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ATP + 2-amino-6-((R)-tetrahydrofuran-2-carboxamido)hexanoic acid + tRNAPyl
AMP + diphosphate + 2-amino-6-((R)-tetrahydrofuran-2-carboxamido)hexanoyl-tRNAPyl
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catalytic efficiency (kcat/Km) is 9% of the catalytic efficiency for L-pyrrolysine
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ATP + 2-amino-6-(cyclopentanecarboxamido)hexanoic acid + tRNAPyl
AMP + diphosphate + 2-amino-6-(cyclopentanecarboxamido)hexanoyl-tRNAPyl
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catalytic efficiency (kcat/Km) is 0.3% of the catalytic efficiency for L-pyrrolysine
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?
ATP + Boc-lysine + tRNAPyl
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Nepsilon-tert-butyloxycarbonyl-L-lysine
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ATP + L-phenylalanine + tRNAPyl
AMP + diphosphate + L-phenylalanyl-tRNAPyl
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mutant enzymes N346A/C348L, A302L/Y306M/N346S/C348L/Y384L, and A302F/Y306L/N346T/C348F/Y384L use L-phenylalanine as substrate
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?
ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
ATP + N-acetyl-L-lysine + tRNAPyl
AMP + diphosphate + N-acetyl-L-lysyl-tRNAPyl
ATP + N-alpha-acetyl-L-lysine + tRNAPyl
?
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?
ATP + N-alpha-benzyloxycarbonyl-L-lysine + tRNAPyl
?
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?
ATP + N-epsilon-cyclopentyloxycarbonyl-L-lysine + tRNAPyl
AMP + diphosphate + N-epsilon-cyclopentyloxycarbonyl-L-lysyl-tRNAPyl
ATP + N-epsilon-D-prolyl-L-lysine + tRNAPyl
AMP + diphosphate + N-epsilon-D-prolyl-L-lysyl-tRNAPyl
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?
ATP + Nepsilon-(N-methylanthraniloyl)-L-lysine + tRNAPyl
AMP + diphosphate + Nepsilon-(N-methylanthraniloyl)-L-lysyl-tRNAPyl
ATP + Nepsilon-(tert-butyloxycarbonyl)-L-lysine + tRNAPyl
AMP + diphosphate + Nepsilon-(tert-butyloxycarbonyl)-L-lysyl-tRNAPyl
ATP + Nepsilon-allyloxycarbonyl-L-lysine + tRNAPyl
AMP + diphosphate + Nepsilon-allyloxycarbonyl-L-lysyl-tRNAPyl
ATP + Nepsilon-benzyloxycarbonyl-L-lysine + tRNAPyl
AMP + diphosphate + Nepsilon-benzyloxycarbonyl-L-lysine-tRNAPyl
ATP + Nepsilon-cyclopentyloxycarbonyl-L-lysine + tRNAPyl
AMP + diphosphate + Nepsilon-cyclopentyloxycarbonyl-L-lysyl-tRNAPyl
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catalytic efficiency (kcat/Km) is 1.8% of the catalytic efficiency for L-pyrrolysine
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?
ATP + Nepsilon-nicotinoyl-L-lysine + tRNAPyl
AMP + diphosphate + Nepsilon-nicotinoyl-L-lysyl-tRNAPyl
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additional information
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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pyrrolysyl-tRNA synthetase PylRS attaches L-pyrrolysine to its cognate tRNA, the special amber suppressor tRNAPyl, encoded by gene pylT
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?
ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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PylRS binds tRNA predominantly along the phosphate backbone of the T-loop, the D-stem and the acceptor stem, while no significant contacts with the anticodon arm occur, the tRNAPyl anticodon is not important for recognition by bacterial PylRS, overview
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?
ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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the bacterial PylRS displays a clear preference for the homologous cognate tRNA, substrate specificity, overview
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?
ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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the enzyme attaches L-pyrrolysine only to tRNA transcripts with a 3'-OH group at A76, whereas no aminoacylation at the 2'-OH group is detected
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?
ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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?
ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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?
ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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the enzyme is specific for L-pyrrolysine
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?
ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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the Methanosarcina acetivorans tRNAhis guanylyltranferase Thg1 gene contains an in-frame TAG codon. Its presence in Methanosarcina mRNA may lead to pyrrolysine incorporation achieved by Pyl-tRNAPyl, the product of pyrrolysyl-tRNA synthetase. Translation of Thg1 mRNA leads to a full-length, Pyl-containing, active enzyme as determined by immunoblotting, mass spectrometry, and biochemical analysis
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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?
ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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?
ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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direct charging of tRNA(CUA) with pyrrolysine in vitro and in vivo
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?
ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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Pyl-tRNAPyl insertion at UAG, a specialized mRNA motif is not essential for stopcodon recoding, unlike for selenocysteine incorporation
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?
ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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direct charging of tRNA(CUA), isolated from Methanosarcina acetivorans strain C2A, with pyrrolysine in vitro and in vivo, PylS activates pyrrolysine with ATP and ligates pyrrolysine to tRNACUA in vitro in reactions specific for pyrrolysine
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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the archaeal enzyme does not distinguish between archaeal and bacterial tRNAPyl species, substrate specificity, overview, residues from the PylRS amino-terminal domain affect activity in vivo
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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the enzyme uses a special amber suppressor tRNA, tRNAPyl, that presumably recognizes this UAG codon, and does not accept L-lysine or tRNALys as substrates, direct transfer of L-pyrroslysine to the UAG codon of tRNAPyl, overview
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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the enzyme attaches attaches L-pyrrolysine only to tRNA transcripts with a 3'-OH group at A76, whereas no aminoacylation at the 2'-OH group is detected
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
the N-terminal region of PylS influences complex formation with tRNAPyl
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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the enzyme uses a special amber suppressor tRNA, tRNAPyl, that presumably recognizes this UAG codon, and does not accept L-lysine or tRNALys as substrates, direct transfer of L-pyrroslysine to the UAG codon of tRNAPyl, overview
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
pyrrolysyl-tRNA synthetase PylRS attaches L-pyrrolysine to its cognate tRNA, the special amber suppressor tRNAPyl, encoded by gene pylT
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
substrate binding, PylRS utilizes a deep hydrophobic pocket for recognition of the Pyl side chain
pyrrolysine-AMPbinds in a deep hydrophobic pocket, with its position coordinated by a hydrogen-bonding network with PylRS, binding structure, overview
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?
ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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the wild type enzyme recognizes the natural lysine derivative as well as many lysine analogs, including Nepsilon-(tert-butoxycarbonyl)-L-lysine (Boc-lysine), with diverse side chain sizes and structures
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?
ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
while the wild type enzyme has a negligible charging activity for N-acetyl-L-lysine, the mutant enzyme is able to acylate only N-acetyl-L-lysine (not natural amino acids) onto tRNAPyl
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?
ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
Methanosarcina mazei ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88
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?
ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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?
ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
while the wild type enzyme has a negligible charging activity for N-acetyl-L-lysine, the mutant enzyme is able to acylate only N-acetyl-L-lysine (not natural amino acids) onto tRNAPyl
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
the archaeal enzyme does not distinguish between archaeal and bacterial tRNAPyl species, substrate specificity, overview
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?
ATP + N-acetyl-L-lysine + tRNAPyl
AMP + diphosphate + N-acetyl-L-lysyl-tRNAPyl
while the wild type enzyme has a negligible charging activity for N-acetyl-L-lysine, the mutant enzyme is able to acylate only N-acetyl-L-lysine (not natural amino acids) onto tRNAPyl
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ATP + N-acetyl-L-lysine + tRNAPyl
AMP + diphosphate + N-acetyl-L-lysyl-tRNAPyl
while the wild type enzyme has a negligible charging activity for N-acetyl-L-lysine, the mutant enzyme is able to acylate only N-acetyl-L-lysine (not natural amino acids) onto tRNAPyl
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?
ATP + N-epsilon-cyclopentyloxycarbonyl-L-lysine + tRNAPyl
AMP + diphosphate + N-epsilon-cyclopentyloxycarbonyl-L-lysyl-tRNAPyl
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substrate specificity, ability of 24 mutant tRNA species to be aminoacylated by the enzyme with the pyrrolysine analog N-epsilon-cyclopentyloxycarbonyl-L-lysine, overview, the discriminator base G73 and the first base pair G1-C72 in the acceptor stem are major identity elements
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ATP + N-epsilon-cyclopentyloxycarbonyl-L-lysine + tRNAPyl
AMP + diphosphate + N-epsilon-cyclopentyloxycarbonyl-L-lysyl-tRNAPyl
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ATP + Nepsilon-(N-methylanthraniloyl)-L-lysine + tRNAPyl
AMP + diphosphate + Nepsilon-(N-methylanthraniloyl)-L-lysyl-tRNAPyl
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?
