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==Pyrrolysyl-tRNA synthetase bound to adenylated pyrrolysine and pyrophosphate==
==Pyrrolysyl-tRNA synthetase bound to adenylated pyrrolysine and pyrophosphate==
<StructureSection load='2q7h' size='340' side='right' caption='[[2q7h]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
<StructureSection load='2q7h' size='340' side='right'caption='[[2q7h]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2q7h]] is a 1 chain structure with 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=2Q7H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q7H FirstGlance]. <br>
<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>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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><br>
</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>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2q7e|2q7e]], [[2q7g|2q7g]], [[2zim|2zim]]</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=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>
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pylS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2209 Methanosarcina mazei])</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=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>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q7h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q7h RCSB], [http://www.ebi.ac.uk/pdbsum/2q7h PDBsum]</span></td></tr>
</table>
<table>
== 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).
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q7/2q7h_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q7/2q7h_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </jmolCheckbox>
</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/chain_selection.php?pdb_ID=2ata ConSurf].
</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].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:17592110<ref>PMID:17592110</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[Pyrrolysyl-tRNA synthetase|Pyrrolysyl-tRNA synthetase]]
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Methanosarcina mazei]]
[[Category: Methanosarcina mazei]]
[[Category: Kavran, J M.]]
[[Category: Kavran JM]]
[[Category: Steitz, T A.]]
[[Category: Steitz TA]]
[[Category: Ligase]]
[[Category: Pyrrolysine]]
[[Category: Pyrrolysyl-trna synthetase]]

Latest revision as of 12:14, 21 February 2024

Pyrrolysyl-tRNA synthetase bound to adenylated pyrrolysine and pyrophosphatePyrrolysyl-tRNA synthetase bound to adenylated pyrrolysine and pyrophosphate

Structural highlights

2q7h is a 1 chain structure with sequence from Methanosarcina mazei. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.1Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PYLS_METMA Catalyzes the attachment of pyrrolysine to tRNA(Pyl). Pyrrolysine is a lysine derivative encoded by the termination codon UAG (By similarity).

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2q7h, resolution 2.10Å

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