Information on EC 6.1.1.21 - histidine-tRNA ligase

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

EC NUMBER
COMMENTARY hide
6.1.1.21
-
RECOMMENDED NAME
GeneOntology No.
histidine-tRNA ligase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + L-histidine + tRNAHis = AMP + diphosphate + L-histidyl-tRNAHis
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Aminoacylation
esterification
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
tRNA charging
-
-
histidine metabolism
-
-
Aminoacyl-tRNA biosynthesis
-
-
SYSTEMATIC NAME
IUBMB Comments
L-histidine:tRNAHis ligase (AMP-forming)
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CAS REGISTRY NUMBER
COMMENTARY hide
9068-78-4
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
SwissProt
Manually annotated by BRENDA team
isozyme HRS1
SwissProt
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
overproducing strain
-
-
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
-
-
-
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
-
UniProt
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
-
Q4DA54
UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
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
ATP + 1-methyl-L-histidine + tRNAHis
AMP + diphosphate + 1-methyl-L-histidyl-tRNAHis
show the reaction diagram
-
-
-
-
?
ATP + 2-thio-L-histidine + tRNAHis
AMP + diphosphate + 2-thio-L-histidyl-tRNAHis
show the reaction diagram
-
low activity
-
-
?
ATP + 3-methyl-L-histidine + tRNAHis
AMP + diphosphate + 3-methyl-L-histidyl-tRNAHis
show the reaction diagram
-
-
-
-
?
ATP + D-histidine + tRNAHis
AMP + diphosphate + D-histidyl-tRNAHis
show the reaction diagram
-
-
-
-
?
ATP + L-histidine + minimalist RNA structures in a resected pseudoknot fold
AMP + diphosphate + L-histidyl-tRNAHis
show the reaction diagram
-
specifically recognized substrate, derived from tyrosine-accepting tRNA-like domain of brome mosaic virus RNA
-
?
ATP + L-histidine + synthetic tRNAHis A-1
AMP + diphosphate + L-histidyl-tRNAHis
show the reaction diagram
-
-
-
?
ATP + L-histidine + synthetic tRNAHis G-1
AMP + diphosphate + L-histidyl-tRNAHis
show the reaction diagram
-
-
-
?
ATP + L-histidine + tRNAHis
AMP + diphosphate + L-histidinyl-tRNAHis
show the reaction diagram
ATP + L-histidine + tRNAHis
AMP + diphosphate + L-histidyl-tRNAHis
show the reaction diagram
ATP + L-histidine + tyrosine-accepting tRNA-like domain of brome mosaic virus RNA
AMP + diphosphate + L-histidyl-tyrosine-accepting tRNA-like domain of brome mosaic virus RNA
show the reaction diagram
-
specifically recognized substrate
-
?
ATP + L-histidine + wild-type full length tRNAHis G-1
AMP + diphosphate + L-histidyl-tRNAHis
show the reaction diagram
-
activity is highly dependent upon the recognition of the unique G-1:C73 base pair and the 5'-monophosphate
-
?