ATP + Nepsilon-(N-methylanthraniloyl)-L-lysine + tRNAPyl
AMP + diphosphate + Nepsilon-(N-methylanthraniloyl)-L-lysyl-tRNAPyl
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ATP + Nepsilon-(tert-butyloxycarbonyl)-L-lysine + tRNAPyl
AMP + diphosphate + Nepsilon-(tert-butyloxycarbonyl)-L-lysyl-tRNAPyl
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ATP + Nepsilon-(tert-butyloxycarbonyl)-L-lysine + tRNAPyl
AMP + diphosphate + Nepsilon-(tert-butyloxycarbonyl)-L-lysyl-tRNAPyl
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ATP + Nepsilon-allyloxycarbonyl-L-lysine + tRNAPyl
AMP + diphosphate + Nepsilon-allyloxycarbonyl-L-lysyl-tRNAPyl
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ATP + Nepsilon-allyloxycarbonyl-L-lysine + tRNAPyl
AMP + diphosphate + Nepsilon-allyloxycarbonyl-L-lysyl-tRNAPyl
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ATP + Nepsilon-benzyloxycarbonyl-L-lysine + tRNAPyl
AMP + diphosphate + Nepsilon-benzyloxycarbonyl-L-lysine-tRNAPyl
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ATP + Nepsilon-benzyloxycarbonyl-L-lysine + tRNAPyl
AMP + diphosphate + Nepsilon-benzyloxycarbonyl-L-lysine-tRNAPyl
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additional information
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enzyme activity with wild-type and different mutant tRNAPyls, overview, 3'-labeled tRNAPyl footprinting with S1 and T1 nuclease digestions, overview
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additional information
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molecular dynamics simulations of the structures of PylRS and its complexes with tRNAPyl and activated pyrrolysine, overview. Identification of key residues and interactions leading to shortest paths of communication in the structure networks of DhPylRS. Dimeric hPylRS in different states of ligation: Sys1 as native DhPylRS, Sys2 as DhPylRS-Pyl-AMP, and Sys3 as DhPylRS-Pyl-AMP-tRNA, detailed overview
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additional information
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the wild type enzyme shows no activity with L-phenylalanine
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additional information
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Methanosarcina cells have two pathways for acylating the suppressor tRNAPyl to ensure efficient translation of the in-frame UAG codon in case of pyrrolysine deficiency and safeguard the biosynthesis of the proteins whose genes contain this special codon, L-pyrrolysine is found in the Methanosarcina barkeri monomethylamine methyltransferase protein in a position that is encoded by an in-frame UAG stop codon in the mRNA, overview
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additional information
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pyrrolysine is required in e.g. methylamine methyltransferase MtmB, overview
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additional information
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while pyrrolysine is the natural substrate of PylRS, lysine is not recognized by the enzyme
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additional information
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structure of endogenous tRNAPyl, overview
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additional information
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synthetic L-pyrrolysine is attached as a free molecule to tRNACUA by PylS, an archaeal class II aminoacyl-tRNA synthetase, inability of recombinant PylS-His6 to synthesize lysyltRNACUA
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additional information
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unlike most aminoacyl-tRNA synthetases, PylRS displays high substrate side chain promiscuity, low selectivity toward its substrate alpha-amine, and low selectivity toward the anticodon of tRNAPyl, overview. PylRS shows low selectivity toward the tRNA anticodon and low selectivity toward the Pyl alpha-amine
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additional information
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the archaeal tRNAPyl features a secondary structure that significantly diverges from that of canonical tRNAs
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additional information
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the recombinant pylS gene product charges tRNAPyl with Pyl, but the recombinant pylS gene product also succeeds in ligating [14C]Lys to tRNA. A mRNA secondary structure is definitely not necessary for the incorporation of Pyl at an amber codon. The binding of the side chain pyrroline of Pyl to the PylRS active site involves essentially van der Waals interactions. Replacing the side chain pyrroline with a similar size chemical component with a hydrophobic nature might retain the PylRS activity to aminoacylate tRNAPyl. PylRS weakly recognizes three non-canonical amino acids and mediates their incorporation into proteins at an amber codon in coordination with tRNAPyl, allowing the synthesis of proteins with site-specific lysine propionylation, butylation, and crotonylation
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additional information
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Methanosarcina cells have two pathways for acylating the suppressor tRNAPyl to ensure efficient translation of the in-frame UAG codon in case of pyrrolysine deficiency and safeguard the biosynthesis of the proteins whose genes contain this special codon, L-pyrrolysine is found in the Methanosarcina barkeri monomethylamine methyltransferase protein in a position that is encoded by an in-frame UAG stop codon in the mRNA, overview
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additional information
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structure of endogenous tRNAPyl, overview
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additional information
