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Information on EC 6.1.1.1 - tyrosine-tRNA ligase and Organism(s) Methanocaldococcus jannaschii and UniProt Accession Q57834
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6.1.1.1 tyrosine-tRNA ligaseSpecify your search results
Word Map
- 6.1.1.1
- synthetases
- aminoacylation
-
tyrosylation
- stearothermophilus
-
anticodon
-
amber
- jannaschii
- trprs
-
aarss
- methanococcus
-
kmsks
-
tryptophanyl-trna
-
charcot-marie-tooth
-
mischarging
-
trna-like
- d-tyrosine
-
self-splicing
- methanocaldococcus
-
half-of-the-sites
- elr
-
non-cognate
- methionyl-trna
-
isoleucyl-trna
- medicine
- biotechnology
-
sideroblastic
-
anticodon-binding
-
tyrts
- 3-iodo-l-tyrosine
- glycyl-trna
- drug development
- pharmacology
- leurs
-
misacylation
- phenylalanyl-trna
-
fersht
-
brome
- hisrs
The taxonomic range for the selected organisms is: Methanocaldococcus jannaschii
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
tyrosyl-trna synthetase, tyrrs, cyt-18, mitochondrial tyrosyl-trna synthetase, mini-tyrrs, tyrrss, cyt-18 protein, tyrosyl trna synthetase, mttyrrs, ldtyrrs, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
Tyrosine translase
-
-
-
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Tyrosine tRNA synthetase
-
-
-
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Tyrosine--tRNA ligase
-
-
-
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Tyrosine-transfer ribonucleate synthetase
-
-
-
-
Tyrosine-transfer RNA ligase
-
-
-
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Tyrosyl--tRNA ligase
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-
-
-
Tyrosyl-transfer ribonucleate synthetase
-
-
-
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Tyrosyl-transfer ribonucleic acid synthetase
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-
-
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Tyrosyl-transfer RNA synthetase
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-
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Tyrosyl-tRNA ligase
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-
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Tyrosyl-tRNA synthetase
TyrRS
Tyrosyl-tRNA synthetase
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-
-
-
TyrRS
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-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Acylation
esterification
-
-
-
-
Acylation
Acylation
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
L-tyrosine:tRNATyr ligase (AMP-forming)
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CAS REGISTRY NUMBER
COMMENTARY
9023-45-4
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + L-tyrosine + tRNATyr
AMP + L-Tyr-tRNATyr + diphosphate
-
-
?
ATP + L-tyrosine + tRNATyr(G34C)
AMP + diphosphate + L-tyrosyl-tRNATyr(G34C)
the enzyme strictly recognizes the C1-G72 base pair, whereas the enzyme from Thermus thermophilus recognizes the G1-C72 in a different manner using different residues
-
-
?
ATP + L-tyrosine + tRNATyr(wild-type)
AMP + diphosphate + L-tyrosyl-tRNATyr(wild-type)
the enzyme strictly recognizes the C1-G72 base pair, whereas the enzyme from Thermus thermophilus recognizes the G1-C72 in a different manner using different residues
-
-
?
ATP + O-methyl-L-tyrosine + tRNATyr
AMP + O-methyl-L-Tyr-tRNATyr + diphosphate
-
-
?
ATP + p-acetyl-L-phenylalanine + tRNATyr
AMP + diphosphate + p-acetyl-L-phenylalanyl-tRNATyr
aminoacyl-tRNA synthetases are designed through a combination of homology modeling, molecular docking and binding affinity computation with the purpose of incorporating pACPhe into proteins in Escherichia coli
-
-
?
ATP + 3-azido-L-tyrosine + tRNATyr
AMP + diphosphate + 3-azido-L-tyrosyl-tRNATyr
-
-
-
-
?
ATP + 3-iodo-L-tyrosine + tRNATyr
AMP + diphosphate + 3-iodo-L-tyrosyl-tRNATyr
-
-
-
-
?
ATP + L-tyrosine + tRNATyr
AMP + diphosphate + L-tyrosyl-tRNATyr
-
-
-
-
?
