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Information on EC 6.1.1.7 - alanine-tRNA ligase and Organism(s) Escherichia coli and UniProt Accession P00957

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Escherichia coli
UNIPROT: P00957 not found.
Word Map
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
The taxonomic range for the selected organisms is: Escherichia coli
Synonyms
AARS2, Ala-tRNA synthetase, ALA1, ALA2, Alanine transfer RNA synthetase, Alanine translase, Alanine tRNA synthetase, Alanine--tRNA ligase, Alanine-transfer RNA ligase, alanine-tRNA ligase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ala-tRNA synthetase
Alanine transfer RNA synthetase
Alanine translase
Alanine tRNA synthetase
Alanine--tRNA ligase
-
-
-
-
Alanine-transfer RNA ligase
alanine-tRNA ligase
246
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alanyl tRNA ligase
246
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Alanyl-transfer ribonucleate synthetase
Alanyl-transfer ribonucleic acid synthetase
Alanyl-transfer RNA synthetase
alanyl-tRNA ligase
246
-
alanyl-tRNA synthase
246
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Alanyl-tRNA synthetase
AlaRS
Synthase, alanyl-transfer ribonucleate
additional information
246
the enzyme belongs to the MurMN/Fem-ABX family of tRNA-dependent ligases
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + L-alanine + tRNAAla = AMP + diphosphate + L-alanyl-tRNAAla
show the reaction diagram
kinetic mechanism, AlaRS belongs to the class II of aminoacyl-tRNA ligases due to the position of aminoacylation on the 3'-terminal tRNA ribose, and the topology and tRNAbinding orientation of the active-site protein fold, class II synthetases are rate-limited by a step prior to aminoacyl transfer, the distinct mechanistic signatures of class I versus class II tRNA synthetases ensure rapid turnover of aminoacyl-tRNAs during protein synthesis
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Aminoacylation
esterification
PATHWAY SOURCE
PATHWAYS
MetaCyc
SYSTEMATIC NAME
IUBMB Comments
L-alanine:tRNAAla ligase (AMP-forming)
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CAS REGISTRY NUMBER
COMMENTARY hide
9031-71-4
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ATP + L-alanine + tRNAAla
AMP + diphosphate + L-alanyl-tRNAAla
show the reaction diagram
-
-
-
-
?
ATP + glycine + tRNAAla
AMP + diphosphate + glycyl-tRNAAla
show the reaction diagram
-
-
-
?
ATP + L-alanine + dual specific tRNAPhe
AMP + diphosphate + L-alanyl-tRNAPhe
show the reaction diagram
-
effects of deoxynucleotide substitutions in the tRNAPhe substrate on the enzyme activity, overview
-
?
ATP + L-alanine + dual specific tRNAPhe(17)
AMP + diphosphate + L-alanyl-tRNAPhe(17)
show the reaction diagram
-
site-specific modification leads to deoxynucleotide substituted yeast tRNA substrate, the backbone is interrupted on the 3'-side of nucleotide 17
-
?
ATP + L-alanine + dual specific tRNAPhe(38)
AMP + diphosphate + L-alanyl-tRNAPhe(38)
show the reaction diagram
-
site-specific modification leads to deoxynucleotide substituted yeast tRNA substrate, the backbone is interrupted on the 3'-side of nucleotide 38
-
?
ATP + L-alanine + dual specific tRNAPhe(57)
AMP + diphosphate + L-alanyl-tRNAPhe(57)
show the reaction diagram
-
site-specific modification leads to deoxynucleotide substituted yeast tRNA substrate, the backbone is interrupted on the 3'-side of nucleotide 57
-
?
ATP + L-alanine + tmRNA
AMP + diphosphate + L-alanyl-tmRNA
show the reaction diagram
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transfer messenger RNA, 75fold reduced activity compared to cognate tRNAAla
-
?
ATP + L-alanine + tRNAAla
AMP + diphosphate + L-alanyl-tRNAAla
show the reaction diagram
ATP + L-alanine + tRNAAla
AMP + diphosphate + L-alanyl-tRNAla
show the reaction diagram
-
-
-
-
?
ATP + L-alanine + tRNAPyl
AMP + diphosphate + L-alanyl-tRNAPyl
show the reaction diagram
-
-
-
-
?
