Information on EC 6.1.1.11 - serine-tRNA ligase

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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea

EC NUMBER
COMMENTARY hide
6.1.1.11
-
RECOMMENDED NAME
GeneOntology No.
serine-tRNA ligase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + L-serine + tRNASer = AMP + diphosphate + L-seryl-tRNASer
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Aminoacylation
esterification
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Aminoacyl-tRNA biosynthesis
-
-
L-selenocysteine biosynthesis I (bacteria)
-
-
L-selenocysteine biosynthesis II (archaea and eukaryotes)
-
-
tRNA charging
-
-
selenocysteine biosynthesis
-
-
SYSTEMATIC NAME
IUBMB Comments
L-serine:tRNASer ligase (AMP-forming)
This enzyme also recognizes tRNASec, the special tRNA for selenocysteine, and catalyses the formation of L-seryl-tRNASec, the substrate for EC 2.9.1.1, L-seryl-tRNASec selenium transferase.
CAS REGISTRY NUMBER
COMMENTARY hide
9023-48-7
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
-
Manually annotated by BRENDA team
two isozymes through poylmorphism at position 197, L197S
UniProt
Manually annotated by BRENDA team
K12
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
C836
-
-
Manually annotated by BRENDA team
gene serS2
SwissProt
Manually annotated by BRENDA team
gene serS
SwissProt
Manually annotated by BRENDA team
strain ATCC 700974
UniProt
Manually annotated by BRENDA team
gene SerS
-
-
Manually annotated by BRENDA team
fragment; gene SerS
SwissProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
-
impairment of zygotic Sars function leads to a significant dilatation of the aortic arch vessels and aberrant branching of cranial and intersegmental vessels
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2'-dATP + L-serine + tRNASer
2'-dAMP + diphosphate + L-seryl-tRNASer
show the reaction diagram
-
-
-
-
-
2-bromoadenosine 5'-triphosphate + L-serine + tRNASer
2-bromoadenosine 5'-monophosphate + diphosphate + L-seryl-tRNASer
show the reaction diagram
-
-
-
-
2-chloroadenosine 5'-triphosphate + L-serine + tRNASer
2-chloroadenosine 5'-monophosphate + diphosphate + L-seryl-tRNASer
show the reaction diagram
-
-
-
-
3'-NH2-ATP + L-serine + tRNASer
3'-NH2-AMP + diphosphate + L-seryl-tRNASer
show the reaction diagram
-
-
-
-
ATP + DL-serine hydroxamate + tRNASer
?
show the reaction diagram
-
very weak activity
-
-
?
ATP + L-cysteine + tRNASer
AMP + diphosphate + L-cysteinyl-tRNASer
show the reaction diagram
-
very weak activity
-
-
?
ATP + L-serine + Fusaro tRNAPyl
AMP + diphosphate + L-seryl-Fusaro tRNAPyl
show the reaction diagram
-
Methanosarcina barkeri Fusaro tRNApyrrolysine (tRNAPyl) can be misacylated with serine by the Methanosarcina barkeri bacterial-type seryl-tRNA synthetase in vitro and in vivo in Escherichia coli. Compared to the Methanosarcina barkeri Fusaro tRNA, the Methanosarcina barkeri MS tRNAPyl contains two base changes: a G3:U70 pair
-
-
?
ATP + L-serine + tRNAPyl
AMP + diphosphate + L-seryl-tRNAPyl
show the reaction diagram
-
-
-
-
?
ATP + L-serine + tRNASec
AMP + diphosphate + L-seryl-tRNASe
show the reaction diagram
-
selenocysteine-incorporating tRNA wild-type and deletion mutants, secondary structures
-
?
ATP + L-serine + tRNASec
AMP + diphosphate + L-seryl-tRNASec
show the reaction diagram
ATP + L-serine + tRNASecUCA
AMP + diphosphate + L-seryl-tRNASecUCA
show the reaction diagram
-
SerRS also aminoacylates tRNASec with serine as the first step for the incorporation of selenocysteine into proteins
-
-
?