ATP + p-iodophenylalanine + tRNATyr
AMP + diphosphate + p-iodophenylalanyl-tRNATyr
-
a variant of the Methanococcus jannaschii tyrosyl synthetase that selectively incorporates para-iodophenylalanine in response to an amber stop codon is identified
-
-
?
ATP + 3-(2-naphthyl)alanine + tRNATyr
AMP + diphosphate + 3-(2-naphthyl)alanyl-tRNATyr
activity of a natural mutant enzyme, NpAla TyrRS activity
-
-
?
ATP + 3-(2-naphthyl)alanine + tRNATyr
AMP + diphosphate + 3-(2-naphthyl)alanyl-tRNATyr
activity of a natural mutant enzyme, NpAla TyrRS activity, altered specificity is due to both side-chain and backbone rearrangements within the active site that modify hydrogen bonds and packing interactions with substrate, as well as disrupt the alpha8-helix, which spans the WT active site
-
-
?
ATP + 4-acetylphenylalanine + tRNATyr
AMP + diphosphate + 4-acetylphenylalanyl-tRNATyr
activity of a natural mutant enzyme
-
-
?
ATP + 4-acetylphenylalanine + tRNATyr
AMP + diphosphate + 4-acetylphenylalanyl-tRNATyr
activity of a natural mutant enzyme, altered specificity is due to both side-chain and backbone rearrangements within the active site that modify hydrogen bonds and packing interactions with substrate, as well as disrupt the alpha8-helix, which spans the WT active site
-
-
?
ATP + 4-bromophenylalanine + tRNATyr
AMP + diphosphate + 4-bromophenylalanyl-tRNATyr
activity of a natural mutant enzyme, p-BrPhe TyrRS activity
-
-
?
ATP + 4-bromophenylalanine + tRNATyr
AMP + diphosphate + 4-bromophenylalanyl-tRNATyr
activity of a natural mutant enzyme, p-BrPhe TyrRS activity, altered specificity is due to both side-chain and backbone rearrangements within the active site that modify hydrogen bonds and packing interactions with substrate, as well as disrupt the alpha8-helix, which spans the WT active site
-
-
?
ATP + L-tyrosine + tRNATyr
AMP + diphosphate + L-tyrosyl-tRNATyr
-
-
-
?
ATP + L-tyrosine + tRNATyr
AMP + diphosphate + L-tyrosyl-tRNATyr
-
-
-
-
?
ATP + L-tyrosine + tRNATyr
AMP + diphosphate + L-tyrosyl-tRNATyr
-
-
-
?
ATP + L-tyrosine + tRNATyr
AMP + diphosphate + L-tyrosyl-tRNATyr
wild-type activity
-
-
?
additional information
?
-
high degree of structural plasticity that is observed in these aminoacyl-tRNA synthetases, overview
-
-
?
additional information
?
-
enzyme TyrRS has a detectable, natural, tRNA-acylation activity for the D-tyrosine stereoisomer, being capable of charging D-Tyr onto tRNATyr to form D-Tyr-tRNA instead of the usual L-Tyr-tRNA
-
-
?
additional information
?
-
-
enzyme TyrRS has a detectable, natural, tRNA-acylation activity for the D-tyrosine stereoisomer, being capable of charging D-Tyr onto tRNATyr to form D-Tyr-tRNA instead of the usual L-Tyr-tRNA
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-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + 3-(2-naphthyl)alanine + tRNATyr
AMP + diphosphate + 3-(2-naphthyl)alanyl-tRNATyr
activity of a natural mutant enzyme, NpAla TyrRS activity
-
-
?
ATP + 4-acetylphenylalanine + tRNATyr
AMP + diphosphate + 4-acetylphenylalanyl-tRNATyr
activity of a natural mutant enzyme
-
-
?
ATP + 4-bromophenylalanine + tRNATyr
AMP + diphosphate + 4-bromophenylalanyl-tRNATyr
activity of a natural mutant enzyme, p-BrPhe TyrRS activity
-
-
?
ATP + L-tyrosine + tRNATyr
AMP + L-Tyr-tRNATyr + diphosphate
-
-
?
ATP + L-tyrosine + tRNATyr
AMP + diphosphate + L-tyrosyl-tRNATyr
-
-
-
-
?
