3vqw: Difference between revisions
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==Crystal structure of the SeMet substituted catalytic domain of pyrrolysyl-tRNA synthetase== | ==Crystal structure of the SeMet substituted catalytic domain of pyrrolysyl-tRNA synthetase== | ||
<StructureSection load='3vqw' size='340' side='right' caption='[[3vqw]], [[Resolution|resolution]] 2.40Å' scene=''> | <StructureSection load='3vqw' size='340' side='right' caption='[[3vqw]], [[Resolution|resolution]] 2.40Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3vqw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3vqw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dsm_2053 Dsm 2053]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VQW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VQW FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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">[[2e3c|2e3c]], [[2zcd|2zcd]], [[2zce|2zce]], [[2zin|2zin]], [[2zio|2zio]], [[3vqv|3vqv]], [[3vqx|3vqx]], [[3vqy|3vqy]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2e3c|2e3c]], [[2zcd|2zcd]], [[2zce|2zce]], [[2zin|2zin]], [[2zio|2zio]], [[3vqv|3vqv]], [[3vqx|3vqx]], [[3vqy|3vqy]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pylS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2209 | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pylS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2209 DSM 2053])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyrrolysine--tRNA(Pyl)_ligase Pyrrolysine--tRNA(Pyl) ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.26 6.1.1.26] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyrrolysine--tRNA(Pyl)_ligase Pyrrolysine--tRNA(Pyl) ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.26 6.1.1.26] </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=3vqw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vqw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vqw RCSB], [http://www.ebi.ac.uk/pdbsum/3vqw PDBsum]</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=3vqw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vqw OCA], [http://pdbe.org/3vqw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vqw RCSB], [http://www.ebi.ac.uk/pdbsum/3vqw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vqw ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 3vqw" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Aminoacyl tRNA Synthetase|Aminoacyl tRNA Synthetase]] | |||
*[[Pyrrolysyl-tRNA synthetase|Pyrrolysyl-tRNA synthetase]] | *[[Pyrrolysyl-tRNA synthetase|Pyrrolysyl-tRNA synthetase]] | ||
== References == | == References == | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Dsm 2053]] | ||
[[Category: Ishii, R]] | [[Category: Ishii, R]] | ||
[[Category: Structural genomic]] | [[Category: Structural genomic]] | ||
Revision as of 18:05, 5 August 2016
Crystal structure of the SeMet substituted catalytic domain of pyrrolysyl-tRNA synthetaseCrystal structure of the SeMet substituted catalytic domain of pyrrolysyl-tRNA synthetase
Structural highlights
Publication Abstract from PubMedStructures of Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS) have been determined in a novel crystal form. The triclinic form crystals contained two PylRS dimers (four monomer molecules) in the asymmetric unit, in which the two subunits in one dimer each bind N()-(tert-butyloxycarbonyl)-L-lysyladenylate (BocLys-AMP) and the two subunits in the other dimer each bind AMP. The BocLys-AMP molecules adopt a curved conformation and the C(alpha) position of BocLys-AMP protrudes from the active site. The beta7-beta8 hairpin structures in the four PylRS molecules represent distinct conformations of different states of the aminoacyl-tRNA synthesis reaction. Tyr384, at the tip of the beta7-beta8 hairpin, moves from the edge to the inside of the active-site pocket and adopts multiple conformations in each state. Furthermore, a new crystal structure of the BocLys-AMPPNP-bound form is also reported. The bound BocLys adopts an unusually bent conformation, which differs from the previously reported structure. It is suggested that the present BocLys-AMPPNP-bound, BocLys-AMP-bound and AMP-bound complexes represent the initial binding of an amino acid (or pre-aminoacyl-AMP synthesis), pre-aminoacyl-tRNA synthesis and post-aminoacyl-tRNA synthesis states, respectively. The conformational changes of Asn346 that accompany the aminoacyl-tRNA synthesis reaction have been captured by X-ray crystallographic analyses. The orientation of the Asn346 side chain, which hydrogen-bonds to the carbonyl group of the amino-acid substrate, shifts by a maximum of 85-90 degrees around the C(beta) atom. A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site.,Yanagisawa T, Sumida T, Ishii R, Yokoyama S Acta Crystallogr D Biol Crystallogr. 2013 Jan;69(Pt 1):5-15. doi:, 10.1107/S0907444912039881. Epub 2012 Dec 20. PMID:23275158[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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