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5ud5

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==Crystal structure of the tRNA binding domain of Pyrrolysyl-tRNA synthetase bound to tRNA(Pyl)==
==Crystal structure of the tRNA binding domain of Pyrrolysyl-tRNA synthetase bound to tRNA(Pyl)==
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<StructureSection load='5ud5' size='340' side='right' caption='[[5ud5]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
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<StructureSection load='5ud5' size='340' side='right'caption='[[5ud5]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5ud5]] is a 4 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=5UD5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UD5 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5ud5]] is a 4 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=5UD5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UD5 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=ZN:ZINC+ION'>ZN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.347&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pylS, MM_1445 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=192952 METMA])</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=5ud5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ud5 OCA], [https://pdbe.org/5ud5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ud5 RCSB], [https://www.ebi.ac.uk/pdbsum/5ud5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ud5 ProSAT]</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=5ud5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ud5 OCA], [http://pdbe.org/5ud5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ud5 RCSB], [http://www.ebi.ac.uk/pdbsum/5ud5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ud5 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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Pyrrolysyl-tRNA synthetase (PylRS) is a major tool in genetic code expansion using noncanonical amino acids, yet its structure and function are not completely understood. Here we describe the crystal structure of the previously uncharacterized essential N-terminal domain of this unique enzyme in complex with tRNAPyl. This structure explains why PylRS remains orthogonal in a broad range of organisms, from bacteria to humans. The structure also illustrates why tRNAPyl recognition by PylRS is anticodon independent: the anticodon does not contact the enzyme. Then, using standard microbiological culture equipment, we established a new method for laboratory evolution-a noncontinuous counterpart of the previously developed phage-assisted continuous evolution. With this method, we evolved novel PylRS variants with enhanced activity and amino acid specificity. Finally, we employed an evolved PylRS variant to determine its N-terminal domain structure and show how its mutations improve PylRS activity in the genetic encoding of a noncanonical amino acid.
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Crystal structures reveal an elusive functional domain of pyrrolysyl-tRNA synthetase.,Suzuki T, Miller C, Guo LT, Ho JML, Bryson DI, Wang YS, Liu DR, Soll D Nat Chem Biol. 2017 Oct 16. doi: 10.1038/nchembio.2497. PMID:29035363<ref>PMID:29035363</ref>
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==See Also==
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*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
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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 5ud5" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Metma]]
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[[Category: Large Structures]]
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[[Category: Soll, D]]
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[[Category: Methanosarcina mazei Go1]]
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[[Category: Suzuki, T]]
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[[Category: Soll D]]
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[[Category: Aminoacyl-trna synthetase]]
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[[Category: Suzuki T]]
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[[Category: Ligase-rna complex]]
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[[Category: Pylr]]
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[[Category: Trna]]
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Current revision

Crystal structure of the tRNA binding domain of Pyrrolysyl-tRNA synthetase bound to tRNA(Pyl)

PDB ID 5ud5

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