ATP + L-tyrosine + tRNATyr
AMP + diphosphate + L-tyrosyl-tRNATyr
-
-
-
?
ATP + L-tyrosine + tRNATyr
AMP + diphosphate + L-tyrosyl-tRNATyr
-
-
-
-
?
ATP + L-tyrosine + tRNATyr
AMP + diphosphate + L-tyrosyl-tRNATyr
-
-
-
?
ATP + L-tyrosine + tRNATyr
AMP + diphosphate + L-tyrosyl-tRNATyr
wild-type activity
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00068
tRNATyr(G34C)
37°C, pH 7.5, mutant enzyme D268R
-
0.00035
tRNATyr(wild-type)
37°C, pH 7.5, wild-type enzyme
-
0.0014
tRNATyr(wild-type)
37°C, pH 7.5, mutant enzyme D268R
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.12
tRNATyr(wild-type)
37°C, pH 7.5, mutant enzyme D268R
-
0.19
tRNATyr(wild-type)
37°C, pH 7.5, wild-type enzyme
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
the enzyme belongs to the class I aminoacyl-tRNA synthetase family
additional information
additional information
molecular dynamics modeling of substrates L- and D-Tyr into the active site of wild-type enzyme and mutants D81R and E36Q using the PDB ID 1J1U X-ray structure, superimposed based on their protein/tRNA environment, enzyme molecular dynamics simulation amd modeling, structure-function analysis, detailed overview
additional information
-
molecular dynamics modeling of substrates L- and D-Tyr into the active site of wild-type enzyme and mutants D81R and E36Q using the PDB ID 1J1U X-ray structure, superimposed based on their protein/tRNA environment, enzyme molecular dynamics simulation amd modeling, structure-function analysis, detailed overview
PDB
SCOP
CATH
UNIPROT
ORGANISM
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant C-terminally His6-tagged tyrosyl aminoacyl-tRNA synthetase, sitting-drop vapor diffusion technique, 15 mg/ml protein in 20 mM Tris, pH 8.5, 50 mM NaCl, 10 mM 2-mercaptoethanol, crystals are grown either in the presence of 2 mM 4-bromophenylalanine or 3-(2-naphthyl)alanine at 20°C or 4°C, against a mother liquor composed of 16-20% PEG 300, 3-5% PEG 8000, 100 mM Tris, pH 8.8-pH 8.2, and 10% glycerol by mixing of equla volumes, X-ray diffraction structure determination and analysis at 1.9 A resolution
sitting-drop vapor-diffusion method. Space group P2(1)2(1)2(1) with two molecules per asymmetric unit, with unit cell dimensions a = 45.12 A, b = 185.29 A, and c = 95.48 A. Crystal structures for the apo wild-type and O-methyl-L-tyrosine-specific mutant enzyme are determined at 2.66 A and 3.0 A
structure of the TyrRS-tRNA(Tyr)-L-tyrosine complex, solved at a resolution of 1.95 A
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D286R
the mutant enzyme aminoacylates the amber suppressor tRNA, as well as the wild-type tRNATyr, whereas the wild-type enzyme aminoacylates the amber suppresssor tRNA about 300fold less efficientyl than the wild-type tRNATyr. The mutant recognizes the amber suppressor tRNA 65fold better than the wild-type enzyme. The activity if the mutant and amber suppressor tRNA pair is as high as 22% that of the wild-type pair. The mutation mainly decreases the KM for tRNA. The kcat is not affected as much
D81R
site-diretced mutagenesis, the mutant shows reduced stereospecificity for L-Tyr compared to wild-type
E36Q
site-diretced mutagenesis, the mutant shows increased, but not inverted, stereospecificity for L-Tyr compared to wild-type
Y32Q/D158A
site-directed mutagenesis, enzyme mutant discriminates between L-tyrosine and O-methyl-L-tyrosine, with a high activity only with the latter
AMSSS
-
TyrRS mutant, a library of more than 200 mutants substituting the ATP binding motif KMSSS is built
KMGCA
-
TyrRS mutant, a library of more than 200 mutants substituting the ATP binding motif KMSSS is built
RMSSS
-
TyrRS mutant, a library of more than 200 mutants substituting the ATP binding motif KMSSS is built
Y32Q/D158A/L162P/D286R
-
The engineered enzyme is improved with specificity for O-methyl-L-tyrosine and 10fold improved incorporation. The optimized synthetase is used for the preparative expression of a modified uvGFP carrying MeTyr at position 66 as part of its fluorophore. This biosynthetic protein shows quantitative incorporation of the non-natural amino acid, The Asp286Arg mutation serves for improved recognition of the CUA anticodon
