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6ab0
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 6ab0 is ON HOLD Authors: Yanagisawa, T., Kuratani, M., Yokoyama, S. Description: Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) compl...) |
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| - | '''Unreleased structure''' | ||
| - | + | ==Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with pAmPyLys== | |
| + | <StructureSection load='6ab0' size='340' side='right'caption='[[6ab0]], [[Resolution|resolution]] 1.44Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[6ab0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_mazei_JCM_9314 Methanosarcina mazei JCM 9314]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AB0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AB0 FirstGlance]. <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]] 1.441Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9UF:N6-{[(6-aminopyridin-3-yl)methoxy]carbonyl}-L-lysine'>9UF</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=6ab0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ab0 OCA], [https://pdbe.org/6ab0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ab0 RCSB], [https://www.ebi.ac.uk/pdbsum/6ab0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ab0 ProSAT]</span></td></tr> | ||
| + | </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). | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Pyrrolysyl-tRNA synthetase (PylRS) and tRNA(Pyl) have been extensively used for genetic-code expansion. A Methanosarcina mazei PylRS mutant bearing the Y306A and Y384F mutations (PylRS(Y306A/Y384F)) encodes various bulky non-natural lysine derivatives by UAG. In this study, we examined how PylRS(Y306A/Y384F) recognizes many amino acids. Among 17 non-natural lysine derivatives, N(varepsilon)-(benzyloxycarbonyl)lysine (ZLys) and 10 ortho/meta/para-substituted ZLys derivatives were efficiently ligated to tRNA(Pyl) and were incorporated into proteins by PylRS(Y306A/Y384F). We determined crystal structures of 14 non-natural lysine derivatives bound to the PylRS(Y306A/Y384F) catalytic fragment. The meta- and para-substituted ZLys derivatives are snugly accommodated in the productive mode. In contrast, ZLys and the unsubstituted or ortho-substituted ZLys derivatives exhibited an alternative binding mode in addition to the productive mode. PylRS(Y306A/Y384F) displayed a high aminoacylation rate for ZLys, indicating that the double-binding mode minimally affects aminoacylation. These precise substrate recognition mechanisms by PylRS(Y306A/Y384F) may facilitate the structure-based design of novel non-natural amino acids. | ||
| - | + | Structural Basis for Genetic-Code Expansion with Bulky Lysine Derivatives by an Engineered Pyrrolysyl-tRNA Synthetase.,Yanagisawa T, Kuratani M, Seki E, Hino N, Sakamoto K, Yokoyama S Cell Chem Biol. 2019 Apr 5. pii: S2451-9456(19)30104-7. doi:, 10.1016/j.chembiol.2019.03.008. PMID:31031143<ref>PMID:31031143</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| - | [[Category: | + | <div class="pdbe-citations 6ab0" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | |
| - | [[Category: | + | ==See Also== |
| + | *[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Methanosarcina mazei JCM 9314]] | ||
| + | [[Category: Kuratani M]] | ||
| + | [[Category: Yanagisawa T]] | ||
| + | [[Category: Yokoyama S]] | ||
Current revision
Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with pAmPyLys
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