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==Pyrrolysyl-tRNA synthetase bound to adenylated pyrrolysine and pyrophosphate== | ==Pyrrolysyl-tRNA synthetase bound to adenylated pyrrolysine and pyrophosphate== | ||
<StructureSection load='2zim' size='340' side='right' caption='[[2zim]], [[Resolution|resolution]] 2.10Å' scene=''> | <StructureSection load='2zim' size='340' side='right'caption='[[2zim]], [[Resolution|resolution]] 2.10Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2zim]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[2zim]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dsm_2053 Dsm 2053]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZIM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZIM FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=YLY:(2R)-2-AMINO-6-({[(2S,3R)-3-METHYLPYRROLIDIN-2-YL]CARBONYL}AMINO)HEXANOYL+[(2S,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+HYDROGEN+(R)-PHOSPHATE'>YLY</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=YLY:(2R)-2-AMINO-6-({[(2S,3R)-3-METHYLPYRROLIDIN-2-YL]CARBONYL}AMINO)HEXANOYL+[(2S,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+HYDROGEN+(R)-PHOSPHATE'>YLY</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2q7g|2q7g]], [[2q7e|2q7e]], [[2q7h|2q7h]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2q7g|2q7g]], [[2q7e|2q7e]], [[2q7h|2q7h]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pylS ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pylS ([https://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'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pyrrolysine--tRNA(Pyl)_ligase Pyrrolysine--tRNA(Pyl) ligase], with EC number [https://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'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zim OCA], [https://pdbe.org/2zim PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zim RCSB], [https://www.ebi.ac.uk/pdbsum/2zim PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zim ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[[ | [[https://www.uniprot.org/uniprot/PYLS_METMA PYLS_METMA]] Catalyzes the attachment of pyrrolysine to tRNA(Pyl). Pyrrolysine is a lysine derivative encoded by the termination codon UAG (By similarity). | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zi/2zim_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zi/2zim_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> | ||
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</div> | </div> | ||
<div class="pdbe-citations 2zim" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 2zim" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Dsm 2053]] | [[Category: Dsm 2053]] | ||
[[Category: Large Structures]] | |||
[[Category: Kavran, J M]] | [[Category: Kavran, J M]] | ||
[[Category: Steitz, T A]] | [[Category: Steitz, T A]] | ||
Revision as of 20:30, 15 December 2021
Pyrrolysyl-tRNA synthetase bound to adenylated pyrrolysine and pyrophosphatePyrrolysyl-tRNA synthetase bound to adenylated pyrrolysine and pyrophosphate
Structural highlights
Function[PYLS_METMA] Catalyzes the attachment of pyrrolysine to tRNA(Pyl). Pyrrolysine is a lysine derivative encoded by the termination codon UAG (By similarity). 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 PubMedPyrrolysine (Pyl), the 22nd natural amino acid and genetically encoded by UAG, becomes attached to its cognate tRNA by pyrrolysyl-tRNA synthetase (PylRS). We have determined three crystal structures of the Methanosarcina mazei PylRS complexed with either AMP-PNP, Pyl-AMP plus pyrophosphate, or the Pyl analogue N-epsilon-[(cylopentyloxy)carbonyl]-L-lysine plus ATP. The structures reveal that PylRS utilizes a deep hydrophobic pocket for recognition of the Pyl side chain. A comparison of these structures with previously determined class II tRNA synthetase complexes illustrates that different substrate specificities derive from changes in a small number of residues that form the substrate side-chain-binding pocket. The knowledge of these structures allowed the placement of PylRS in the aminoacyl-tRNA synthetase (aaRS) tree as the last known synthetase that evolved for genetic code expansion, as well as the finding that Pyl arose before the last universal common ancestral state. The PylRS structure provides an excellent framework for designing new aaRSs with altered amino acid specificity. Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation.,Kavran JM, Gundllapalli S, O'Donoghue P, Englert M, Soll D, Steitz TA Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11268-73. Epub 2007 Jun 25. PMID:17592110[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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