2q7h

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[[Image:2q7h.gif|left|200px]]<br /><applet load="2q7h" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2q7h, resolution 2.10&Aring;" />
 
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'''pyrrolysyl-tRNA synthetase bound to adenylated pyrrolysine and pyrophosphate'''<br />
 
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==Overview==
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==Pyrrolysyl-tRNA synthetase bound to adenylated pyrrolysine and pyrophosphate==
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Pyrrolysine (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.
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<StructureSection load='2q7h' size='340' side='right'caption='[[2q7h]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2q7h]] 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=2Q7H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q7H FirstGlance]. <br>
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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]] 2.1&#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=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>
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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=2q7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q7h OCA], [https://pdbe.org/2q7h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q7h RCSB], [https://www.ebi.ac.uk/pdbsum/2q7h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q7h ProSAT]</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/q7/2q7h_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=2q7h ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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2Q7H is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Methanosarcina_mazei Methanosarcina mazei] with <scene name='pdbligand=EDO:'>EDO</scene>, <scene name='pdbligand=YLY:'>YLY</scene> and <scene name='pdbligand=POP:'>POP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q7H OCA].
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*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17592110 17592110]
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[[Category: Large Structures]]
[[Category: Methanosarcina mazei]]
[[Category: Methanosarcina mazei]]
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[[Category: Single protein]]
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[[Category: Kavran JM]]
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[[Category: Kavran, J M.]]
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[[Category: Steitz TA]]
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[[Category: Steitz, T A.]]
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[[Category: EDO]]
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[[Category: POP]]
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[[Category: YLY]]
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[[Category: pyrrolysine]]
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[[Category: pyrrolysyl-trna synthetase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:36:48 2008''
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Current revision

Pyrrolysyl-tRNA synthetase bound to adenylated pyrrolysine and pyrophosphate

PDB ID 2q7h

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