ATP + L-serine + tRNASer
?
show the reaction diagram
-
-
-
-
-
ATP + L-serine + tRNASer
AMP + diphosphate + L-seryl-tRNASer
show the reaction diagram
ATP + L-serine + tRNASerCGA
AMP + diphosphate + L-seryl-tRNASerCGA
show the reaction diagram
-
-
-
-
?
ATP + L-serine + tRNASerGCU
AMP + diphosphate + L-seryl-tRNASerGCU
show the reaction diagram
ATP + L-serine + tRNASerUGA
AMP + diphosphate + L-seryl-tRNASerUGA
show the reaction diagram
ATP + L-threonine + tRNASer
AMP + diphosphate + L-threonyl-tRNASer
show the reaction diagram
-
very weak activity
-
-
?
dATP + L-serine + tRNASer
dAMP + diphosphate + L-seryl-tRNASer
show the reaction diagram
-
-
-
-
-
formycin 5'-triphosphate + L-serine + tRNASer
formycin 5'-monophosphate + diphosphate + L-seryl-tRNASer
show the reaction diagram
-
-
-
-
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + L-serine + tRNASec
AMP + diphosphate + L-seryl-tRNASec
show the reaction diagram
ATP + L-serine + tRNASer
?
show the reaction diagram
-
-
-
-
-
ATP + L-serine + tRNASer
AMP + diphosphate + L-seryl-tRNASer
show the reaction diagram
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
KCl
-
50 mM, required for optimal activity
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(E)-3-(3-ethynyl-4-hydroxyphenyl)-1-(2-hydroxy-4-methoxy-3-(3-methylbut-2-en-1-yl)phenyl)prop-2-en-1-one
-
-
2-mercaptoethanol
-
-
4-hydroxyderricin
-
-
5'-O-[N-(L-Seryl)-sulfamoyl]adenosine
diphosphate
-
-
DL-Serine hydroxamate
Mg2+
-
inhibition by dead-end complex formation between the ternary complex, E-ATP-Ser, and either free Mg2+ or Mg2P2O7
p-hydroxymercuribenzoate
Phenylalanyl adenosine 5'-phosphate
-
-
Poly-arginine
-
-
serinamide
-
inhibition of methanogenic type seryl-tRNA synthetase, no inhibition of bacterial type seryl-tRNA synthetase
serine hydroxamate
serine methyl ester
-
-
Seryl adenosine 5'-phosphate
-
-
tRNASer-C-C
-
weak
-
tRNASer-C-C-3'dA
-
weak
-
tRNASer-C-C-Aoxi
-
weak
-
tRNASer-C-C-Foxi-red
-
weak
-
tRNASer-I-G-A oxidized with NaIO4
-
-
-
additional information
-
Trypanosoma brucei is highly sensitive to the action of specific selenoprotein inhibitors
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Intact SH-groups
-
required for activity
-
Pex21p
-
the enzyme interacts with the peroxisome biogenesis-related factor Pex21p, the C-terminally appended domain of yeast seryl-tRNA synthetase does not participate in substrate binding, but instead is required for association with Pex21p, Pex21p does not directly bind tRNA, and nor does it possess a tRNA-binding motif, but it instead participates in the formation of a specific ternary complex with seryl-tRNA synthetase and tRNASer, strengthening the interaction of seryl-tRNA synthetase with its cognate tRNASer, overview
-
tRNASer
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.4
2-Bromoadenosine 5'-triphosphate
-
-
0.05
2-Chloroadenosine 5'-triphosphate
-
-
1
3'-NH2-ATP
-
-
0.000068 - 0.55
ATP
0.00067
chloroplastic tRNASer from maize
-
mitochondrial isozyme, pH 7.5, 30°C
-
0.2
D-Ser
0.065
dATP
-
-
2.35
DL-Serine hydroxamate
-
in 50 mM HEPES pH 7.0, 25 mM KCl, 20 mM MgCl2, temperature not specified in the publication
2
Formycin 5'-triphosphate
-
-
29
L-cysteine
-
in 50 mM HEPES pH 7.0, 25 mM KCl, 20 mM MgCl2, temperature not specified in the publication
0.0061 - 2.879
L-Ser
0.000104 - 0.9
L-serine
2 - 3.4
L-threonine
-
in 50 mM HEPES pH 7.0, 25 mM KCl, 20 mM MgCl2, temperature not specified in the publication
0.00025
mitochondrial tRNASer from maize
-
mitochondrial isozyme, pH 7.5, 30°C
-
0.0004