additional information
additional information
computational design of possible mutants with altered substrate specificity by prediction of the binding structure and calculation of binding energies of mutants to amino acids, overview
additional information
-
computational design of possible mutants with altered substrate specificity by prediction of the binding structure and calculation of binding energies of mutants to amino acids, overview
additional information
structural comparison of wild-type enzyme and naturally occuring mutant variant p-BrPhe TyrRSs, the latter shows an altered substrate specificity charging 4-bromophenylalanine, 3-(2-naphthyl)alanine, or 4-acetylphenylalanine, overview
additional information
60 aminoacyl-tRNA synthetases are modeled using the conformation of Methanococcus jannaschii tRNATyr/tyrosyl-tRNA synthetase as template
additional information
-
60 aminoacyl-tRNA synthetases are modeled using the conformation of Methanococcus jannaschii tRNATyr/tyrosyl-tRNA synthetase as template
additional information
-
the Escherichia coli TyrRS-tRNATyr pair is functionally replaced by the Methanocaldococcus jannaschii tyrosine pair
additional information
-
development of a one-plasmid expression system encoding an inducible modified tyrosyl-tRNA synthetase, the orthogonal cognate suppressor tRNA, and eGFPUAG in an individually regulatable fashion, overview. Assessment of the system for the incorporation of a non-natural amino acid yielding a fluorescent readout. Mutant library construction by random mutagenesis, and selection for O-methyl-L-tyrosine-specific mutant variants
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant C-terminally His6-tagged tyrosyl aminoacyl-tRNA synthetase from Escherichia coli by nickel affinity and ion exchange chromatography to homogeneity
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
DNA and amino acid sequence determination and analysis of two enzymes types, expression of tyrosyl aminoacyl-tRNA synthetase as C-terminally His6-tagged enzyme in Escherichia coli
a library of more than 200 mutants substituting the ATP binding motif KMSSS, Lys204-Met205-Ser206-Ser207-Ser208, is built, mutants and wild-type of MjYRS are cloned into the vector pET41a+
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
biotechnology
incorporation of unusual specific amino acids into proteins in in vitro translation systems by mutant enzyme with altered substrate specificity. e.g. mutant Y32Q/D158A
biotechnology
biotechnology
-
a mutant Methanococcus jannaschii tyrosyl amber suppressor tRNA, Tyr MjtRNA CUR/tyrosyl-tRNA synthetase (MjTyrRS) pair is developed to uniquely incorporate phenylselenocysteine in response to the amber TAG codon in Escherichia coli. After being efficiently converted into dehydroalanine under mild conditions, Michael addition reactions with the corresponding thiols can be used to synthesize N-methyl- and N-acetyl-lysine analogues
biotechnology
-
Escherichia coli-based cell-free system for the production of proteins with a non-natural amino acid incorporated site-specifically is described. A mutant Methanococcus jannaschii tyrosyl-tRNA synthetase (mTyrRS) and tRNATyr pair are used as orthogonal elements. The mTyrRS experienced proteolysis and modified protein yields improves with higher synthetase addition (200-300 mg/mL)
biotechnology
-
a rapid, straightforward, one plasmid dual positive/negative selection system for the evolution of aminoacyl-tRNA synthetases with altered specifities in Escherichia coli is developed
biotechnology
-
the present engineering allows Escherichia coli TyrRS variants for non-natural amino acids to be developed in Escherichia coli, for use in both eukaryotic and bacterial cells for genetic code expansion
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Zhang, D.; Vaidehi, N.; Goddard, W.A.3rd.; Danzer, J.F.; Debe, D.
