6ab8: Difference between revisions
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<StructureSection load='6ab8' size='340' side='right'caption='[[6ab8]], [[Resolution|resolution]] 1.75Å' scene=''> | <StructureSection load='6ab8' size='340' side='right'caption='[[6ab8]], [[Resolution|resolution]] 1.75Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6ab8]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AB8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AB8 FirstGlance]. <br> | <table><tr><td colspan='2'>[[6ab8]] is a 1 chain structure with sequence from [http://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=6AB8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AB8 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9VC:(2S)-2-azanyl-6-(phenylmethoxycarbonylamino)hexanoic+acid'>9VC</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></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9VC:(2S)-2-azanyl-6-(phenylmethoxycarbonylamino)hexanoic+acid'>9VC</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></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6aac|6aac]], [[6aad|6aad]], [[6aan|6aan]], [[6aao|6aao]], [[6aap|6aap]], [[6aaq|6aaq]], [[6aaz|6aaz]], [[6ab0|6ab0]], [[6ab1|6ab1]], [[6ab2|6ab2]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6aac|6aac]], [[6aad|6aad]], [[6aan|6aan]], [[6aao|6aao]], [[6aap|6aap]], [[6aaq|6aaq]], [[6aaz|6aaz]], [[6ab0|6ab0]], [[6ab1|6ab1]], [[6ab2|6ab2]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pylS, DU43_20175, DU67_18120 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1293038 Methanosarcina mazei JCM 9314])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyrrolysine--tRNA(Pyl)_ligase Pyrrolysine--tRNA(Pyl) ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.26 6.1.1.26] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyrrolysine--tRNA(Pyl)_ligase Pyrrolysine--tRNA(Pyl) ligase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ab8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ab8 OCA], [http://pdbe.org/6ab8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ab8 RCSB], [http://www.ebi.ac.uk/pdbsum/6ab8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ab8 ProSAT]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ab8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ab8 OCA], [http://pdbe.org/6ab8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ab8 RCSB], [http://www.ebi.ac.uk/pdbsum/6ab8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ab8 ProSAT]</span></td></tr> | ||
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== Function == | == Function == | ||
[[http://www.uniprot.org/uniprot/A0A0F8JXW8_METMZ A0A0F8JXW8_METMZ]] Catalyzes the attachment of pyrrolysine to tRNA(Pyl). Pyrrolysine is a lysine derivative encoded by the termination codon UAG.[HAMAP-Rule:MF_01573] | [[http://www.uniprot.org/uniprot/A0A0F8JXW8_METMZ A0A0F8JXW8_METMZ]] Catalyzes the attachment of pyrrolysine to tRNA(Pyl). Pyrrolysine is a lysine derivative encoded by the termination codon UAG.[HAMAP-Rule:MF_01573] | ||
<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> | |||
</div> | |||
<div class="pdbe-citations 6ab8" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Methanosarcina mazei jcm 9314]] | |||
[[Category: Kuratani, M]] | [[Category: Kuratani, M]] | ||
[[Category: Yanagisawa, T]] | [[Category: Yanagisawa, T]] | ||
Revision as of 10:26, 23 May 2019
Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with ZLysCrystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with ZLys
Structural highlights
Function[A0A0F8JXW8_METMZ] Catalyzes the attachment of pyrrolysine to tRNA(Pyl). Pyrrolysine is a lysine derivative encoded by the termination codon UAG.[HAMAP-Rule:MF_01573] Publication Abstract from PubMedPyrrolysyl-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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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