mitochondrial tRNASer from yeast subtype 2
-
mitochondrial isozyme, pH 7.5, 30°C
-
0.00034 - 0.89
Ser
0.0033
tRNASec
-
pH 7.6, 37°C
-
0.004
tRNASec mutant without anticodon arm
-
pH 7.6, 37°C
-
0.0004
tRNASecUCA
-
pH 7.6, 37°C, recombinant enzyme
-
0.00004 - 1.191
tRNASer
0.0005
tRNASer from Escherichia coli
-
mitochondrial isozyme, pH 7.5, 30°C
-
0.0011
tRNASer mutant without anticodon arm
-
pH 7.6, 37°C
-
0.0029 - 0.003
tRNASer(CGA)
-
0.0013 - 0.0053
tRNASer(GCU)
-
0.0026 - 0.0047
tRNASer(GGA)
-
0.003
tRNASer-C-C-2'dA
-
-
-
0.0009
tRNASer-C-C-A
-
-
-
0.001
tRNASer-C-C-F
-
-
-
0.00125
tRNASer-CmCA
-
-
-
0.00084 - 0.0014
tRNASer-I-G-A
-
0.0032
tRNASerCGA
-
pH 7.6, 37°C, recombinant enzyme
-
0.35 - 0.37
tRNASerGCU
-
0.22 - 0.29
tRNASerUGA
-
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.031 - 6.08
ATP
0.9
chloroplastic tRNASer from maize
Zea mays
-
mitochondrial isozyme, pH 7.5, 30°C
-
2.433
DL-Serine hydroxamate
Zea mays
-
in 50 mM HEPES pH 7.0, 25 mM KCl, 20 mM MgCl2, temperature not specified in the publication
0.078
L-cysteine
Zea mays
-
in 50 mM HEPES pH 7.0, 25 mM KCl, 20 mM MgCl2, temperature not specified in the publication
0.172 - 3.7
L-Ser
0.0014 - 7
L-serine
0.14
L-threonine
Zea mays
-
in 50 mM HEPES pH 7.0, 25 mM KCl, 20 mM MgCl2, temperature not specified in the publication
0.2
mitochondrial tRNASer from maize
Zea mays
-
mitochondrial isozyme, pH 7.5, 30°C
-
0.5
mitochondrial tRNASer from yeast subtype 2
Zea mays
-
mitochondrial isozyme, pH 7.5, 30°C
-
0.03 - 3.8
Ser
0.833
SertRNASer
Saccharomyces cerevisiae
-
-
-
0.007
tRNASec
Homo sapiens
-
pH 7.6, 37°C
-
0.005
tRNASec mutant without anticodon arm
Homo sapiens
-
pH 7.6, 37°C
-
0.000000011 - 1.48
tRNASer
1.2
tRNASer from Escherichia coli
Zea mays
-
mitochondrial isozyme, pH 7.5, 30°C
-
0.023
tRNASer mutant without anticodon arm
Homo sapiens
-
pH 7.6, 37°C
-
1.07 - 3.05
tRNASer(CGA)
-
0.92 - 1.13
tRNASer(GCU)
-
0.9 - 4.4
tRNASer(GGA)
-
0.35 - 6.08
tRNASerGCU
-
0.63 - 6.08
tRNASerUGA
-
additional information
additional information
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.04
DL-Serine hydroxamate
Zea mays
-
in 50 mM HEPES pH 7.0, 25 mM KCl, 20 mM MgCl2, temperature not specified in the publication
29972
0.0027
L-cysteine
Zea mays
-
in 50 mM HEPES pH 7.0, 25 mM KCl, 20 mM MgCl2, temperature not specified in the publication
74
0.016 - 13.9
L-serine
95
0.006
L-threonine
Zea mays
-
in 50 mM HEPES pH 7.0, 25 mM KCl, 20 mM MgCl2, temperature not specified in the publication
250
1275
tRNASer
Zea mays
-
in 50 mM HEPES pH 7.0, 25 mM KCl, 20 mM MgCl2, temperature not specified in the publication
887
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.21 - 3.1
5'-O-[N-(L-Seryl)-sulfamoyl]adenosine
0.0032 - 1
serinamide
0.18 - 18.1
serine hydroxamate
0.55 - 3.5
serine methyl ester
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0238
(E)-3-(3-ethynyl-4-hydroxyphenyl)-1-(2-hydroxy-4-methoxy-3-(3-methylbut-2-en-1-yl)phenyl)prop-2-en-1-one
Staphylococcus aureus
-
in 100 mM HEPES (pH 7.2), 10 mM MgCl2, 30 mM KCl, at 37°C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.0068
-
purified mitochondrial isozyme
0.093
-
-
0.15
-
-
0.76
-
-
10.87
-
-
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.1 - 8.1
-
in phosphate and Tris buffer
7.8
-
Hepes or Tris-HCl buffer
8.1
-
Hepes buffer
8.2 - 8.8
-
aminoacylation
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 8
-
25°C, acylation rate increases when pH is raised from 6.0 to 8.0
7.3 - 10
-
7.3: about 30% of maximal activity, 10: about 60% of activity maximum
