan.org/Proteins/RSGI/2dxi TOPSAN]</span></td></tr>
-|RELATEDENTRY=[[2cuz|2CUZ]], [[2cv0|2CV0]], [[2cv1|2CV1]], [[2cv2|2CV2]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dxi OCA], [http://www.ebi.ac.uk/pdbsum/2dxi PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dxi RCSB]</span>
+== 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/dx/2dxi_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=2dxi ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Glutamyl-tRNA synthetase (GluRS) is one of the aminoacyl-tRNA synthetases that require the cognate tRNA for specific amino acid recognition and activation. We analyzed the role of tRNA in amino acid recognition by crystallography. In the GluRS*tRNA(Glu)*Glu structure, GluRS and tRNA(Glu) collaborate to form a highly complementary L-glutamate-binding site. This collaborative site is functional, as it is formed in the same manner in pretransition-state mimic, GluRS*tRNA(Glu)*ATP*Eol (a glutamate analog), and posttransition-state mimic, GluRS*tRNA(Glu)*ESA (a glutamyl-adenylate analog) structures. In contrast, in the GluRS*Glu structure, only GluRS forms the amino acid-binding site, which is defective and accounts for the binding of incorrect amino acids, such as D-glutamate and L-glutamine. Therefore, tRNA(Glu) is essential for formation of the completely functional binding site for L-glutamate. These structures, together with our previously described structures, reveal that tRNA plays a crucial role in accurate positioning of both L-glutamate and ATP, thus driving the amino acid activation.
-'''2.2 A crystal structure of glutamyl-tRNA synthetase from Thermus thermophilus complexed with tRNA(Glu), ATP, and L-glutamol'''
+Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase.,Sekine S, Shichiri M, Bernier S, Chenevert R, Lapointe J, Yokoyama S Structure. 2006 Dec;14(12):1791-9. PMID:17161369<ref>PMID:17161369</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2dxi" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Glutamyl-tRNA synthetase (GluRS) is one of the aminoacyl-tRNA synthetases that require the cognate tRNA for specific amino acid recognition and activation. We analyzed the role of tRNA in amino acid recognition by crystallography. In the GluRS*tRNA(Glu)*Glu structure, GluRS and tRNA(Glu) collaborate to form a highly complementary L-glutamate-binding site. This collaborative site is functional, as it is formed in the same manner in pretransition-state mimic, GluRS*tRNA(Glu)*ATP*Eol (a glutamate analog), and posttransition-state mimic, GluRS*tRNA(Glu)*ESA (a glutamyl-adenylate analog) structures. In contrast, in the GluRS*Glu structure, only GluRS forms the amino acid-binding site, which is defective and accounts for the binding of incorrect amino acids, such as D-glutamate and L-glutamine. Therefore, tRNA(Glu) is essential for formation of the completely functional binding site for L-glutamate. These structures, together with our previously described structures, reveal that tRNA plays a crucial role in accurate positioning of both L-glutamate and ATP, thus driving the amino acid activation.
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
-==About this Structure==
+== References ==
-DXI is a [[Single protein]] structure of sequence 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=2DXI OCA].
+<references/>
+__TOC__
-==Reference==
+</StructureSection>
-Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase., Sekine S, Shichiri M, Bernier S, Chenevert R, Lapointe J, Yokoyama S, Structure. 2006 Dec;14(12):1791-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17161369 17161369]
+[[Category: Large Structures]]
-[[Category: Glutamate--tRNA ligase]]
-[[Category: Single protein]]
 [[Category: Thermus thermophilus]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Sekine S]]
-[[Category: Sekine, S.]]
+[[Category: Yokoyama S]]
-[[Category: Yokoyama, S.]]
-[[Category: ligase]]
-[[Category: national project on protein structural and functional analyse]]
-[[Category: nppsfa]]
-[[Category: riken structural genomics/proteomics initiative]]
-[[Category: rna]]
-[[Category: rsgi]]
-[[Category: structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:40:59 2008''