3vqy: Difference between revisions
No edit summary |
No edit summary |
||
| (One intermediate revision by the same user not shown) | |||
| Line 3: | Line 3: | ||
<StructureSection load='3vqy' size='340' side='right'caption='[[3vqy]], [[Resolution|resolution]] 2.40Å' scene=''> | <StructureSection load='3vqy' size='340' side='right'caption='[[3vqy]], [[Resolution|resolution]] 2.40Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3vqy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3vqy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_mazei Methanosarcina mazei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VQY FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=LBY:N~6~-(TERT-BUTOXYCARBONYL)-L-LYSINE'>LBY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=3vqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vqy OCA], [https://pdbe.org/3vqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vqy RCSB], [https://www.ebi.ac.uk/pdbsum/3vqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vqy ProSAT]</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=3vqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vqy OCA], [https://pdbe.org/3vqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vqy RCSB], [https://www.ebi.ac.uk/pdbsum/3vqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vqy ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| Line 27: | Line 25: | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Methanosarcina mazei]] | ||
[[Category: | [[Category: Ishii R]] | ||
[[Category: Sumida | [[Category: Sumida T]] | ||
[[Category: Yanagisawa | [[Category: Yanagisawa T]] | ||
[[Category: Yokoyama | [[Category: Yokoyama S]] | ||
Latest revision as of 15:33, 8 November 2023
Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with BocLys and AMPPNP (form 2)Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with BocLys and AMPPNP (form 2)
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
|
| ||||||||||||||||||