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
22
aminoacylation assay at room temperature
35
aminoacylation assay at
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.8
-
isoelectric focusing
7.9
-
isoelectric focusing
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
expression at low level
Manually annotated by BRENDA team
-
high expression
Manually annotated by BRENDA team
-
high expression
Manually annotated by BRENDA team
-
low expression
Manually annotated by BRENDA team
-
-
Manually annotated by BRENDA team
-
-
Manually annotated by BRENDA team
-
middle, high abundance in this organ may result from an adaption of this organ to the production of the serine-rich protein, sericin
Manually annotated by BRENDA team
-
expression at low level
Manually annotated by BRENDA team
-
low expression
Manually annotated by BRENDA team
-
low expression
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
-
dual localization is established by the virtue of an ambiguous targeting peptid at the very N-terminus
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
UNIPROT
Aquifex aeolicus (strain VF5)
Candida albicans (strain SC5314 / ATCC MYA-2876)
Candida albicans (strain SC5314 / ATCC MYA-2876)
Candida albicans (strain SC5314 / ATCC MYA-2876)
Candida albicans (strain SC5314 / ATCC MYA-2876)
Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)
Methanosarcina barkeri (strain Fusaro / DSM 804)
Methanosarcina barkeri (strain Fusaro / DSM 804)
Methanosarcina barkeri (strain Fusaro / DSM 804)
Methanosarcina barkeri (strain Fusaro / DSM 804)
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Trypanosoma brucei brucei (strain 927/4 GUTat10.1)
Trypanosoma brucei brucei (strain 927/4 GUTat10.1)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
47000
-
2 * 47000, sedimentation studies after dissociation in 6 M guanidine hydrochloride
48700
x * 48700, recombinant enzyme, SDS-PAGE
49000
-
2 * 49000, SDS-PAGE
55000
-
2 * 55000, SDS-PAGE
57000
-
2 * 57000, recombinant mitochondrial isozyme, SDS-PAGE
59000
-
SDS-PAGE
60000
-
2 * 60000, SDS-PAGE
81000
-
gel filtration, sedimentation velocity
87000
-
2 * 87000 (alpha), SDS-PAGE
88000
-
sedimentation equilibrium measurement
89000
-
equilibrium ultracentrifugation method
95000
-
sedimentation studies
100000
-
gel filtration
103000
-
meniscus depletion method
109000
-
recombinant mitochondrial isozyme, gel filtration
110000
-
gel filtration
114000
-
sucrose density gradient centrifugation
124000
-
gel filtration, sedimentation velocity
170000
-
gel filtration
additional information
-
-
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystal structure of mtRS in complex with seryl adenylate at 1.65 A resolution, space group P222(1) with unit cell parameters a = 79.9, b = 230 A, c = 135.6 A
-
recombinant enzyme, hanging drop vapor-diffusion method. Crystals diffract well beyond a resolution of 1.16 A and belong to the orthorhombic space group C222(1), with unit cell parameters a = 79.89, b = 230.42, c = 13560. There is one dimer in the asymmetric unit, with a solvent content of 55%
-
sitting-drop vapour-diffusion method. Crystals grew in a very narrow range of conditions using PEG 8000 as precipitant at room temperature. An appropriate concentration of lithium sulfate was critical for crystal nucleation. Crystals diffracted well beyond a resolution of 1.6 A and were found to belong to the orthorhombic space group C222(1), with unit-cell parameters a = 79.89 A, b = 230.42 A, c = 135.60 A. There is one dimer in the asymmetric unit, with a solvent content of 55%