ATP + L-serine + tRNAAla
AMP + diphosphate + L-seryl-tRNAAla
show the reaction diagram
-
-
-
?
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + L-alanine + tRNAAla
AMP + diphosphate + L-alanyl-tRNAAla
show the reaction diagram
-
-
-
-
?
ATP + L-alanine + tRNAAla
AMP + diphosphate + L-alanyl-tRNAAla
show the reaction diagram
ATP + L-alanine + tRNAAla
AMP + diphosphate + L-alanyl-tRNAla
show the reaction diagram
-
-
-
-
?
additional information
?
-
-
analysis of the deacylation activities of the wild type and five different Escherichia coli AlaRS editing site substitution mutants using the free-standing Pyrococcus horikoshii AlaX editing domain complexed with serine as a model and both Ser-tRNAAla and Ala-tRNAAla as substrates, overview
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
-
required
Zinc
-
thightly bound
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5'-O-[N-(L-alanyl)-sulfamoyl]adenosine
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5'-O-[N-(L-glycinyl)sulfamoyl]-adenosine
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5,5'-dithiobis(2-nitrobenzoate)
guanidine hydrochloride
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at 0.8 M guanidine hydrochloride, the enzyme forms a molten globule like intermediate, which is enzymatically inactive
monobromobimane
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p-Hydroxymercuriphenylsulfonic acid
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Urea
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denaturation at 3.3 M, the Zn2+-depleted enzyme is much more sensitive to denaturation by urea than the native enzyme
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.23 - 1.41
alanine
0.083 - 0.21
ATP
26 - 493
glycine
0.05 - 502
L-alanine
31 - 600
L-serine
0.024
tmRNA
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pH 7.6, 37°C, recombinant His-tagged enzyme
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0.023
tRNA
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mutant AlaRS(K73E), aminoacylation
0.0011 - 0.028
tRNAAla
0.0021
tRNAPhe
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native dual specific tRNAPhe derivative substrate from Saccharomyces cerevisiae, pH 7.5, 37°C
0.0019
tRNAPhe(17)
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tRNAPhe mutant tRNAPhe(17), pH 7.5, 37°C
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0.0031
tRNAPhe(38)
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tRNAPhe mutant tRNAPhe(38), pH 7.5, 37°C
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0.017
tRNAPhe(57)
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tRNAPhe mutant tRNAPhe(57), pH 7.5, 37°C
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additional information
additional information
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
79 - 120
ATP
0.0035 - 3.7
glycine
0.0074 - 1.4
L-alanine
0.0028 - 2.4
L-serine
0.043
tmRNA
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pH 7.6, 37°C, 0.001 mg recombinant His-tagged enzyme
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0.19 - 2
tRNAAla
0.25
tRNAPhe
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native dual specific tRNAPhe substrate from Saccharomyces cerevisiae, pH 7.5, 37°C
0.25
tRNAPhe(17)
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tRNAPhe mutant tRNAPhe(17), pH 7.5, 37°C
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0.46
tRNAPhe(38)
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tRNAPhe mutant tRNAPhe(38), pH 7.5, 37°C
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0.12
tRNAPhe(57)
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tRNAPhe mutant tRNAPhe(57), pH 7.5, 37°C
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
additional information
-
the wild-type AlaRS editing domain deacylates Ser-tRNAAla with a kcat/Km of 66 mM/s, equivalent to a rate enhancement of 6000 over the rate of enzyme-independent deacylation but only 12.2fold greater than the rate with Ala-tRNAAla. While the E664A and T567G substitutions only minimally decrease kcat/Km, Q584H, I667E, and C666A AlaRS are more compromised in activity, with decreases in kcat/Km in the range of 6fold, 6.6fold, and 15fold. C666A AlaRS is 1.7fold more active on Ala-tRNAAla relative to Ser-tRNAAl. Deacylation rates of Ser-tRNAAla and Ala-tRNAAla in the absence of enzyme are determined by fitting the progress curves to equations describing a first-order decay
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0000002
5'-O-[N-(L-alanyl)-sulfamoyl]adenosine
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in 20 mM Tris-HCl (pH 8.0), at 30°C
0.000004
5'-O-[N-(L-glycinyl)sulfamoyl]-adenosine
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in 20 mM Tris-HCl (pH 8.0), at 30°C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5
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assay at
7.6
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assay at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37
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assay at
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
10 - 37
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independent of temperature in this range