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enzyme evolution study, PylRS can be placed in the aminoacyl-tRNA synthetase tree as the last known synthetase that evolved for genetic code expansion, pyrrolysine arose before the last universal common ancestral state
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additional information
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enzyme evolution study, PylRS can be placed in the aminoacyl-tRNA synthetase tree as the last known synthetase that evolved for genetic code expansion, pyrrolysine arose before the last universal common ancestral state
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additional information
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substrate-binding specificity of PylRS, overview
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additional information
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substrate-binding specificity of PylRS, overview
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additional information
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Nepsilon-(p-azidobenzoyl)-L-lysine, Nepsilon-biotinyl-L-lysine, and Nepsilon-(9-fluorenylmethoxycarbonyl)-L-lysine, which have even larger substituents at the N3-carbonyl group, are not detectably esterified to tRNAPyl. The enzyme exhibits no ligation activity for lysine derivatives without the Nepsilon-carbonyl group, such as Nepsilon-methyl-L-lysine, Nepsilon-dimethyl-L-lysine, Nepsilon-trimethyl-L-lysine, Nepsilon-isopropyl-L-lysine, Nepsilon-dansyl-L-lysine, Nepsilon-(o,p-dinitrophenyl)-L-lysine, Nepsilon-(p-toluenesulfonyl)-L-lysine, and Nepsilon-(DL-2-amino-2-carboxyethyl)-L-lysine, regardless of the size of the Nepsilon-substituent
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additional information
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unlike most aminoacyl-tRNA synthetases, PylRS displays high substrate side chain promiscuity, low selectivity toward its substrate alpha-amine, and low selectivity toward the anticodon of tRNAPyl, overview. PylRS shows low selectivity toward the tRNA anticodon and low selectivity toward the Pyl alpha-amine
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additional information
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the structure of Methanosarcina mazei PylRS catalytic core reveals a deep hydrophobic pocket for the binding of Pyl. Residues A302, L305, Y306, L309, N346, C348, and W417 form a bulky cavity for the binding of the side chain (4R,5R)-4-methyl-pyrroline-5-caboxylate of Pyl. The Pyl side chain also forms two hydrogen bonds at the PylRS active site, with one involving the side chain amide nitrogen of N346 and the Pyl side chain amide oxygen and the other involving the pyrroline nitrogen and the phenolic oxygen of Y384. Residue Y384 is at a flexible loop region that is random in the absence of Pyl but serves as a cap for the binding of Pyl to the active site. PylRS displays remarkably high tolerance toward variations of the substrate side chain, especially when a variation is at the pyrroline region. PylRS recognizes desmethyl-Pyl and is able to direct its incorporation at amber codon when in coordination with tRNAPyl. The binding of the side chain pyrroline of Pyl to the PylRS active site involves essentially van der Waals interactions. Replacing the side chain pyrroline with a similar size chemical component with a hydrophobic nature might retain the PylRS activity to aminoacylate tRNAPyl
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additional information
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Methanosarcina mazei ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88
unlike most aminoacyl-tRNA synthetases, PylRS displays high substrate side chain promiscuity, low selectivity toward its substrate alpha-amine, and low selectivity toward the anticodon of tRNAPyl, overview. PylRS shows low selectivity toward the tRNA anticodon and low selectivity toward the Pyl alpha-amine
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additional information
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Methanosarcina mazei ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88
the structure of Methanosarcina mazei PylRS catalytic core reveals a deep hydrophobic pocket for the binding of Pyl. Residues A302, L305, Y306, L309, N346, C348, and W417 form a bulky cavity for the binding of the side chain (4R,5R)-4-methyl-pyrroline-5-caboxylate of Pyl. The Pyl side chain also forms two hydrogen bonds at the PylRS active site, with one involving the side chain amide nitrogen of N346 and the Pyl side chain amide oxygen and the other involving the pyrroline nitrogen and the phenolic oxygen of Y384. Residue Y384 is at a flexible loop region that is random in the absence of Pyl but serves as a cap for the binding of Pyl to the active site. PylRS displays remarkably high tolerance toward variations of the substrate side chain, especially when a variation is at the pyrroline region. PylRS recognizes desmethyl-Pyl and is able to direct its incorporation at amber codon when in coordination with tRNAPyl. The binding of the side chain pyrroline of Pyl to the PylRS active site involves essentially van der Waals interactions. Replacing the side chain pyrroline with a similar size chemical component with a hydrophobic nature might retain the PylRS activity to aminoacylate tRNAPyl
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additional information
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Nepsilon-(p-azidobenzoyl)-L-lysine, Nepsilon-biotinyl-L-lysine, and Nepsilon-(9-fluorenylmethoxycarbonyl)-L-lysine, which have even larger substituents at the N3-carbonyl group, are not detectably esterified to tRNAPyl. The enzyme exhibits no ligation activity for lysine derivatives without the Nepsilon-carbonyl group, such as Nepsilon-methyl-L-lysine, Nepsilon-dimethyl-L-lysine, Nepsilon-trimethyl-L-lysine, Nepsilon-isopropyl-L-lysine, Nepsilon-dansyl-L-lysine, Nepsilon-(o,p-dinitrophenyl)-L-lysine, Nepsilon-(p-toluenesulfonyl)-L-lysine, and Nepsilon-(DL-2-amino-2-carboxyethyl)-L-lysine, regardless of the size of the Nepsilon-substituent