-
purified isozymes, sitting-drop vapour-diffusion method, 8-14 mg/ml protein in 50 mM Na HEPES, pH 7.6, 150 mM KCl, 10 mM MgCl2, and 8% v/v glycerol, is mixed with reservoir solution containing 100 mM Na MES pH 5.6-5.8, 3.2-3.4 M ammonium sulfate and 0-2% v/v glycerol, equilibration against 0.5 ml of reservoir solution. Binary complexes SerRS-SerSA and SerRS-ATP, SerRS_Ser197 with 15 mM 5'-O-[N-(l-seryl)sulfamoyl]adenosine or 10 mM ATP, are mixed with 100 mM Na MES pH 5.8-6.2, 3.3-3.4 M ammonium sulfate and 0-5% v/v glycerol as precipitant solution, 2-3 days, X-ray diffraction structure determination and analysis at 2.0 A resolution, molecular replacement for analysis of crystal structures of unliganded SerRS and of its complexes with ATP and with a seryl-adenylate analogue
in complex with 5'-O-(N-(L-seryl)-sulfamoyl)adenosine, sitting drop vapor diffusion method, using 20% (w/v) PEG 3350, 0.2 M ammonium fluoride or ammonium formate, and 0.1 M HEPES pH 7.0
purified hsSerRS, sitting-drop vapour diffusion method, 0.01875 ml of protein solution containing 10 mg/ml protein in HCl, pH 7.9, 100 mM NaCl, 10 mM MgCl2, 5% glycerol, 5 mM DTT, with 0.00625 ml of reservoir solution containing 100 mM ammonium sulfate, 22% w/v PEG 3350, 5% glycerol, 200 mM sodium formate pH 7.2, supplemented with 20% v/v glycerol, and equilibration against 0.5 ml of reservoir solution, 12°C, 2 weeks, X-ray diffraction structure determination and analysis at 3.1 A resolution
-
in complex with tRNASec from Aquifex aeolicus, sitting drop vapor diffusion method, using 100 mM trisodium citrate-HCl buffer pH 5.6 containing 2.0 M ammonium sulfate and 200 mM potassium sodium tartrate
-
SerRS free and in complex with ATP, serine and the nonhydrolysable seryl-adenylate analogue 5'-O-(N-serylsulfamoyl) adenosine, X-ray diffraction structure determination and anaylsis at 2.5 A resolution
-
crystal structures of the SerRS from the archaeon Pyrococcus horikoshii bound with 5'-O-[N-(L-seryl)-sulfamoyl]-adenosine are solved at 2.6 A, with ATP at 2.8 A, and in the apo form at 3.0 A. SerRS recognizes the seryl and adenylate moieties in a manner similar to those of the bacterial and mitochondrial SerRSs from Thermus thermophilus and Bos taurus, respectively, but different from that of the unusual SerRS from the methanogenic archaeon Methanosarcina barkeri
crystal structure analysis for identification of the amino acid substrate discrimination mechanism
-
enzyme complexes: 1. with seryl-AMP, 2. with 5'-O-[N-(L-seryl)-sulfamoyl]adenosine
-
structure at 2.3-2.6 A resolution, of enzyme complexes: 1. with ATP and Mn2+, 2. containing seryl-adenylate in the active site, 3. between the enzyme, Ap4A and Mn2+
-
tRNASer-seryl-tRNA synthetase complex, X-ray diffraction structure determination and analysis at 2.9 A resolution, the 1.8 A-resolution tRNASer acceptor stem crystal structure is superimposed to a 2.9 A-resolution crystal structure of a tRNASer-seryl-tRNA synthetase complex for a visualization of the binding environment of the tRNASer microhelix, modeling
-
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4 - 6
-
37°C, stability gradually decreases when pH is lowered from 6 to 4
81
additional information
-
glycerol stabilizes at low pH
81
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
42
-
30 min, about 80% loss of activity of full-length enzyme, about 5% loss of activity of truncated enzyme
additional information
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
