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2zio

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{{Seed}}
 
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[[Image:2zio.png|left|200px]]
 
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<!--
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==Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with AlocLys-AMP and PNP==
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The line below this paragraph, containing "STRUCTURE_2zio", creates the "Structure Box" on the page.
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<StructureSection load='2zio' size='340' side='right'caption='[[2zio]], [[Resolution|resolution]] 2.06&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2zio]] 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=2ZIO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZIO FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.06&#8491;</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=2PN:IMIDODIPHOSPHORIC+ACID'>2PN</scene>, <scene name='pdbligand=AYB:5-O-[(S)-({(2S)-2-AMINO-6-[(PROPOXYCARBONYL)AMINO]HEXANOYL}OXY)(HYDROXY)PHOSPHORYL]ADENOSINE'>AYB</scene></td></tr>
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{{STRUCTURE_2zio| PDB=2zio | SCENE= }}
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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=2zio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zio OCA], [https://pdbe.org/2zio PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zio RCSB], [https://www.ebi.ac.uk/pdbsum/2zio PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zio ProSAT], [https://www.topsan.org/Proteins/RSGI/2zio TOPSAN]</span></td></tr>
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</table>
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== Function ==
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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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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zi/2zio_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2zio ConSurf].
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<div style="clear:both"></div>
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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) esterifies pyrrolysine to tRNA(Pyl). In this study, N(epsilon)-(tert-butyloxycarbonyl)-L-lysine (BocLys) and N(epsilon)-allyloxycarbonyl-L-lysine (AlocLys) were esterified to tRNA(Pyl) by PylRS. Crystal structures of a PylRS catalytic fragment complexed with BocLys and an ATP analog and with AlocLys-AMP revealed that PylRS requires an N(epsilon)-carbonyl group bearing a substituent with a certain size. A PylRS(Y384F) mutant obtained by random screening exhibited higher in vitro aminoacylation and in vivo amber suppression activities with BocLys, AlocLys, and pyrrolysine than those of the wild-type PylRS. Furthermore, the structure-based Y306A mutation of PylRS drastically increased the in vitro aminoacylation activity for N(epsilon)-benzyloxycarbonyl-L-lysine (ZLys). A PylRS with both the Y306A and Y384F mutations enabled the large-scale preparation (&gt;10 mg per liter medium) of proteins site-specifically containing N(epsilon)-(o-azidobenzyloxycarbonyl)-L-lysine (AzZLys). The AzZLys-containing protein was labeled with a fluorescent probe, by Staudinger ligation.
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===Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with AlocLys-AMP and PNP===
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Multistep engineering of pyrrolysyl-tRNA synthetase to genetically encode N(epsilon)-(o-azidobenzyloxycarbonyl) lysine for site-specific protein modification.,Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S Chem Biol. 2008 Nov 24;15(11):1187-97. PMID:19022179<ref>PMID:19022179</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 2zio" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_19022179}}, adds the Publication Abstract to the page
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*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 19022179 is the PubMed ID number.
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== References ==
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-->
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<references/>
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{{ABSTRACT_PUBMED_19022179}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2ZIO is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Methanosarcina_mazei Methanosarcina mazei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZIO OCA].
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==Reference==
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Multistep Engineering of Pyrrolysyl-tRNA Synthetase to Genetically Encode N(varepsilon)-(o-Azidobenzyloxycarbonyl) lysine for Site-Specific Protein Modification., Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S, Chem Biol. 2008 Nov;15(11):1187-97. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/19022179 19022179]
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[[Category: Methanosarcina mazei]]
[[Category: Methanosarcina mazei]]
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[[Category: Single protein]]
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[[Category: Ishii R]]
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[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
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[[Category: Yanagisawa T]]
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[[Category: Aminoacyl-trna synthetase]]
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[[Category: Yokoyama S]]
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[[Category: Atp analogue]]
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[[Category: Atp-binding]]
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[[Category: Cytoplasm]]
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[[Category: Ligase]]
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[[Category: National project on protein structural and functional analyse]]
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[[Category: Non-natural amino acid]]
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[[Category: Nppsfa]]
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[[Category: Nucleotide-binding]]
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[[Category: Protein biosynthesis]]
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[[Category: Pyrrolysine]]
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[[Category: Pyrrolysyl-trna synthetase]]
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[[Category: Riken structural genomics/proteomics initiative]]
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[[Category: Rsgi]]
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[[Category: Structural genomic]]
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[[Category: Trna]]
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[[Category: Unnatural amino acid]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 10 20:03:14 2008''
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Current revision

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with AlocLys-AMP and PNP

PDB ID 2zio

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