6ab0: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6ab0 is ON HOLD
+==Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with pAmPyLys==
+<StructureSection load='6ab0' size='340' side='right'caption='[[6ab0]], [[Resolution|resolution]] 1.44&Aring;' 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]] 1.441&#8491;</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.
-Authors:
+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>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6ab0" style="background-color:#fffaf0;"></div>
+==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]]