Literature summary for 6.1.1.3 extracted from

Zhou, X.L.; Chen, Y.; Fang, Z.P.; Ruan, Z.R.; Wang, Y.; Liu, R.J.; Xue, M.Q.; Wang, E.D.
Translational quality control by bacterial threonyl-tRNA synthetases (2016), J. Biol. Chem., 291, 21208-21221 .

Search for more literature for 6.1.1.3

Cloned(Commentary)

Cloned (Comment)	Organism
gene thrS, sequence comparisons, recombinant expression of wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)	Escherichia coli
gene thrS, sequence comparisons, recombinant expression of wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)	Mesomycoplasma mobile
gene thrS, sequence comparisons, recombinant expression of wild-type enzyme in Escherichia coli strain BL21(DE3)	Mycoplasma capricolum

Protein Variants

Protein Variants	Comment	Organism
D46E	site-directed mutagenesis, the mutant has a modest reduction in its aminoacylation activity compared to wild-type, and its post-transfer editing activity is abolished	Escherichia coli
D46E/H186G	site-directed mutagenesis, the mutant EcThrRS strongly supports growth of a yeast thrS deletion strain (ScDELTAthrS)	Escherichia coli
D46E/Y173F	site-directed mutagenesis, the mutant EcThrRS supports growth of a yeast thrS deletion strain (ScDELTAthrS)	Escherichia coli
D46E/Y173H	site-directed mutagenesis, the mutant does not support growth of a yeast thrS deletion strain (ScDELTAthrS)	Escherichia coli
D46E/Y173K	site-directed mutagenesis, the mutant does not support growth of a yeast thrS deletion strain (ScDELTAthrS)	Escherichia coli
D46E/Y173R	site-directed mutagenesis, the mutant does not support growth of a yeast thrS deletion strain (ScDELTAthrS)	Escherichia coli
D46E/Y173S	site-directed mutagenesis, the mutant does not support growth of a yeast thrS deletion strain (ScDELTAthrS)	Escherichia coli
D46R	site-directed mutagenesis, the mutant has a modest reduction in its aminoacylation activity compared to wild-type, and its post-transfer editing activity is abolished	Escherichia coli
H186G	site-directed mutagenesis, the mutant EcThrRS strongly supports growth of a yeast thrS deletion strain (ScDELTAthrS)	Escherichia coli
H9A/H13A	site-directed mutagenesis, the post-transfer editing of MmThrRS mutant H9A/H13A is reduced compared with that of wild-type MmThrRS, the in vivo mutation of more crucial residues is required to abolish the post-transfer editing	Mesomycoplasma mobile
H9A/H13A/K86A/D117A/C119A/H123A	site-directed mutagenesis, the post-transfer editing of mutant MmThrRS-N2M is completely lost	Mesomycoplasma mobile
K136A	site-directed mutagenesis, the mutant EcThrRS supports growth of a yeast thrS deletion strain (ScDELTAthrS)	Escherichia coli
K136E	site-directed mutagenesis, the mutant does not support growth of a yeast thrS deletion strain (ScDELTAthrS)	Escherichia coli
K136R	site-directed mutagenesis, the mutant EcThrRS supports growth of a yeast thrS deletion strain (ScDELTAthrS)	Escherichia coli
additional information	the mutant EcThrRS-DELTAN1 lacking domain N1 shows no post-transfer editing activity	Escherichia coli
Y173D	site-directed mutagenesis, the mutant has a modest reduction in its aminoacylation activity compared to wild-type, and its post-transfer editing activity is abolished	Escherichia coli
Y173R	site-directed mutagenesis, the mutant has a modest reduction in its aminoacylation activity compared to wild-type, and its post-transfer editing activity is abolished	Escherichia coli

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
additional information	-	additional information	kinetics of the enzyme for cognate Thr and noncognate Ser are determined with an ATP-phosphate exchange reaction	Mycoplasma capricolum
additional information	-	additional information	kinetics of the enzyme for cognate Thr and noncognate Ser are determined with an ATP-phosphate exchange reaction	Mesomycoplasma mobile
3.39	-	L-threonine	pH 7.5, 30°C	Mycoplasma capricolum
4.4	-	L-threonine	pH 7.5, 30°C	Mesomycoplasma mobile
582.37	-	L-serine	pH 7.5, 30°C	Mycoplasma capricolum
939.72	-	L-serine	pH 7.5, 30°C	Mesomycoplasma mobile

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	required	Escherichia coli
Mg2+	required	Mesomycoplasma mobile