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
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the enzyme belongs to the class IIa aminoacyl-tRNA synthestase family
physiological function
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the relatively modest specificity of the AlaRS editing domain may provide a rationale for the widespread phylogenetic distribution of AlaX free-standing editing domains, thereby contributing a further mechanism to lower concentrations of misacylated tRNAAla
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
Sequence
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
95000
96000
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1 * 96000, recombinant His-tagged enzyme, SDS-PAGE
179000
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Zn2+-depleted enzyme, sedimentation coefficient and analytical ultracentrifugation
186000
245000
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gel filtration
360000
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gel filtration
380000
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gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
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2 * 96000, analytical ultracentrifugation
monomer
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1 * 96000, recombinant His-tagged enzyme, SDS-PAGE
tetramer
additional information
CRYSTALLIZATION/commentary
ORGANISM
UNIPROT
LITERATURE
molecular replacement with the apo-AlaRS structure from Aquifex aeolicus,Protein Data Bank accession code 1RIQ, as the initial model
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of small fragments
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
G674D
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site-directed mutagenesis, a point mutation in the C-terminal domain, the mutation produces a monomeric variant with a fivefold reduced aminoacylation activity compared to the wild-type enzyme
C290S
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mutant enzymes with replacement of Cys residues, Cys76Ser, Cys290Ser, Cys412Ser, Cys665Ser. Mutation of Cys665 to serine induces a 120-fold decrease in catalytic efficiency
C665S
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mutant enzymes with replacement of Cys residues, Cys76Ser, Cys290Ser, Cys412Ser, Cys665Ser. Mutation of Cys665 to serine induces a 120-fold decrease in catalytic efficiency
C666A
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site-directed mutagenesis, the mutant shows reduced deacylation rates of tRNAAla compared to the wild-type enzyme
C666A/Q584H
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aminoacylation activity is unchanged from that of wild-type. In contrast to the wild-type protein mutant protein mischarges Ser onto tRNAAla. Consistent with this mischarging, deacylation of Ser-tRNA Ala by the mutant protein is undetecable. Mutant protein is sensitive to high concentrations of serine; Serine toxicity, experienced by a strain harboring an C666A/Q584H editing-defective alanyl-tRNA synthetase mutant, is rescued by an AlaXp-encoding transgene from Methanosarcina mazei. AlaXp is a free-standing editing domain homolog of AlaRS. Rescue is dependent on amino acid residues in AlaXp that are needed for its in vitro catalytic activity
C76S
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mutant enzymes with replacement of Cys residues, Cys76Ser, Cys290Ser, Cys412Ser, Cys665Ser. Mutation of Cys665 to serine induces a 120-fold decrease in catalytic efficiency
D235A
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no improvement in the discrimination between alanine and serine
D235E
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no improvement in the discrimination between alanine and serine
D235N
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no improvement in the discrimination between alanine and serine
D235Q
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no improvement in the discrimination between alanine and serine
DELTA1-437
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mutant protein containing a deleted aminoacylation domain: mutant protein is fully active for clearance of Ser-tRNAAla but it is inactive deacylate Ser-tRNAAla
DELTA1-437/731-875
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mutant protein containing a deleted aminoacylation domain: mutant protein is inactive for clearance of Ser-tRNAAla. Using RNA-binding assays, it is shown that the inactivity of the mutant correlates with a lack of binding of tRNAAla. However, at much higher concentrations, mutant is able of specifically deacylating misacylated tRNAAla. Thus, the catalytic site for editing is not disrupted instead, the reduction in editing activity results from a loss of affinity for tRNA
DELTA1-437/R693K
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a region important for tRNA-specificity is further localized to a predicted strand-loop-strand motif within the region 438-875. Arg 693 is highly conserved. Mutant R693K has relaxed specificity for tRNAThr, and deacylated Ser-tRNAThr. Thus, the AlaRS editing domain shares a second, independent way to recognize tRNAAla
