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4ch5

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<StructureSection load='4ch5' size='340' side='right'caption='[[4ch5]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='4ch5' size='340' side='right'caption='[[4ch5]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4ch5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Metma Metma]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CH5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CH5 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4ch5]] 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=4CH5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CH5 FirstGlance]. <br>
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</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=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=YLP:(S)-2-AMINO-6-PROPIONAMIDOHEXANOIC(((2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL)METHYL+PHOSPHORIC)+ANHYDRIDE'>YLP</scene></td></tr>
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</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=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=YLP:(S)-2-AMINO-6-PROPIONAMIDOHEXANOIC(((2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL)METHYL+PHOSPHORIC)+ANHYDRIDE'>YLP</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ch3|4ch3]], [[4ch4|4ch4]], [[4ch6|4ch6]]</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ch5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ch5 OCA], [https://pdbe.org/4ch5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ch5 RCSB], [https://www.ebi.ac.uk/pdbsum/4ch5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ch5 ProSAT]</span></td></tr>
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<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>
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<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=4ch5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ch5 OCA], [http://pdbe.org/4ch5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ch5 RCSB], [http://www.ebi.ac.uk/pdbsum/4ch5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ch5 ProSAT]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://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).
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[[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).
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Posttranslational 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.
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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<ref>PMID:24760130</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 4ch5" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Metma]]
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[[Category: Methanosarcina mazei Go1]]
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[[Category: Fluegel, V]]
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[[Category: Fluegel V]]
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[[Category: Schneider, S]]
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[[Category: Schneider S]]
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[[Category: Vrabel, M]]
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[[Category: Vrabel M]]
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[[Category: Ligase]]
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[[Category: Non-natural amino acid]]
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[[Category: Pyrrolysine]]
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Revision as of 17:45, 7 September 2022

Structure of pyrrolysyl-tRNA synthetase in complex with adenylated propionyl lysine

PDB ID 4ch5

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