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
ATP + L-serine + tRNAThr	Mycoplasma capricolum	reaction of EC 6.1.1.11, mischarging of tRNAThr	AMP + diphosphate + L-seryl-tRNAThr	-	?
ATP + L-serine + tRNAThr	Mesomycoplasma mobile	reaction of EC 6.1.1.11, mischarging of tRNAThr, low activity	AMP + diphosphate + L-seryl-tRNAThr	-	?
ATP + L-serine + tRNAThr	Mesomycoplasma mobile ATCC 43663	reaction of EC 6.1.1.11, mischarging of tRNAThr, low activity	AMP + diphosphate + L-seryl-tRNAThr	-	?
ATP + L-threonine + tRNAThr	Mycoplasma capricolum	-	AMP + diphosphate + L-threonyl-tRNAThr	-	?
ATP + L-threonine + tRNAThr	Escherichia coli	-	AMP + diphosphate + L-threonyl-tRNAThr	-	?
ATP + L-threonine + tRNAThr	Mesomycoplasma mobile	-	AMP + diphosphate + L-threonyl-tRNAThr	-	?
ATP + L-threonine + tRNAThr	Mesomycoplasma mobile ATCC 43663	-	AMP + diphosphate + L-threonyl-tRNAThr	-	?

Organism

Organism	UniProt	Comment	Textmining
Escherichia coli	P0A8M3	-	-
Mesomycoplasma mobile	Q6KH76	-	-
Mesomycoplasma mobile ATCC 43663	Q6KH76	-	-
Mycoplasma capricolum	-	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant wild-type and mutant enzymes from Escherichia coli strain Bl21(DE3)	Escherichia coli
recombinant wild-type and mutant enzymes from Escherichia coli strain Bl21(DE3)	Mesomycoplasma mobile

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
ATP + L-serine + tRNAThr	reaction of EC 6.1.1.11, mischarging of tRNAThr	Mycoplasma capricolum	AMP + diphosphate + L-seryl-tRNAThr	-	?
ATP + L-serine + tRNAThr	reaction of EC 6.1.1.11, mischarging of tRNAThr, low activity	Mesomycoplasma mobile	AMP + diphosphate + L-seryl-tRNAThr	-	?
ATP + L-serine + tRNAThr	reaction of EC 6.1.1.11, mischarging of tRNAThr, low activity	Mesomycoplasma mobile ATCC 43663	AMP + diphosphate + L-seryl-tRNAThr	-	?
ATP + L-threonine + tRNAThr	-	Mycoplasma capricolum	AMP + diphosphate + L-threonyl-tRNAThr	-	?
ATP + L-threonine + tRNAThr	-	Escherichia coli	AMP + diphosphate + L-threonyl-tRNAThr	-	?
ATP + L-threonine + tRNAThr	-	Mesomycoplasma mobile	AMP + diphosphate + L-threonyl-tRNAThr	-	?
ATP + L-threonine + tRNAThr	-	Mesomycoplasma mobile ATCC 43663	AMP + diphosphate + L-threonyl-tRNAThr	-	?

Subunits

Subunits	Comment	Organism
More	enzyme domain structure, threonyl-tRNA synthetase (ThrRS) contains multiple domains, including an N2 editing domain, overview	Mycoplasma capricolum
More	enzyme domain structure, threonyl-tRNA synthetase (ThrRS) contains multiple domains, including an N2 editing domain, overview	Escherichia coli
More	enzyme domain structure, threonyl-tRNA synthetase (ThrRS) contains multiple domains, including an N2 editing domain, overview	Mesomycoplasma mobile

Synonyms

Synonyms	Comment	Organism
EcThrRS	-	Escherichia coli
McThrRS	-	Mycoplasma capricolum
MmThrRS	-	Mesomycoplasma mobile
Threonyl-tRNA synthetase	-	Mycoplasma capricolum
Threonyl-tRNA synthetase	-	Escherichia coli
Threonyl-tRNA synthetase	-	Mesomycoplasma mobile
ThrRS	-	Mycoplasma capricolum
ThrRS	-	Escherichia coli
ThrRS	-	Mesomycoplasma mobile
ThrS	-	Mycoplasma capricolum
ThrS	-	Escherichia coli
ThrS	-	Mesomycoplasma mobile

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
30	-	assay at	Mycoplasma capricolum
30	-	assay at	Escherichia coli
30	-	assay at	Mesomycoplasma mobile

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism	Structure
0.55	-	L-serine	pH 7.5, 30°C	Mesomycoplasma mobile
1.15	-	L-serine	pH 7.5, 30°C	Mycoplasma capricolum
2.16	-	L-threonine	pH 7.5, 30°C	Mesomycoplasma mobile
6.31	-	L-threonine	pH 7.5, 30°C	Mycoplasma capricolum