E664A
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site-directed mutagenesis, the mutant shows reduced deacylation rates of tRNAAla compared to the wild-type enzyme
G237A
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mutation G237A introduces bulk into the alanine-binding pocket, with little other change in the pocket or the surrounding atoms. Shrinking of the alanine-binding pocket sharply raises the Km for alanine but does not greatly perturb the Km for serine
I667E
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site-directed mutagenesis, the mutant shows reduced deacylation rates of tRNAAla compared to the wild-type enzyme
L73A
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mutant enzymes with replacement of Lys73 with Gln, Asn, Ala or Glu show reduction in catalytic efficiency in aminoacylation assay. Glu substitution causes a 5-fold decrease in affinity for alanine
L73E
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mutant enzymes with replacement of Lys73 with Gln, Asn, Ala or Glu show reduction in catalytic efficiency in aminoacylation assay. Glu substitution causes a 5-fold decrease in affinity for alanine
L73N
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mutant enzymes with replacement of Lys73 with Gln, Asn, Ala or Glu show reduction in catalytic efficiency in aminoacylation assay. Glu substitution causes a 5-fold decrease in affinity for alanine
L73Q
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mutant enzymes with replacement of Lys73 with Gln, Asn, Ala or Glu show reduction in catalytic efficiency in aminoacylation assay. Glu substitution causes a 5-fold decrease in affinity for alanine
Q584N
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site-directed mutagenesis, the mutant shows reduced deacylation rates of tRNAAla compared to the wild-type enzyme
T567G
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site-directed mutagenesis, the mutant shows reduced deacylation rates of tRNAAla compared to the wild-type enzyme
additional information
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
the Zn2+-depleted enzyme shows reduced viscosity at 10°C compared to 37°C
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
Zn2+ stabilizes the enzyme
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PURIFICATION/commentary
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged wild-type and mutant enzmyes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
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Ni-NTA agarose column chromatography, and gel filtration
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purified by Ni-NTA chromatography and SDS gel electrophoresis
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Superose 12 column chromatography, Q Sepharose column chromatography and Sephacryl S200 gel filtration
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CLONED/commentary
ORGANISM
UNIPROT
LITERATURE
gene alaS, recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
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expressed in Escherichia coli BL21(DE3) cells
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expressed in Escherichia coli BL21DE3star cells
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expression in Escherichia coli
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RENATURED/Commentary
ORGANISM
UNIPROT
LITERATURE
after refolding from denatured state, the dimeric full-length alaRS gets back similar activity as the native enzyme, while the monomeric, truncated or point mutants do not, secondary structure analysis, unfolding profiles, overview
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a complete reversibility of enzyme activity is observed on refolding by dilution from 5 to 0.5 M guanidine hydrochloride
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
molecular biology
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the unique widespread distribution of the free-standing editing domain homolog AlaXp is most probably due to singular difficulties, for translation, poised by alanine
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Schimmel, P.
Alanine transfer synthetase. Structure-function relationships and molecular recognition of transfer RNA
Adv. Enzymol. Relat. Areas Mol. Biol.
63
233-270
1990
Escherichia coli, Escherichia coli overproducing
Manually annotated by BRENDA team
Sood, S.M.; Slattery, C.W.; Filley, S.J.; Wu, M.X.; Hill, K.A.
Further characterization of Escherichia coli alanyl-tRNA synthetase
Arch. Biochem. Biophys.
328
295-301
1996
Escherichia coli
Manually annotated by BRENDA team
Shiba, K.; Ripmaster, T.; Suzuki, N.; Nichols, R.; Plotz, P.; Noda, T.; Schimmel, P.
Human alanyl-tRNA synthetase. Conservation in evolution of catalytic core and microhelix recognition
Biochemistry
34
10340-10349
1995
Escherichia coli, Homo sapiens
Manually annotated by BRENDA team
Filley, S.J.; Hill, K.A.W.
Amino acid substitutions at position 73 in motif 2 of Escherichia coli alanyl-tRNA synthetase
Arch. Biochem. Biophys.
307
46-51
1993
Escherichia coli
Manually annotated by BRENDA team
Wu, M.X.; Filley, S.J.; Xiong, J.; Lee, J.J.; Hill, K.A.W.