dATP + L-histidine + tRNAHis
dAMP + diphosphate + L-histidyl-tRNAHis
show the reaction diagram
-
very poor substrate
-
-
-
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-histidine + tRNAHis
AMP + diphosphate + L-histidinyl-tRNAHis
show the reaction diagram
ATP + L-histidine + tRNAHis
AMP + diphosphate + L-histidyl-tRNAHis
show the reaction diagram
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
KCl
-
optimal concentration is 45 mM in absence of KCl, 5 mM in presence of 160 mM KCl
PO43-
-
enzyme contains phosphoserine, phosphoprotein
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(6-bromopyridin-2-yl)methanol
Q4DA54;
-
1,2,4-Triazole-3-alanine
-
-
2-aminoquinolin-8-ol
Q4DA54;
-
2-bromo-N-(quinolin-3-yl)acetamide
Q4DA54;
-
Argininosuccinic acid
-
poor inhibitor
D-histidine
-
-
diphosphate
-
weak
Imidazoleglycerol phosphate
-
-
Indoleglycerol phosphate
-
-
L-Histidinol
L-Histidyl-L-histidine sesquihydrate
-
-
L-Hydrazinoimidazoylpropionic acid
-
-
-
Mg2+
-
inhibition at 15 mM, optimal activation at 5-10 mM
Myositis-specific anti-Jo-1 autoantibody
-
N-(5-hydroxynaphthalen-2-yl)prop-2-enamide
Q4DA54;
-
N-(quinolin-3-yl)acetamide
Q4DA54;
-
N-(quinolin-3-yl)prop-2-enamide
Q4DA54;
-
N-Acetylhistidine
ornithine
-
poor inhibitor
p-chloromercuribenzoate
-
L-His, ATP, and Mg2+ protect
p-hydroxymercuribenzoate
-
-
quinolin-3-amine
Q4DA54;
-
RNAi
Q4DA54;
-
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Hematin
-
can substitute for hemoglobin in stimulation
hemoglobin
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2 mg/ml, stimulates
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0442 - 1.763
ATP
0.0006 - 0.08
His
0.0005
L-His
-
-
0.008 - 0.6872
L-histidine
0.0038 - 0.124
RNA microhelix
-
0.00096 - 0.0063
synthetic tRNAHis A-1
-
0.0012 - 0.0178
synthetic tRNAHis G-1
-
0.000006 - 0.034
tRNAHis
0.0055 - 0.013
tRNAHisCUA
-
0.000004
tRNAHisII
-
substrate from rabbit reticuloytes
0.00031 - 0.0016
U73tRNAHisGUG
-
0.00034 - 0.015
wild-type full length tRNAHis G-1
-
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.17 - 130
ATP
0.1 - 142
His
0.39 - 130
L-histidine
0.0013 - 0.024
RNA microhelix
-
0.002 - 0.024
synthetic tRNAHis A-1
-
0.11 - 6.08
synthetic tRNAHis G-1
-
0.0004 - 5.4
tRNAHis
0.26 - 1.5
tRNAHisCUA
-
0.005 - 0.016
U73tRNAHisGUG
-
0.12 - 4
wild-type full length tRNAHis G-1
-
0.64 - 2.6
wild-type tRNAHis
-
additional information
additional information
-
-
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.15 - 130
ATP
3 - 500
L-histidine
1000 - 6900
tRNAHis
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2
(6-bromopyridin-2-yl)methanol
Trypanosoma cruzi;
Q4DA54
IC50 above 2.0 mM, at pH 7.5 and 25°C
2
2-aminoquinolin-8-ol
Trypanosoma cruzi;
Q4DA54
IC50 above 2.0 mM, at pH 7.5 and 25°C
0.8
2-bromo-N-(quinolin-3-yl)acetamide
Trypanosoma cruzi;
Q4DA54
at pH 7.5 and 25°C
1.65
N-(5-hydroxynaphthalen-2-yl)prop-2-enamide
Trypanosoma cruzi;
Q4DA54
at pH 7.5 and 25°C
2
N-(quinolin-3-yl)acetamide
Trypanosoma cruzi;
Q4DA54
IC50 above 2.0 mM, at pH 7.5 and 25°C
0.85
N-(quinolin-3-yl)prop-2-enamide
Trypanosoma cruzi;
Q4DA54
at pH 7.5 and 25°C
2
quinolin-3-amine
Trypanosoma cruzi;
Q4DA54
IC50 above 2.0 mM, at pH 7.5 and 25°C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
121.8
-
-
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.4
-
histidyl-tRNA formation
8
-
diphosphate exchange assay at
8 - 9
-
histidine-dependent ATP-diphosphate exchange
8
-
diphosphate exchange assay at
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.5 - 9
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enzyme activity does not vary much in this range
6.5 - 7.8
-
6.5: about 40% of maximal activity, 7.2-7.8: maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25
-
assay at
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25 - 45
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25°C: about 40% of maximal activity, 45°C: about 20% of maximal activity
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
UNIPROT
ORGANISM
B0VKR7
Acinetobacter baumannii (strain SDF);
C8WUX4
Alicyclobacillus acidocaldarius subsp. acidocaldarius (strain ATCC 27009 / DSM 446 / JCM 5260 / NBRC 15652 / NCIMB 11725 / NRRL B-14509 / 104-1A);