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additional information
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Methanosarcina species pyrrolysyl-tRNA synthetase (PylRS) attaches Pyl to its cognate amber suppressor tRNA. The introduction of two mutations (Y384F and Y306A) into PylRS generates a mutant, designated LysZ-RS, that is able to attach N-benzyloxycarbonyl-L-lysine (LysZ) to its cognate tRNA
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additional information
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the amino-terminal extension present in archaeal PylRSs is dispensable for in vitro activity, but required for PylRS function in vivo
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Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
additional information
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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pyrrolysyl-tRNA synthetase PylRS attaches L-pyrrolysine to its cognate tRNA, the special amber suppressor tRNAPyl, encoded by gene pylT
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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the enzyme attaches L-pyrrolysine only to tRNA transcripts with a 3'-OH group at A76, whereas no aminoacylation at the 2'-OH group is detected
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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direct charging of tRNA(CUA) with pyrrolysine in vitro and in vivo
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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Pyl-tRNAPyl insertion at UAG, a specialized mRNA motif is not essential for stopcodon recoding, unlike for selenocysteine incorporation
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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the enzyme attaches attaches L-pyrrolysine only to tRNA transcripts with a 3'-OH group at A76, whereas no aminoacylation at the 2'-OH group is detected
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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-
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
pyrrolysyl-tRNA synthetase PylRS attaches L-pyrrolysine to its cognate tRNA, the special amber suppressor tRNAPyl, encoded by gene pylT
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
Methanosarcina mazei ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
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additional information
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-
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the wild type enzyme shows no activity with L-phenylalanine
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-
?
additional information
?
-
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Methanosarcina cells have two pathways for acylating the suppressor tRNAPyl to ensure efficient translation of the in-frame UAG codon in case of pyrrolysine deficiency and safeguard the biosynthesis of the proteins whose genes contain this special codon, L-pyrrolysine is found in the Methanosarcina barkeri monomethylamine methyltransferase protein in a position that is encoded by an in-frame UAG stop codon in the mRNA, overview
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additional information
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pyrrolysine is required in e.g. methylamine methyltransferase MtmB, overview
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additional information
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while pyrrolysine is the natural substrate of PylRS, lysine is not recognized by the enzyme
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additional information
?
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unlike most aminoacyl-tRNA synthetases, PylRS displays high substrate side chain promiscuity, low selectivity toward its substrate alpha-amine, and low selectivity toward the anticodon of tRNAPyl, overview. PylRS shows low selectivity toward the tRNA anticodon and low selectivity toward the Pyl alpha-amine
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additional information
?
-
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Methanosarcina cells have two pathways for acylating the suppressor tRNAPyl to ensure efficient translation of the in-frame UAG codon in case of pyrrolysine deficiency and safeguard the biosynthesis of the proteins whose genes contain this special codon, L-pyrrolysine is found in the Methanosarcina barkeri monomethylamine methyltransferase protein in a position that is encoded by an in-frame UAG stop codon in the mRNA, overview
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additional information
?
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enzyme evolution study, PylRS can be placed in the aminoacyl-tRNA synthetase tree as the last known synthetase that evolved for genetic code expansion, pyrrolysine arose before the last universal common ancestral state
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additional information
?
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enzyme evolution study, PylRS can be placed in the aminoacyl-tRNA synthetase tree as the last known synthetase that evolved for genetic code expansion, pyrrolysine arose before the last universal common ancestral state
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?
additional information
?
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unlike most aminoacyl-tRNA synthetases, PylRS displays high substrate side chain promiscuity, low selectivity toward its substrate alpha-amine, and low selectivity toward the anticodon of tRNAPyl, overview. PylRS shows low selectivity toward the tRNA anticodon and low selectivity toward the Pyl alpha-amine
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additional information
?