A cysteine in the C-terminal region of alanyl-tRNA synthetase is important for aminoacylation activity
Biochemistry
33
12260-12266
1994
Escherichia coli
Manually annotated by BRENDA team
Putney, S.D.; Sauer, R.T.; Schimmmel, P.R.
Purification and properties of alanine tRNA synthetase from Escherichia coli
J. Biol. Chem.
256
198-204
1981
Escherichia coli
Manually annotated by BRENDA team
Chen, Z.Q.; Park Kim, J.J.; Lai, C.S.; Mehler, A.H.
Reactions of the sulfhydryl groups of alanyl-tRNA synthetase
Arch. Biochem. Biophys.
233
611-616
1984
Escherichia coli
Manually annotated by BRENDA team
Sood, S.M.; Wu, M.X.; Hill, K.A.; Slattery, C.W.
Characterization of zinc-depleted alanyl-tRNA synthetase from Escherichia coli: role of zinc
Arch. Biochem. Biophys.
368
380-384
1999
Escherichia coli
Manually annotated by BRENDA team
Barends, S.; Wower, J.; Kraal, B.
kinetic parameters for tmRNA binding to alanyl-tRNA synthetase and elongation factor Tu from Escherichia coli
Biochemistry
39
2652-2658
2000
Escherichia coli
Manually annotated by BRENDA team
Pleiss, J.A.; Wolfson, A.D.; Uhlenbeck, O.C.
Mapping contacts between Escherichia coli alanyl tRNA synthetase and 2' hydroxyls using a complete tRNA molecule
Biochemistry
39
8250-8258
2000
Escherichia coli
Manually annotated by BRENDA team
Zhang, C.M.; Perona, J.J.; Ryu, K.; Francklyn, C.; Hou, Y.M.
Distinct kinetic mechanisms of the two classes of aminoacyl-tRNA synthetases
J. Mol. Biol.
361
300-311
2006
Escherichia coli
Manually annotated by BRENDA team
Gundllapalli, S.; Ambrogelly, A.; Umehara, T.; Li, D.; Polycarpo, C.; Soell, D.
Misacylation of pyrrolysine tRNA in vitro and in vivo
FEBS Lett.
582
3353-3358
2008
Escherichia coli
Manually annotated by BRENDA team
Chong, Y.E.; Yang, X.L.; Schimmel, P.
Natural homolog of tRNA synthetase editing domain rescues conditional lethality caused by mistranslation
J. Biol. Chem.
283
30073-30078
2008
Escherichia coli
Manually annotated by BRENDA team
Beebe, K.; Mock, M.; Merriman, E.; Schimmel, P.
Distinct domains of tRNA synthetase recognize the same base pair
Nature
451
90-93
2008
Escherichia coli
Manually annotated by BRENDA team
Guo, M.; Chong, Y.E.; Shapiro, R.; Beebe, K.; Yang, X.L.; Schimmel, P.
Paradox of mistranslation of serine for alanine caused by AlaRS recognition dilemma
Nature
462
808-812
2009
Escherichia coli (P00957)
Manually annotated by BRENDA team
Pasman, Z.; Robey-Bond, S.; Mirando, A.C.; Smith, G.J.; Lague, A.; Francklyn, C.S.
Substrate specificity and catalysis by the editing active site of alanyl-tRNA synthetase from Escherichia coli
Biochemistry
50
1474-1482
2011
Escherichia coli
Manually annotated by BRENDA team
Dignam, J.D.; Guo, J.; Griffith, W.P.; Garbett, N.C.; Holloway, A.; Mueser, T.
Allosteric interaction of nucleotides and tRNA(Ala) with E. coli alanyl-tRNA synthetase
Biochemistry
50
9886-9900
2011
Escherichia coli
Manually annotated by BRENDA team
Banerjee, B.; Banerjee, R.
Guanidine hydrochloride mediated denaturation of E. coli alanyl-tRNA Synthetase: identification of an inactive dimeric intermediate
Protein J.
33
119-127
2014
Escherichia coli
Manually annotated by BRENDA team
Banerjee, B.; Banerjee, R.
Urea unfolding study of E. coli alanyl-tRNA synthetase and its monomeric variants proves the role of C-terminal domain in stability
J. Amino Acids
2015
805681
2015
Escherichia coli, Escherichia coli (P00957)
Manually annotated by BRENDA team
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