Q2SWE3
Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264);
Escherichia coli (strain K12);
Homo sapiens;
Q8YMC2
Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576);
P60911
Staphylococcus aureus;
Q9HLX5
Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165);
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039);
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579);
Q584V0
Trypanosoma brucei brucei (strain 927/4 GUTat10.1);
Trypanosoma cruzi (strain CL Brener);
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
41100
x * 41100, amino acid sequence determination
42500
-
2 * 42500, SDS-PAGE
46600
x * 46600, amino acid sequence determination
46900
-
2 * 46900, fully purified native enzyme
47100
x * 47100, amino acid sequence determination
47300
x * 47300, amino acid sequence determination
47800
x * 47800, amino acid sequence determination
47932
-
2 * 47932, calculation from nucleotide sequence, wild-type enzyme
48800
x * 48800, amino acid sequence determination
49200
x * 49200, amino acid sequence determination
49800
x * 49800, amino acid sequence determination
50000
-
2 * 50000, SDS-PAGE
52300
-
x * 52300
53700
-
2 * 53700, SDS-PAGE with or without reduction
55000
2 * 55000, dimeric quarternary structure
55300
x * 55300, amino acid sequence determination
60000
x * 60000, amino acid sequence determination
62500
-
2 * 62500, SDS-PAGE
78000
-
high speed equilibrium centrifugation
80000
-
2 * 80000, SDS-PAGE
94000
-
gel filtration, active fusion HisRS
96000
-
gel filtration, measurement of the sedimentation coefficient
108200
-
nondenaturing PAGE, active fusion HisRS
115000
-
gel filtration
122000
-
sucrose density gradient centrifugation
125000
-
gel filtration
153000
-
gel filtration, cytoplasmic
154000
-
gel filtration, mitochondrial
160000
-
electrophoresis under nondenaturing conditions
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
oligomer
-
-
additional information
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
proteolytic modification
-
lung HisRS cleavage by the cytotoxic lymphocyte serine protease granzyme B in vitro at LGPD48, caspase 6, which shares a tetrapeptide specificity similar to that of granzyme B, cleaves HisRS, producing a fragment of similar size, but cleavage sites are nonoverlapping
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystal structure analysis
-
crystal structure of enzyme-substrate complex with histidyl-tRNA synthetase, ATP, and the amino acid analog histidinyl
-
crystal structure of histidyl-tRNA synthetase complexed with histidyl-adenylate, at 2.6 A
-
vapor diffusion method, using 0.1 M Tris pH 8.5, 0.2 M MgCl2 and 25% (w/v) PEG 3350
-
purified recombinant apoenzyme at 8 mg/ml, sitting drop method, protein solution: 20 mM Tris, pH 7.5, 0.2 M NaCl, 1 mM EDTA, 1 mM DTT, plus equal volume of well solution: 0.1 M sodium citrate, pH 5.6, 0.2 M sodium/potassium tartrate, 1.8 M ammonium sulfate, several days at room temperature, X-ray diffraction structure determination at 2.7 A resolution, and analysis
crystal structure analysis
enzyme complexed with tRNAHis, L-histidine, and AMPPNP, hanging drop vapor diffusion method, using 5% (w/v) PEG 4000 and 0.1 M NaOAc (pH4.5)
enzyme in complex with histidine
-
HisRS and its complex with histidine and its cognate tRNAHis
-
the structure of histidyl-tRNA synthetase is determined to a resolution of 2.7 A
Q4DA54;
hanging drop vapor diffusion method, using 0.2 M lithium sulfate or ammonium sulfate, 26% (w/v) PEG 3350, 0.1 M bis-Tris pH 5.5, 1 mM TCEP
Q4DA54;
the structure of histidyl-tRNA synthetase in complex with L-histidine is determined to a resolution of 1.8 A , in complex with histidyl-adenosinemonophosphate to a resolution of 3.05 A
Q4DA54;
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37
-
in presence of 2-mercaptoethanol stable for 5 h, 40% loss of activity after 12 h. In absence of 2-mercaptoethanol total loss of activity in a few min
51.7
-
melting temperature
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
2-mercaptoethanol stabilizes the enzyme
4°C, in dilute solutions stable for a few days
