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==Crystal Structure Analysis of B. stearothermophilus Tryptophanyl-tRNA Synthetase Complexed with Tryptophan, AMP, and Inorganic Phosphate== | ==Crystal Structure Analysis of B. stearothermophilus Tryptophanyl-tRNA Synthetase Complexed with Tryptophan, AMP, and Inorganic Phosphate== | ||
<StructureSection load='3fi0' size='340' side='right' caption='[[3fi0]], [[Resolution|resolution]] 2.70Å' scene=''> | <StructureSection load='3fi0' size='340' side='right'caption='[[3fi0]], [[Resolution|resolution]] 2.70Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3fi0]] is a 18 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3fi0]] is a 18 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FI0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FI0 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr> | ||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3fhj|3fhj]], [[1d2r|1d2r]], [[1mb2|1mb2]], [[1m83|1m83]], [[1mau|1mau]], [[2ov4|2ov4]], [[1i6k|1i6k]], [[1maw|1maw]], [[1i6l|1i6l]], [[1i6m|1i6m]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3fhj|3fhj]], [[1d2r|1d2r]], [[1mb2|1mb2]], [[1m83|1m83]], [[1mau|1mau]], [[2ov4|2ov4]], [[1i6k|1i6k]], [[1maw|1maw]], [[1i6l|1i6l]], [[1i6m|1i6m]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TrpS ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TrpS ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Tryptophan--tRNA_ligase Tryptophan--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.2 6.1.1.2] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3fi0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fi0 OCA], [https://pdbe.org/3fi0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fi0 RCSB], [https://www.ebi.ac.uk/pdbsum/3fi0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fi0 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
| Line 15: | Line 15: | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fi/3fi0_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fi/3fi0_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
| Line 30: | Line 30: | ||
</div> | </div> | ||
<div class="pdbe-citations 3fi0" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 3fi0" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
| Line 35: | Line 38: | ||
</StructureSection> | </StructureSection> | ||
[[Category: Atcc 12980]] | [[Category: Atcc 12980]] | ||
[[Category: Large Structures]] | |||
[[Category: Tryptophan--tRNA ligase]] | [[Category: Tryptophan--tRNA ligase]] | ||
[[Category: Carter, C W]] | [[Category: Carter, C W]] | ||
Revision as of 11:02, 2 March 2022
Crystal Structure Analysis of B. stearothermophilus Tryptophanyl-tRNA Synthetase Complexed with Tryptophan, AMP, and Inorganic PhosphateCrystal Structure Analysis of B. stearothermophilus Tryptophanyl-tRNA Synthetase Complexed with Tryptophan, AMP, and Inorganic Phosphate
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedTwo new crystal structures of Bacillus stearothermophilus tryptophanyl-tRNA synthetase (TrpRS) afford evidence that a closed interdomain hinge angle requires a covalent bond between AMP and an occupant of either pyrophosphate or tryptophan subsite. They also are within experimental error of a cluster of structures observed in a nonequilibrium molecular dynamics simulation showing partial active-site assembly. Further, the highest energy structure in a minimum action pathway computed by using elastic network models for Open and Pretransition state (PreTS) conformations for the fully liganded TrpRS monomer is intermediate between that simulated structure and a partially disassembled structure from a nonequilibrium molecular dynamics trajectory for the unliganded PreTS. These mutual consistencies provide unexpected validation of inferences drawn from molecular simulations. Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations.,Laowanapiban P, Kapustina M, Vonrhein C, Delarue M, Koehl P, Carter CW Jr Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):1790-5. Epub 2009 Jan 27. PMID:19174517[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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