EDTA, 10-50 mM, stabilizes purified enzyme at 2-4°C and at 37°C, no protective effect at 45°C
-
glycerol and DTT enhance stability of the enzyme
-
glycerol stabilizes at low pH
-
not particularly susceptible to inactivation from by freezing and thawing
-
unstable to dialysis against 0.15 M KCl for 3 h at 4°C
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, 10 mM potassium phosphate buffer, pH 6.8, containing 20 mM 2-mercaptoethanol, 0.5 mM EDTA and 10% glycerol
-
-20°C, 6 months, 50-75% of the original activity is retained
-
4°C, 50 mM potassium phosphate buffer, pH 7.5, 20% glycerol, 5 mM magnesium acetate, 0.2 mM EDTA, 0.5 mM DTT, 0.5 mM PMSF, 1 week, less than 20% loss of activity
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2400fold from liver, mitochondrial isozyme
-
ammonium sulfate precipitation and Toyopearl phenyl 650 column chromatography
-
by affinity chromatography on nickel-nitrilotriacetc acid-agarose and cation exchange chromatography on a Resource S column
-
by glutathione Sepharose beads
carried out with Ni-nitriloacetic acid spin columns; carried out with Ni-nitriloacetic acid spin columns
GST-MtArgRS shows the ability to co-purify with His-tagged MtSerRS by nickel affinity chromatography, co-elution of the two enzymes during gel filtration
-
Ni-NTA column chromatography, Resource Q column chromatography, and Superdex 200 gel filtration
purified by Ni-NTA chromatography and SDS gel electrophoresis
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recombinant
recombinant enzyme
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recombinant His-tagged hsSerRS from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
-
recombinant His-tagged isozymes from Escherichia coli strain BL21 (DE3) by nickel affinity and anion exchange chromatography, followed by ultrafiltration and gel filtration
recombinant His-tagged SerRS from Escherichia coli by nickel affinity chromatography
recombinant His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3) by nickel affinity chromatography, recombinant mutant enzymes from strain L40 by anion and cation exchange chromatography
-
recombinant mitochondrial isozyme from overexpression in Escherichia coli BL21(DE3), to homogeneity
-
recombinant SerRS from Escherichia coli by Ni2þ-chelating and cation-exchange chromatography, and gel filtration
-
recombinant wild-type and mutants from Escherichia coli
-
wild-type and mutant enzymes
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
co-expression of MtSerRS with arginyl-tRNA synthetase, MtArgRS, EC 6.1.1.19, from in the Saccharomyces cerevisiae two-hybrid system using yeast strain MaV203
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DNA and amino acid sequence determination and analysis
DNA and amino acid sequence determination and analysis, chromosomal localization at 19q13.1
DNA and amino acid sequence determination and analysis, overexpression in Escherichia coli
expressed as a His-tagged fusion protein in Escherichia coli
expressed in Escherichia coli
expressed in Escherichia coli as a C-terminal Flag-tagged fusion protein
-
expressed in Escherichia coli BL21(DE3) cells
expressed in Escherichia coli Rosetta 2 (DE3) cells
-
expressed in Escherichia coli strain KL229
-
expression in Escherichia coli
-
expression in strain L40, SerRS mutant enzyme-Pex21p interaction analysis using the yeast two-hybrid system, overview, expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
-
expression of SerRS in Escherichia coli
-
