View source for 3fhj


==Independent saturation of three TrpRS subsites generates a partially-assembled state similar to those observed in molecular simulations==
<StructureSection load='3fhj' size='340' side='right'caption='[[3fhj]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3fhj]] is a 6 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=3FHJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FHJ FirstGlance]. <br>
</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1d2r|1d2r]], [[1mb2|1mb2]], [[1m83|1m83]], [[2ov4|2ov4]], [[1i6k|1i6k]], [[3fi0|3fi0]], [[1mau|1mau]], [[1i6m|1i6m]], [[1i6l|1i6l]]</div></td></tr>
<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'>[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'>[https://proteopedia.org/fgij/fg.htm?mol=3fhj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fhj OCA], [https://pdbe.org/3fhj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fhj RCSB], [https://www.ebi.ac.uk/pdbsum/3fhj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fhj ProSAT]</span></td></tr>
</table>
== 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/fh/3fhj_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=3fhj ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Two 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<ref>PMID:19174517</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3fhj" style="background-color:#fffaf0;"></div>

==See Also==
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Atcc 12980]]
[[Category: Large Structures]]
[[Category: Tryptophan--tRNA ligase]]
[[Category: Carter, C W]]
[[Category: Delarue, M]]
[[Category: Kapustina, M]]
[[Category: Koehl, P]]
[[Category: Laowanapiban, P]]
[[Category: Vonrhein, C]]
[[Category: Aminoacyl-trna synthetase]]
[[Category: Atp-binding]]
[[Category: Cytoplasm]]
[[Category: Ligand-dependent domain rearrangement]]
[[Category: Ligase]]
[[Category: Mechanistic pathway]]
[[Category: Molecular simulation]]
[[Category: Nucleotide-binding]]
[[Category: Protein biosynthesis]]
[[Category: Translation]]