4ch4: Difference between revisions
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<StructureSection load='4ch4' size='340' side='right'caption='[[4ch4]], [[Resolution|resolution]] 2.16Å' scene=''> | <StructureSection load='4ch4' size='340' side='right'caption='[[4ch4]], [[Resolution|resolution]] 2.16Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4ch4]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[4ch4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_mazei_Go1 Methanosarcina mazei Go1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CH4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CH4 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=YLC:5-O-[({(2R)-2-AMINO-6-[(2E)-BUT-2-ENOYLAMINO]HEXANOYL}OXY)PHOSPHINATO]ADENOSINE'>YLC</scene | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.16Å</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=YLC:5-O-[({(2R)-2-AMINO-6-[(2E)-BUT-2-ENOYLAMINO]HEXANOYL}OXY)PHOSPHINATO]ADENOSINE'>YLC</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=4ch4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ch4 OCA], [https://pdbe.org/4ch4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ch4 RCSB], [https://www.ebi.ac.uk/pdbsum/4ch4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ch4 ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</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). | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Methanosarcina mazei Go1]] | ||
[[Category: Fluegel | [[Category: Fluegel V]] | ||
[[Category: Schneider | [[Category: Schneider S]] | ||
[[Category: Vrabel | [[Category: Vrabel M]] | ||
Latest revision as of 15:10, 20 December 2023
Structure of pyrrolysyl-tRNA synthetase in complex with adenylated crotonyl lysineStructure of pyrrolysyl-tRNA synthetase in complex with adenylated crotonyl lysine
Structural highlights
FunctionPYLS_METMA Catalyzes the attachment of pyrrolysine to tRNA(Pyl). Pyrrolysine is a lysine derivative encoded by the termination codon UAG (By similarity). Publication Abstract from PubMedPosttranslational modifications (PTMs) of proteins determine their structure-function relationships, interaction partners, as well as their fate in the cell and are crucial for many cellular key processes. For instance chromatin structure and hence gene expression is epigenetically regulated by acetylation or methylation of lysine residues in histones, a phenomenon known as the 'histone code'. Recently it was shown that these lysine residues can furthermore be malonylated, succinylated, butyrylated, propionylated and crotonylated, resulting in significant alteration of gene expression patterns. However the functional implications of these PTMs, which only differ marginally in their chemical structure, is not yet understood. Therefore generation of proteins containing these modified amino acids site specifically is an important tool. In the last decade methods for the translational incorporation of non-natural amino acids using orthogonal aminoacyl-tRNA synthetase (aaRS):tRNAaaCUA pairs were developed. A number of studies show that aaRS can be evolved to use non-natural amino acids and expand the genetic code. Nevertheless the wild type pyrrolysyl-tRNA synthetase (PylRS) from Methanosarcina mazei readily accepts a number of lysine derivatives as substrates. This enzyme can further be engineered by mutagenesis to utilize a range of non-natural amino acids. Here we present structural data on the wild type enzyme in complex with adenylated epsilon-N-alkynyl-, epsilon-N-butyryl-, epsilon-N-crotonyl- and epsilon-N-propionyl-lysine providing insights into the plasticity of the PylRS active site. This shows that given certain key features in the non-natural amino acid to be incorporated, directed evolution of this enzyme is not necessary for substrate tolerance. Structural basis for the site-specific incorporation of lysine derivatives into proteins.,Flugel V, Vrabel M, Schneider S PLoS One. 2014 Apr 23;9(4):e96198. doi: 10.1371/journal.pone.0096198. eCollection, 2014. PMID:24760130[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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