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Methanosarcina mazei ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88
unlike most aminoacyl-tRNA synthetases, PylRS displays high substrate side chain promiscuity, low selectivity toward its substrate alpha-amine, and low selectivity toward the anticodon of tRNAPyl, overview. PylRS shows low selectivity toward the tRNA anticodon and low selectivity toward the Pyl alpha-amine
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additional information
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the amino-terminal extension present in archaeal PylRSs is dispensable for in vitro activity, but required for PylRS function in vivo
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A302F/Y306L/N346T/C348F/Y384L
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the mutant acylates tRNAPyl with L-phenylalanine
A302L/Y306M/N346S/C348L/Y384L
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the mutant acylates tRNAPyl with L-phenylalanine
N346A/C348A
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the mutant displays specific recognition toward non-canonical amino acids and has a broad substrate spectrum with specific recognition of L-phenylalanine
N346A/C348L
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the mutant acylates tRNAPyl with L-phenylalanine
D2A
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site-directed mutagenesis, the mutant shows 95% reduced activity compared to the wild-type enzyme
D2A/K4A
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site-directed mutagenesis, the mutant shows almost completely reduced activity compared to the wild-type enzyme
D7A
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site-directed mutagenesis, the mutant shows only slightly reduced activity compared to the wild-type enzyme
G21L
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site-directed mutagenesis, the mutant shows only slightly reduced activity compared to the wild-type enzyme
H24A
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site-directed mutagenesis, the mutant shows 95% reduced activity compared to the wild-type enzyme
I26G
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site-directed mutagenesis, the mutant shows 80% reduced activity compared to the wild-type enzyme
K3A
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site-directed mutagenesis, the mutant shows 80% reduced activity compared to the wild-type enzyme
K4A
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site-directed mutagenesis, the mutant shows 95% reduced activity compared to the wild-type enzyme
R19A
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site-directed mutagenesis, the mutant shows only slightly reduced activity compared to the wild-type enzyme
S11A
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site-directed mutagenesis, the mutant shows 95% reduced activity compared to the wild-type enzyme
S11A/T13A
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site-directed mutagenesis, the mutant shows almost completely reduced activity compared to the wild-type enzyme
S18A
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site-directed mutagenesis, the mutant shows only slightly reduced activity compared to the wild-type enzyme
T13A
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site-directed mutagenesis, the mutant shows 95% reduced activity compared to the wild-type enzyme
W16A
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site-directed mutagenesis, the mutant shows 35% reduced activity compared to the wild-type enzyme
Y349F
the pyrrolysyl-tRNA synthetase/tRNAPyl pair is the most versatile and widespread system for the incorporation of non-canonical amino acids (ncAAs) into proteins in mammalian cells. Low yields of ncAA incorporation severely limit its applicability to relevant biological targets. Generation of two tRNAPyl variants that significantly boost the performance of the pyrrolysine system. Compared to the original tRNAPyl, the engineered tRNAs feature a canonical hinge between D- and T-loop, show higher intracellular concentrations and bear partially distinct post-transcriptional modifications. They allow efficient ncAA incorporation into a G-protein coupled receptor (GPCR) and simultaneous ncAA incorporation at two GPCR sites. Different combinations of recognition motifs for PylRS are introduced into Bos taurus mt-tRNASerCUA. Bicistronic plasmids are generated combining each tRNA with the PylRS from Methanosarcina barkeri, which bears the mutation Y349F for enhanced activity (PylRSF). In the presence of the PylRS substrate Lys(Boc), four tRNAs in the M series and five in the C series yield higher amber suppression compared to the tRNAPyl, whereas the other tRNAs show either lower efficiency or no amber suppression at all, overview
L301M/Y306L/C348S/A315V
while the wild type enzyme has a negligible charging activity for N-acetyl lysine, the mutant enzyme is able to acylate only N-acetyl lysine (not natural amino acids) onto tRNAPyl
L301M/Y306L/L309A/C348F
while the wild type enzyme has a negligible charging activity for N-acetyl lysine, the mutant enzyme is able to acylate only N-acetyl lysine (not natural amino acids) onto tRNAPyl
L309A/C348V
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designated as ZLysRS has the L309A and C348V substitutions at the pyrrolysine binding pocket and three mutations at the other sites
Y306/Y384F
together with tRNAPyl the mutant enzyme provides a good yield of the in vivo amber-suppression product containing Nepsilon-benzyloxycarbonyl-L-lysine
Y306A
mutation of PylRS drastically increases the in vitro aminoacylation activity for Nepsilon-benzyloxycarbonyl-L-lysine
Y384F/A302T/N346V/C348W/V401L
the mutant specifically incorporates the cognate unnatural amino acid O-methyl-L-tyrosine into proteins
L301M/Y306L/C348S/A315V
