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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
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 + 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-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-nicotinoyl-L-lysine + tRNAPyl
AMP + diphosphate + Nepsilon-nicotinoyl-L-lysyl-tRNAPyl
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ATP + Boc-lysine + tRNAPyl
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Nepsilon-tert-butyloxycarbonyl-L-lysine
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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
ATP + N-alpha-acetyl-L-lysine + tRNAPyl
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ATP + N-alpha-benzyloxycarbonyl-L-lysine + tRNAPyl
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?
additional information
?
-
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
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
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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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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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ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-tRNAPyl
ATP + L-pyrrolysine + tRNAPyl
AMP + diphosphate + L-pyrrolysyl-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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?
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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?
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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1.75 A X-ray crystal structure of the enzyme complexed with O-methyl-L-tyrosine and a non-hydrolyzable ATP analogue
apo-PylRS and PylRS complexes with different ligands, X-ray diffraction structure determination and analysis
crystal structures of a catalytic fragment of the enzyme complexed with N3-(tert-butyloxycarbonyl)-L-lysine and an ATP analog and with Nepsilon-allyloxycarbonyl-L-lysine reveals that the enzyme requires an Nepsilon-carbonyl group bearing a substituent with a certain size
crystal structures of the PylRS catalytic fragment in the substrate-free, ATP analogue (AMPPNP)-bound, and AMPPNP/pyrrolysine-bound forms, compared with other PylRS structures
hanging-drop vapour-diffusion method at 21°C, the triclinic form crystals contain two PylRS dimers (four monomer molecules) in the asymmetric unit, in which the two subunits in one dimer each bind Nepsilon-(tert-butyloxycarbonyl)-L-lysyladenylate and the two subunits in the other dimer each bind AMP
mutant Y384F/A302T/N346V/C348W/V401L in complex with O-methyl-L-tyrosine, hanging drop vapor diffusion method, using
purified recombinant N-terminally His-tagged catalytic domain of PylRS complexed with either AMP-PNP, pyrrolysine-AMP plus pyrophosphate, or the pyrrolysine analogue N-epsilon-[(cylopentyloxy)carbonyl]-L-lysine plus ATP, vapour diffusion method, 10 mg/ml protein in 100 mM Tris, pH 7.0-8.0, 8-14% PEG 2000 monomethyl ether, 10 mM pyrrolysine, and10 mM AMP-PNP or other ligands, overnight at 16°C, stabilization and cryoprotection by 5 mM EDTA, 10 mM AMP-PNP, 5 mM MgCl2, 30% ethylen glycol, and additional 2% PEG, hexagonal-shaped crystals, X-ray diffraction structure determination and analysis at 1.8 A resolution
purified recombinant His-tagged N-terminally truncated enzyme form PylRS(c270) in complex with an ATP analogue AMP-PNP, hanging drop vapour diffusion method, in 100 mM sodium cacodylate, pH 6.8, containing 0.25 M NaCl, 5 mM MgSO4 and 5% w/v PEG 4000, 20°C, hexagonal crystals, X-ray diffraction structure determination and analysis at 1.9-2.6 A resolution
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the crystal structures of the enzyme reveals that it has a unique, large pocket for amino acid binding
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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
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
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
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
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
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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
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
11268-11273
2007
Methanosarcina mazei (Q8PWY1), Methanosarcina mazei
brenda
Mukai, T.; Kobayashi, T.; Hino, N.; Yanagisawa, T.; Sakamoto, K.; Yokoyama, S.
Adding l-lysine derivatives to the genetic code of mammalian cells with engineered pyrrolysyl-tRNA synthetases
Biochem. Biophys. Res. Commun.
371
818-822
2008
Methanosarcina mazei
brenda
Yanagisawa, T.; Ishii, R.; Fukunaga, R.; Kobayashi, T.; Sakamoto, K.; Yokoyama, S.
Crystallographic studies on multiple conformational states of active-site loops in pyrrolysyl-tRNA synthetase
J. Mol. Biol.
378
634-652
2008
Methanosarcina mazei (Q8PWY1), Methanosarcina mazei
brenda
Wang, Y.S.; Russell, W.K.; Wang, Z.; Wan, W.; Dodd, L.E.; Pai, P.J.; Russell, D.H.; Liu, W.R.
The de novo engineering of pyrrolysyl-tRNA synthetase for genetic incorporation of L-phenylalanine and its derivatives
Mol. Biosyst.
7
714-717
2011
Methanocaldococcus jannaschii, Methanosarcina mazei
brenda
Takimoto, J.K.; Dellas, N.; Noel, J.P.; Wang, L.
Stereochemical basis for engineered pyrrolysyl-tRNA synthetase and the efficient in vivo incorporation of structurally divergent non-native amino acids
ACS Chem. Biol.
6
733-743
2011
Methanosarcina mazei (Q8PWY1), Methanosarcina mazei, Methanosarcina mazei DSM 3647 (Q8PWY1)
brenda
Yanagisawa. T.; Sumida, T.; Ishii, R.; Yokoyama, S.
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
Acta Crystallogr. Sect. D
69
5-15
2013
Methanosarcina mazei (Q8PWY1), Methanosarcina mazei, Methanosarcina mazei DSM 3647 (Q8PWY1)
brenda
Yanagisawa, T.; Ishii, R.; Fukunaga, R.; Kobayashi, T.; Sakamoto, K.; Yokoyama, S.
Multistep engineering of pyrrolysyl-tRNA synthetase to genetically encode N(epsilon)-(o-azidobenzyloxycarbonyl) lysine for site-specific protein modification
Chem. Biol.
15
1187-1197
2008
Methanosarcina mazei (Q8PWY1), Methanosarcina mazei DSM 3647 (Q8PWY1)
brenda
Lacey, V.; Louie, G.; Noel, J.; Wang, L.
Expanding the library and substrate diversity of the pyrrolysyl-tRNA synthetase to incorporate unnatural amino acids containing conjugated rings
ChemBioChem
14
2100-2105
2013
Methanosarcina mazei
brenda
Umehara, T.; Kim, J.; Lee, S.; Guo, L.T.; Sll, D.; Park, H.S.
N-Acetyl lysyl-tRNA synthetases evolved by a CcdB-based selection possess N-acetyl lysine specificity in vitro and in vivo
FEBS Lett.
586
729-733
2012
Methanosarcina mazei (Q8PWY1), Methanosarcina mazei, Methanosarcina mazei DSM 3647 (Q8PWY1)
brenda
Kobayashi, T.; Yanagisawa, T.; Sakamoto, K.; Yokoyama, S.
Recognition of non-alpha-amino substrates by pyrrolysyl-tRNA synthetase
J. Mol. Biol.
385
1352-1360
2009
Methanosarcina mazei
brenda
Wan, W.; Tharp, J.M.; Liu, W.R.
Pyrrolysyl-tRNA synthetase an ordinary enzyme but an outstanding genetic code expansion tool
Biochim. Biophys. Acta
1844
1059-1070
2014
Methanosarcina barkeri (Q6WRH6), Methanosarcina mazei (Q8PWY1), Methanosarcina mazei ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88 (Q8PWY1)
brenda