expression of the archaeal SerRS in Escherichia coli, wild-type strain KL229 and derivatives, and Saccharomyces cerevisiae. Although SerRSs from methanogenic archaea recognize tRNAsSer from all three domains of life in vitro, the toxicity presumably precludes the complementation of endogenous SerRS function in both, Escherichia coli and Saccharomyces cerevisiae. But coexpression of methanogenic-type SerRS with its cognate tRNA leads to complementation suppressing the bacterial amber mutation
-
expression of the mitochondrial isozyme in an enzyme-deficient Saccharomyces cerevisiae strain, caused by gene disruption, leads to functional complementation, overexpression of the mitochondrial isozyme in Escherichia coli BL21(DE3)
-
expression of wild type or mutant C315A archaeal SerRS in Escherichia coli, wild-type strain KL229 and derivatives, and Saccharomyces cerevisiae. Although SerRSs from methanogenic archaea recognize tRNAsSer from all three domains of life in vitro, the toxicity presumably precludes the complementation of endogenous SerRS function in both, Escherichia coli and Saccharomyces cerevisiae. But coexpression of methanogenic-type SerRS with its cognate tRNA leads to complementation suppressing the bacterial amber mutation
-
expression of wild-type and mutants in Escherichia coli BL21(DE3)
-
expresssion of the mitochondrial isozyme in Escherichia coli BL21(DE3)
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gene encoding SerRS, DNA and amino acid sequence determination and analysis, sequence comparison, phylogenetic analysis, expression of His-tagged SerRS in Escherichia coli
gene SerS, DNA and amino acid sequence determination and analysis, sequence comparison, phylogenetic analysis
-
gene serS, phylogenetic analysis
gene serS2, phylogenetic analysis
gene SerZMm, DNA and amino acid sequence determination and analysis, functional complementation by expression of the mature enzyme in a temperature-sensitive serS mutant strain of Escherichia coli, overexpression in Escherichia coli BL21(DE3)
genes vlmL and svsR, DNA and amino acid sequence determination and analysis from strain MG456-hF10, phylogenetic analysis, overexpression of soluble VlmL and SvsR in Escherichia coli strain BL21(DE3)
hsSerRS DNA and amino acid sequence determination, analysis, and comparisons, expression as His-tagged enzyme in Escherichia coli coli BL21 (DE3)
-
into the vector pET15b for expression in Escherichia coli cells, and into the vector pBAD24
-
into the vector pGEX6p3 for expression in Escherichia coli cells
into the vectors pET30a+ and pUC19; into the vectors pET30a+, pSUP and pUC19, the H270G PCR product is cloned into the vector pET15b
large-scale expression of His-tagged isozymes in Escherichia coli strain BL21 (DE3)
overexpression in Escherichia coli
the seryl-tRNA synthetase expression vector pET15bmMbSerRs is utilized, SerRS proteins are expressed in Escherichia coli cells
-
the vectors pET15b, pET20b, and pET28b are used for expression of the proteins in Escherichia coli BL21 cells, the vectors pACT2 and pAB151 are used in yeast two-hybrid analysis
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
DELTA_C
-
mutant, enzymatically inactive
ko095
-
mutant lacking aminoacylation activity
SerRSDELTA35-97
-
truncated mutants with a deletion of the N-terminal arm of the enzyme: SerRSDELTA35-97 and SerRSDELTA56-72. Both mutant have lost their specificity for tRNASer and charge also non-cognate type 1 tRNAs. The deletion has no effect on the amino acid activation step of the reaction, but reduces aminoacylation activity dramatically