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while the wild type enzyme has a negligible charging activity for N-acetyl lysine, the mutant enzyme is able to acylate only N-acetyl lysine (not natural amino acids) onto tRNAPyl
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L301M/Y306L/L309A/C348F
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while the wild type enzyme has a negligible charging activity for N-acetyl lysine, the mutant enzyme is able to acylate only N-acetyl lysine (not natural amino acids) onto tRNAPyl
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Y306/Y384F
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together with tRNAPyl the mutant enzyme provides a good yield of the in vivo amber-suppression product containing Nepsilon-benzyloxycarbonyl-L-lysine
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Y306A
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mutation of PylRS drastically increases the in vitro aminoacylation activity for Nepsilon-benzyloxycarbonyl-L-lysine
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Y384F/A302T/N346V/C348W/V401L
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the mutant specifically incorporates the cognate unnatural amino acid O-methyl-L-tyrosine into proteins
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Y384F/Y306A
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site-directed mutagenesis, the mutant can also incorporate L-lysine derivatives N-benzyloxycarbonyl-L-lysines, i.e. LysZ
Y384F
mutation increases the aminoacylation rate
Y384F
the mutation increases the aminoacylation activity of the enzyme regardless of the amino acid substrate
Y384F
the mutation increases the aminoacylation rate
Y384F
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mutation increases the aminoacylation rate
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Y384F
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the mutation increases the aminoacylation rate
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Y384F
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the mutation increases the aminoacylation activity of the enzyme regardless of the amino acid substrate
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additional information
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usage of evolved pyrrolysyl-tRNA synthetase-tRNAPylCUA pairs for genetic incorporation of L-phenylalanine, p-iodo-L-phenylalanine and p-bromo-L-phenylalanine into proteins at amber mutation sites in Escherichia coli
additional information
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in vivo ability of lysK/lysS to replace pylS for tRNAPyl-dependent amber suppression in a recombinant system, overview
additional information
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construction of several truncation mutants, which show 90-99% reduced activity compared to the wild-type enzyme, overview
additional information
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the genetic code of Escherichia coli can be expanded to include UAG-directed pyrrolysine incorporation into proteins
additional information
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variant pyrrolysyl-tRNA synthetase/tRNACUA Pyl pairs created in Escherichia coli can be used to expand the genetic code of Saccharomyces cerevisiae through a simple system, overview. Variant pyrrolysyl-tRNA synthetase/tRNACUA Pyl pairs are site-specifically incorporated into proteins in yeast
additional information
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truncation of the N-terminal region of PylS (DELTA92PylS) eliminates detectable tRNAPyl binding, but not catalytic activity
additional information
truncation of the N-terminal region of PylS (DELTA92PylS) eliminates detectable tRNAPyl binding, but not catalytic activity
additional information
engineering of mutants that display higher activities for their genetic incorporation than the wild-type PylRS and increased specificities, overview
additional information
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four substitutions (L305I, Y306F, L309A, and C348F) at the binding pocket out of the six mutations found in AcLysRS from Methanosarcina barkeri are transplanted into Methanosarcina mazei PylRS to create mAcLysRS
additional information
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evolving a PylRS mutant that specifically acylates tRNAPylCUA with L-phenylalanine, p-iodo-L-phenylalanine and p-bromo-L-phenylalanine by standard positive and negative selections of the pRS1 plasmid library in Escherichia coli. The pRS1 plasmid library contains the Methanosarcina mazei PylRS gene with randomization at six active-site residues, L305, Y306, L309, N346, C348, and W417, method, overview
additional information
engineering of mutants that display higher activities for their genetic incorporation than the wild-type PylRS and increased specificities, overview
additional information
Methanosarcina mazei ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88
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engineering of mutants that display higher activities for their genetic incorporation than the wild-type PylRS and increased specificities, overview
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additional information
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liposome-based in vitro compartmentalization (IVC) for LysZRS evolution, directed evolution of LysZ-RS, overview
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Yanagisawa, T.; Ishii, R.; Fukunaga, R.; Nureki, O.; Yokoyama, S.
Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of pyrrolysyl-tRNA synthetase from the methanogenic archaeon Methanosarcina mazei
Acta Crystallogr. Sect. F
62
1031-1033
2006
Methanosarcina mazei
brenda
Polycarpo, C.R.; Herring, S.; Berube, A.; Wood, J.L.; Soll, D.; Ambrogelly, A.
Pyrrolysine analogues as substrates for pyrrolysyl-tRNA synthetase
FEBS Lett.
580
6695-6700
2006
Methanosarcina barkeri
brenda
Herring, S.; Ambrogelly, A.; Gundllapalli, S.; O'Donoghue, P.; Polycarpo, C.R.; Soll, D.