Structure-based design of mutant Methanococcus jannaschii tyrosyl-tRNA synthetase for incorporation of O-methyl-L-tyrosine
Proc. Natl. Acad. Sci. USA
99
6579-6584
2002
Methanocaldococcus jannaschii (Q57834), Methanocaldococcus jannaschii
Zhang, Y.; Wang, L.; Schultz, P.G.; Wilson, I.A.
Crystal structures of apo wild-type M. jannaschii tyrosyl-tRNA synthetase (TyrRS) and an engineered TyrRS specific for O-methyl-L-tyrosine
Protein Sci.
14
1340-1349
2005
Methanocaldococcus jannaschii (Q57834), Methanocaldococcus jannaschii
Turner, J.M.; Graziano, J.; Spraggon, G.; Schultz, P.G.
Structural plasticity of an aminoacyl-tRNA synthetase active site
Proc. Natl. Acad. Sci. USA
103
6483-6488
2006
Methanocaldococcus jannaschii (Q57834)
Goerke, A.R.; Swartz, J.R.
High-level cell-free synthesis yields of proteins containing site-specific non-natural amino acids
Biotechnol. Bioeng.
102
400-416
2008
Methanocaldococcus jannaschii
Park, H.; Davidson, E.; King, M.P.
Overexpressed mitochondrial leucyl-tRNA synthetase suppresses the A3243G mutation in the mitochondrial tRNA(Leu(UUR)) gene
RNA
14
2407-2416
2008
Methanocaldococcus jannaschii
Sun, R.; Zheng, H.; Fang, Z.; Yao, W.
Rational design of aminoacyl-tRNA synthetase specific for p-acetyl-L-phenylalanine
Biochem. Biophys. Res. Commun.
391
709-715
2010
Methanocaldococcus jannaschii (Q57834), Methanocaldococcus jannaschii
Melancon, C.E.; Schultz, P.G.
One plasmid selection system for the rapid evolution of aminoacyl-tRNA synthetases
Bioorg. Med. Chem. Lett.
19
3845-3847
2009
Methanocaldococcus jannaschii
Kamijo, S.; Fujii, A.; Onodera, K.; Wakabayashi, K.
Analyses of conditions for KMSSS loop in tyrosyl-tRNA synthetase by building a mutant library
J. Biochem.
146
241-250
2009
Methanocaldococcus jannaschii
Iraha, F.; Oki, K.; Kobayashi, T.; Ohno, S.; Yokogawa, T.; Nishikawa, K.; Yokoyama, S.; Sakamoto, K.
Functional replacement of the endogenous tyrosyl-tRNA synthetase-tRNATyr pair by the archaeal tyrosine pair in Escherichia coli for genetic code expansion
Nucleic Acids Res.
38
3682-3691
2010
Saccharomyces cerevisiae, Methanocaldococcus jannaschii, Escherichia coli (P0AGJ9), Escherichia coli
Kuhn, S.M.; Rubini, M.; Fuhrmann, M.; Theobald, I.; Skerra, A.
Engineering of an orthogonal aminoacyl-tRNA synthetase for efficient incorporation of the non-natural amino acid O-methyl-L-tyrosine using fluorescence-based bacterial cell sorting
J. Mol. Biol.
404
70-87
2010
Methanocaldococcus jannaschii
Kobayashi, T.; Nureki, O.; Ishitani, R.; Yaremchuk, A.; Tukalo, M.; Cusack, S.;, Sakamoto K, Yokoyama S.
Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion
Nat. Struct. Biol.
10
425-432
2003
Methanocaldococcus jannaschii (Q57834), Methanocaldococcus jannaschii, Methanocaldococcus jannaschii DSM 2661 (Q57834)
Druart, K.; Guennec, M.L.; Palmai, Z.; Simonson, T.
Probing the stereospecificity of tyrosyl- and glutaminyl-tRNA synthetase with molecular dynamics
J. Mol. Graph. Model.
71
192-199
2017
Methanocaldococcus jannaschii (Q57834), Methanocaldococcus jannaschii, Methanocaldococcus jannaschii TCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 (Q57834)
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