DELTAG254-N261
the mutant shows 72% activity compared to the wild type enzyme
DELTAG75-N97
the mutant shows 13% activity compared to the wild type enzyme
DELTAG75-N97/DELTAG254-N261
the mutant shows 7% activity compared to the wild type enzyme
C315A
-
site-directed mutagenesis
E273A
-
E273A replacement in helix 9 located in the C-terminal domain
E273A/D277A/K280A
-
triple replacement in helix 9
E338A
-
Km (mM)(tRNASer): 0.0021, kcat (1/sec) (tRNASer): 0.059
F397P/A399G
-
the mutant shows deleterious effects in both kcat and KM values compared to the wild type enzyme
G340V/G341A
-
Km (mM)(tRNASer): 0.0067, kcat (1/sec) (tRNASer): 0.000000011
G402A/G405A
-
the double substitution displays an order of magnitude higher KM but only 2.5fold lower kcat
H250A
-
the mutant is highly efficient in serine activation: kcat is reduced by only 3fold, while KM is reduced relative to the wild type parameters
H250A/Q400A
-
the mutant is highly efficient in serine activation: kcat is reduced by only 3fold, while KM is reduced relative to the wild type parameters
K141A
-
mutated enzyme, serylation rate lowered
K164A
-
K164A replacement in the linker peptide
K79A
-
mutated enzyme, significant drop in the serylation rate
K87A
-
mutated enzyme, retains the serylation ability comparable with the wild-type enzyme
K88A
-
mutated enzyme, retains the serylation ability comparable with the wild-type enzyme
K90A
-
mutated enzyme, retains the serylation ability comparable with the wild-type enzyme
mC306A
-
active site mutant
mC306A/C461A
-
active site mutant
mE338A
-
active site mutant
mG340V/G341A
-
active site mutant
mMbSerRS-CTD
-
START codon introduced at position 167, which generates the C-terminal domain
mMbSerRS-CTDDELTAHTH
-
START codon introduced at position 167 of mMbSerRS-DELTAHTH, generating the C-terminal domain without the helix-turn-helix motif
mMbSerRS-DELTAHTH
-
deleted helix-turn-helix motif
mMbSerRS-NTD
-
STOP codon introduced at position 164, which generates the N-terminal domain
mR267A
-
active site mutant
mR347A
-
active site mutant
mW396A
-
active site mutant
N142A
-
mutated enzyme, serylation rate lowered
N435A
-
Km (mM) (L-Ser): 0.07028, kcat (1/sec) (L-Ser): 0.172, Km (mM)(tRNASer): 0.283, kcat (1/sec) (tRNASer): 0.435
N435A/S437A
-
Km (mM) (L-Ser): 0.689, kcat (1/sec) (L-Ser): 0.576, Km (mM)(tRNASer): 0.509, kcat (1/sec) (tRNASer): 0.361
N435A/S437A/W396A
-
Km (mM) (L-Ser): 0.2879, kcat (1/sec) (L-Ser): 1.32, Km (mM)(tRNASer): 1.191, kcat (1/sec) (tRNASer): 0.175
P395A
-
the mutant shows 6.5fold reduced enzyme efficiency compared to the wild type
Q400A
-
the mutation produces only small kinetic effects: KM is elevated 2fold while kcat is reduced 2fold
R143A
-
mutated enzyme, serylation rate lowered
R147A
-
R147A replacement in helix 4 located in the N-terminal domain
R267A
-
Km (mM)(tRNASer): 0.0034, kcat (1/sec) (tRNASer): 0.032
R347A
-
Km (mM)(tRNASer): 0.0063, kcat (1/sec) (tRNASer): 0.0026
R38A
-
mutated enzyme, serylation rate lowered
R76A
-
mutated enzyme, serylation ability completely lost
R78A
-
mutated enzyme, retains the serylation ability comparable with the wild-type enzyme
R94A
-
mutated enzyme, significant drop in the serylation rate
S437A
-
Km (mM) (L-Ser): 0.573, kcat (1/sec) (L-Ser): 0.729, Km (mM)(tRNASer): 0.412, kcat (1/sec) (tRNASer): 0.396
W396A
-
Km (mM)(L-Ser): 0.2645, kcat (1/sec) (L-Ser): 0.287, Km (mM)(tRNASer): 0.760, kcat (1/sec) (tRNASer): 0.239
Y89A
-
mutated enzyme, retains the serylation ability comparable with the wild-type enzyme