2zce: Difference between revisions

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<StructureSection load='2zce' size='340' side='right'caption='[[2zce]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='2zce' size='340' side='right'caption='[[2zce]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2zce]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dsm_2053 Dsm 2053]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZCE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZCE FirstGlance]. <br>
<table><tr><td colspan='2'>[[2zce]] 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=2ZCE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZCE FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PYL:PYRROLYSINE'>PYL</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2e3c|2e3c]], [[2zcd|2zcd]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PYL:PYRROLYSINE'>PYL</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pylS ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2209 DSM 2053])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pyrrolysine--tRNA(Pyl)_ligase Pyrrolysine--tRNA(Pyl) ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.26 6.1.1.26] </span></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=2zce FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zce OCA], [https://pdbe.org/2zce PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zce RCSB], [https://www.ebi.ac.uk/pdbsum/2zce PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zce ProSAT], [https://www.topsan.org/Proteins/RSGI/2zce TOPSAN]</span></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=2zce FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zce OCA], [https://pdbe.org/2zce PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zce RCSB], [https://www.ebi.ac.uk/pdbsum/2zce PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zce ProSAT], [https://www.topsan.org/Proteins/RSGI/2zce TOPSAN]</span></td></tr>
</table>
</table>
== Function ==
== 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).  
[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]]
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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=2zce 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=2zce ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Pyrrolysine, a lysine derivative with a bulky pyrroline ring, is the "22nd" genetically encoded amino acid. In the present study, the carboxy-terminal catalytic fragment of Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS) was analyzed by X-ray crystallography and site-directed mutagenesis. The catalytic fragment ligated tRNA(Pyl) with pyrrolysine nearly as efficiently as the full-length PylRS. We determined the crystal structures of the PylRS catalytic fragment in the substrate-free, ATP analogue (AMPPNP)-bound, and AMPPNP/pyrrolysine-bound forms, and compared them with the previously-reported PylRS structures. The ordering loop and the motif-2 loop undergo conformational changes from the "open" states to the "closed" states upon AMPPNP binding. On the other hand, the beta 7-beta 8 hairpin exhibits multiple conformational states, the open, intermediate (beta 7-open/beta 8-open and beta 7-closed/beta 8-open), and closed states, which are not induced upon substrate binding. The PylRS structures with a docked tRNA suggest that the active-site pocket can accommodate the CCA terminus of tRNA when the motif-2 loop is in the closed state and the beta 7-beta 8 hairpin is in the open or intermediate state. The entrance of the active-site pocket is nearly closed in the closed state of the beta 7-beta 8 hairpin, which may protect the pyrrolysyladenylate intermediate in the absence of tRNA(Pyl). Moreover, a structure-based mutational analysis revealed that hydrophobic residues in the amino acid-binding tunnel are important for accommodating the pyrrolysine side chain and that Asn346 is essential for anchoring the side-chain carbonyl and alpha-amino groups of pyrrolysine. In addition, a docking model of PylRS with tRNA was constructed based on the aspartyl-tRNA synthetase/tRNA structure, and was confirmed by a mutational analysis.
Crystallographic studies on multiple conformational states of active-site loops in pyrrolysyl-tRNA synthetase.,Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S J Mol Biol. 2008 May 2;378(3):634-52. Epub 2008 Feb 29. PMID:18387634<ref>PMID:18387634</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2zce" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Dsm 2053]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Ishii, R]]
[[Category: Methanosarcina mazei]]
[[Category: Structural genomic]]
[[Category: Ishii R]]
[[Category: Yanagisawa, T]]
[[Category: Yanagisawa T]]
[[Category: Yokoyama, S]]
[[Category: Yokoyama S]]
[[Category: Aminoacyl-trna synthetase]]
[[Category: Atp-binding]]
[[Category: Ligase]]
[[Category: National project on protein structural and functional analyse]]
[[Category: Nppsfa]]
[[Category: Nucleotide-binding]]
[[Category: Protein biosynthesis]]
[[Category: Protein3000]]
[[Category: Pyrrolysine]]
[[Category: Pyrrolysyl-trna synthetase]]
[[Category: Rsgi]]
[[Category: Trna]]

Latest revision as of 13:57, 13 March 2024

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with pyrrolysine and an ATP analogue

2zce, resolution 1.80Å

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