-
bovine serum albumin required to prevent inactivation
hemoglobin partially preserves the enzyme activity of preparations during storage at -80°C
-
hemoglobin, 2 mg/ml, partially restores the activity of the enzyme stored at low concentrations, below 0.01 mg/ml
-
loss of activity after freezing and thawing
-
no stabilization by glycerol or His, ATP or unfractionated tRNA at concentrations similar to those in the enzyme assay
-
stability is reduced at protein concentrations of less than 0.015 mg/ml
-
stabilization of the isolated enzyme by hemoglobin and hematin
sulfhydryl groups are involved in the stabilization of the native structure of the enzyme
-
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
the tRNA aminoacylation activity of the enzyme is increased upon oxidative modification by hydrogen peroxide
-
726891
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, 10 mM Hepes, pH 7.4, 1 mM magnesium acetate, 1 mM KCl, 0.5 mM DTT, 0.1 mM phenylmethylsulfonyl fluoride, 50% glycerol, stable for 6 months
-
-20°C, 50% glycerol, 2 mM 2-mercaptoethanol, stable for months
-
-20°C, 50% glycerol, 5 mM 2-mercaproethanol, stable for more than 4 months
-
-20°C, no loss of activity after 6 months
-
-85°C, stable for many months
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
by a Ni-NTA affinity column followed by a XK26/60 Superdex 75 column
employing Q-Sepharose and hydroxyapatite chromatography, by utilizing the His-tag
-
native HisRS and fusion HisRS
-
Ni-NTA column chromatography
Ni-NTA column chromatography and Superdex 200 gel filtration
Ni-NTA column chromatography, and Superdex 200 gel filtration
-
Ni-NTA column chromatography, Mono S cation-exchange column chromatography, and Superdex 200 gel filtration
Q4DA54;
partially 351fold, fully 820fold purified, recombinant from overexpression in large scale
-
recombinant from Escherichia coli
recombinant maltose-binding fusion HisRS active site fragments, HisRS1-HisRS4, from Escherichia coli strain BL21(DE3)pLysS by amylose affinity chromatography, fusion protein cleavage by TEV. The fusion protein does not affect urzyme activity
-
recombinant wild-type enzyme and mutants
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
determination of DNA sequence, genomic organization, and chromosome mapping to 5q31.3
DNA and amino acid sequence determination and analysis of HisRS gene variants, HisRS genes, which map closely to the Egr1 locus, have conserved the 129/Sv haplotype despite numerous back-crossing of the null mice progeny with C57Bl/6J animals, genetic analysis of isozymes of HisRS encoded by the 129/Sv haplotype, allelic difference for mortalin and HisRS between 129/Sv and C57Bl/6J strains, overview
-
DNA sequence determination and analysis, phylogenetic development
DNA sequence determination and expression in strain JM105 of wild-type and mutant enzymes
-
expressed in Escherichia coli BL21(DE3) cells
expressed in Escherichia coli MEOV1 cells
-
expression as enzyme-green fluorescent protein or as green fluorescent protein-enzyme construct
-
expression in Cos-1 cells
-
expression of C-terminally epitope-tagged wild-type and mutant HARS2 in 293T cells mitochondria
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gene hisS, expression of HisRS active site fragments, HisRS1-HisRS4, as maltose-binding proteins fusion proteins in Escherichia coli strain BL21(DE3)pLysS
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HTS1, phylogenetic analysis, expression in Escherichia coli strain BL21(DE3)
-
overexpression
-
overexpression in Escherichia coli DH5alpha
overexpression in Escherichia coli of a fusion HisRS, with additional 15 amino acids between the initiator Met and the second amino acid Lys
-
overexpression in Escherichia coli, as a fusion protein containing an additional 15 amino acids
-
recombinant HisRS allows complete histidylation of a Caulobacter crescentus tRNAHis transcript lacking G-1, addition of G-1 does not improve the aminoacylation
-
the full-length and a truncated variant is cloned into the Escherichia coli expression vector AVA0421 derived from vector pET14b
the vectors pWY30 anf pQE30 are used
-