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[[Image: | ==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=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3fi0]] is a 18 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. 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 [http://oca.weizmann.ac.il/oca-docs/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> | |||
<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]], [[1m83|1m83]], [[1mau|1mau]], [[2ov4|2ov4]]</td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TrpS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tryptophan--tRNA_ligase Tryptophan--tRNA ligase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3fi0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fi0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fi0 RCSB], [http://www.ebi.ac.uk/pdbsum/3fi0 PDBsum]</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/fi/3fi0_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/chain_selection.php?pdb_ID=2ata 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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
< | |||
[[Category: Geobacillus stearothermophilus]] | [[Category: Geobacillus stearothermophilus]] | ||
[[Category: Tryptophan--tRNA ligase]] | [[Category: Tryptophan--tRNA ligase]] | ||
[[Category: Carter, C W | [[Category: Carter, C W]] | ||
[[Category: Delarue, M | [[Category: Delarue, M]] | ||
[[Category: Kapustina, M | [[Category: Kapustina, M]] | ||
[[Category: Koehl, P | [[Category: Koehl, P]] | ||
[[Category: Laowanapiban, P | [[Category: Laowanapiban, P]] | ||
[[Category: Vonrhein, C | [[Category: Vonrhein, C]] | ||
[[Category: Aminoacyl-trna synthetase]] | [[Category: Aminoacyl-trna synthetase]] | ||
[[Category: Atp-binding]] | [[Category: Atp-binding]] | ||
Revision as of 13:30, 3 December 2014
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. References
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