The amino-terminal domain of pyrrolysyl-tRNA synthetase is dispensable in vitro but required for in vivo activity
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581
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2007
Desulfitobacterium hafniense, Methanosarcina barkeri, Methanosarcina thermophila (Q1L6A3)
brenda
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Class I and class II lysyl-tRNA synthetase mutants and the genetic encoding of pyrrolysine in Methanosarcina spp.
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64
1306-1318
2007
Methanosarcina acetivorans
brenda
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Direct charging of tRNA(CUA) with pyrrolysine in vitro and in vivo
Nature
431
333-335
2004
Methanosarcina barkeri
brenda
Herring, S.; Ambrogelly, A.; Polycarpo, C.R.; Soll, D.
Recognition of pyrrolysine tRNA by the Desulfitobacterium hafniense pyrrolysyl-tRNA synthetase
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35
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2007
Desulfitobacterium hafniense
brenda
Polycarpo, C.; Ambrogelly, A.; Berube, A.; Winbush, S.M.; McCloskey, J.A.; Crain, P.F.; Wood, J.L.; Soll, D.
An aminoacyl-tRNA synthetase that specifically activates pyrrolysine
Proc. Natl. Acad. Sci. USA
101
12450-12454
2004
Methanosarcina barkeri, Methanosarcina barkeri Fusaro / DSM 804
brenda
Kavran, J.M.; Gundllapalli, S.; O'Donoghue, P.; Englert, M.; Soll, D.; Steitz, T.A.
Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation
Proc. Natl. Acad. Sci. USA
104
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2007
Methanosarcina mazei (Q8PWY1), Methanosarcina mazei
brenda
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Adding l-lysine derivatives to the genetic code of mammalian cells with engineered pyrrolysyl-tRNA synthetases
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371
818-822
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Methanosarcina mazei
brenda
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Structure of Desulfitobacterium hafniense PylSc, a pyrrolysyl-tRNA synthetase
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374
470-474
2008
Desulfitobacterium hafniense
brenda
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Misacylation of pyrrolysine tRNA in vitro and in vivo
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582
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Methanosarcina barkeri str. Fusaro
brenda
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Crystallographic studies on multiple conformational states of active-site loops in pyrrolysyl-tRNA synthetase
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378
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Methanosarcina mazei (Q8PWY1), Methanosarcina mazei
brenda
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Genetic encoding and labeling of aliphatic azides and alkynes in recombinant proteins via a pyrrolysyl-tRNA Synthetase/tRNA(CUA) pair and click chemistry
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131
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Methanosarcina barkeri
brenda
Nozawa, K.; ODonoghue, P.; Gundllapalli, S.; Araiso, Y.; Ishitani, R.; Umehara, T.; Soell, D.; Nureki, O.
Pyrrolysyl-tRNA synthetase-tRNA(Pyl) structure reveals the molecular basis of orthogonality
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457
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Desulfitobacterium hafniense (B0S4P3), Desulfitobacterium hafniense
brenda
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The appearance of pyrrolysine in tRNAHis guanylyltransferase by neutral evolution
Proc. Natl. Acad. Sci. USA
106
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Methanosarcina acetivorans
brenda
Bhattacharyya, M.; Vishveshwara, S.
Probing the allosteric mechanism in pyrrolysyl-tRNA synthetase using energy-weighted network formalism
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50
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Desulfitobacterium hafniense
brenda
Hancock, S.M.; Uprety, R.; Deiters, A.; Chin, J.W.
Expanding the genetic code of yeast for incorporation of diverse unnatural amino acids via a pyrrolysyl-tRNA synthetase/tRNA pair
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132
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Methanosarcina barkeri
brenda
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The de novo engineering of pyrrolysyl-tRNA synthetase for genetic incorporation of L-phenylalanine and its derivatives
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7
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Methanocaldococcus jannaschii, Methanosarcina mazei
brenda
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The complete biosynthesis of the genetically encoded amino acid pyrrolysine from lysine
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Methanosarcina barkeri
brenda
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6
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Methanosarcina mazei (Q8PWY1), Methanosarcina mazei, Methanosarcina mazei DSM 3647 (Q8PWY1)
brenda
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A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site
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69
5-15
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Methanosarcina mazei (Q8PWY1), Methanosarcina mazei, Methanosarcina mazei DSM 3647 (Q8PWY1)
brenda
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Expanding the library and substrate diversity of the pyrrolysyl-tRNA synthetase to incorporate unnatural amino acids containing conjugated rings
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Escherichia coli
brenda
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Escherichia coli
brenda
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32738-32746
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brenda
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385
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Methanosarcina barkeri
brenda
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brenda
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1059-1070
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brenda
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16
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brenda
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46
1-10
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Methanosarcina barkeri (Q6WRH6)
brenda