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.5	-	assay at	Mycoplasma capricolum
7.5	-	assay at	Escherichia coli
7.5	-	assay at	Mesomycoplasma mobile

Cofactor

Cofactor	Comment	Organism	Structure
ATP	-	Escherichia coli
ATP	-	Mesomycoplasma mobile

General Information

General Information	Comment	Organism
evolution	crucial importance of the only absolutely conserved residue within the N1 domain in regulating post-transfer editing activityand editing active sites by mediating an N1-N2 domain interaction in Escherichia coli ThrRS. Translational quality control of various ThrRSs and the role of the N1 domain in translational fidelity, overview	Escherichia coli
evolution	ThrRSs from Mycoplasma species exhibit differences in their domain composition and editing active sites compared with the canonical ThrRSs. The Mycoplasma capricolum ThrRS, which harbors an N1 domain and a degenerate N2 domain, is editing-defective, and is thus not capable to support the growth of a yeast thrS deletion strain (ScDELTAthrS). Translational quality control of various ThrRSs and the role of the N1 domain in translational fidelity, overview. McThrRS has lost its post-transfer editing activity, probably because of its degenerate editing active site in the N2 domain. MmThrRS has negligible tRNA-dependent pretransfer editing capacities	Mycoplasma capricolum
evolution	ThrRSs from Mycoplasma species exhibit differences in their domain composition and editing active sites compared with the canonical ThrRSs. The Mycoplasma mobile ThrRS, the first example of a ThrRS naturally lacking the N1 domain, displays efficient post-transfer editing activity. Mycoplasma mobile ThrRS is able to support the growth of a yeast thrS deletion strain (ScDELTAthrS). Translational quality control of various ThrRSs and the role of the N1 domain in translational fidelity, overview	Mesomycoplasma mobile
additional information	structure analysis of EcThrRS, functional importance of the Asp46 in the N1 domain and the Tyr173 in the N2 domain	Escherichia coli
physiological function	correct aminoacyl-tRNA generation is critical for the faithful transduction of genetic information, which is supported by the high levels of amino acid conservation in editing active sites of specific aaRSs across the three domains of life. Enzyme EcThrRS is an editing-capable enzyme, that can remove noncognate Ser. The N1 domain is essential for editing by EcThrRS. The enzyme shows strong tRNA-dependent editing, including the pre- and post-transfer editing of EcThrRS	Escherichia coli
physiological function	correct aminoacyl-tRNA generation is critical for the faithful transduction of genetic information, which is supported by the high levels of amino acid conservation in editing active sites of specific aaRSs across the three domains of life. The enzyme misactivates noncognate Ser and therefore requires an editing function to ensure the correct Thr-tRNAThr formation. Enzyme McThrRS is not able to hydrolyze Ser-tRNAThr and remove noncognate Ser. The degeneration of the crucial editing active sites of McThrRS impairs its posttransfer editing, McThrRS has lost its post-transfer editing activity, probably because of its degenerate editing active site in the N2 domain. McThrRS is unable to complement the loss of Saccharomyces cerevisiae thrS in vivo, because of its lack of editing activity	Mycoplasma capricolum
physiological function	correct aminoacyl-tRNA generation is critical for the faithful transduction of genetic information, which is supported by the high levels of amino acid conservation in editing active sites of specific aaRSs across the three domains of life. The enzyme misactivates noncognate Ser and therefore requires an editing function to ensure the correct Thr-tRNAThr formation. Enzyme MmThrRS is able to hydrolyze Ser-tRNAThr and remove noncognate Ser. MmThrRS, which has an intact N2 domain, has post-transfer editing activity, editing-crucial residues include Lys86, Asp117, Cys119, and His123. MmThrRS has negligible tRNA-dependent pretransfer editing capacities. MmThrRS can complement the loss of Saccharomyces cerevisiae thrS in vivo, because of its lack of editing activity. The absence of the N1 domain of MmThrRS increases in vivo activity and optimizes enzyme protein structure/stability	Mesomycoplasma mobile

kcat/KM [mM/s]

kcat/KM Value [1/mMs^-1]	kcat/KM Value Maximum [1/mMs^-1]	Substrate	Comment	Organism	Structure
0.00059	-	L-serine	pH 7.5, 30°C	Mesomycoplasma mobile
0.00122	-	L-serine	pH 7.5, 30°C	Mycoplasma capricolum
0.49	-	L-threonine	pH 7.5, 30°C	Mesomycoplasma mobile
1.86	-	L-threonine	pH 7.5, 30°C	Mycoplasma capricolum

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Release 2023.1 (January 2023)