Information on EC 6.1.1.21 - histidine-tRNA ligase

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

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
Aminoacyl-tRNA biosynthesis
-
-
tRNA charging
-
-
histidine metabolism
-
-
SYSTEMATIC NAME
IUBMB Comments
L-histidine:tRNAHis ligase (AMP-forming)
-
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
K12
-
-
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
residues 44-477
UniProt
Manually annotated by BRENDA team
residues 45-478
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 + 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
1,2,4-Triazole-3-alanine
-
-
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-Acetylhistidine
ornithine
-
poor inhibitor
p-chloromercuribenzoate
-
L-His, ATP, and Mg2+ protect
p-hydroxymercuribenzoate
-
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Hematin
-
can substitute for hemoglobin in stimulation
hemoglobin
-
2 mg/ml, stimulates
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.14 - 0.89
ATP
0.0006 - 0.08
His
0.0005
L-His
-
-
0.009 - 0.03
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
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.17 - 130
ATP
0.1 - 142
His
40 - 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 - 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
Oryctolagus cuniculus
-
-
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1000 - 1231
tRNAHis
2422
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
121.8
-
-
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.4
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histidyl-tRNA formation
8 - 9
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histidine-dependent ATP-diphosphate exchange
8
-
diphosphate exchange assay at
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
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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
-
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
ORGANISM
UNIPROT
Acinetobacter baumannii (strain SDF)
Alicyclobacillus acidocaldarius subsp. acidocaldarius (strain ATCC 27009 / DSM 446 / JCM 5260 / NBRC 15652 / NCIMB 11725 / NRRL B-14509 / 104-1A)
Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)
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 HB27 / ATCC BAA-163 / DSM 7039)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Trypanosoma brucei brucei (strain 927/4 GUTat10.1)
Trypanosoma cruzi (strain CL Brener)
Trypanosoma cruzi (strain CL Brener)
Trypanosoma cruzi (strain CL Brener)
Trypanosoma cruzi (strain CL Brener)
Trypanosoma cruzi (strain CL Brener)
Trypanosoma cruzi (strain CL Brener)
Trypanosoma cruzi (strain CL Brener)
Trypanosoma cruzi (strain CL Brener)
Trypanosoma cruzi (strain CL Brener)
Trypanosoma cruzi (strain CL Brener)
Trypanosoma cruzi (strain CL Brener)
Trypanosoma cruzi (strain CL Brener)
Trypanosoma cruzi (strain CL Brener)
Trypanosoma cruzi (strain CL Brener)
Trypanosoma cruzi (strain CL Brener)
Trypanosoma cruzi (strain CL Brener)
Trypanosoma cruzi (strain CL Brener)
Trypanosoma cruzi (strain CL Brener)
Trypanosoma cruzi (strain CL Brener)
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
-
HARS2 functions in vivo as a homodimer, HARS2 structure analysis, overview
oligomer
-
-
additional information
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
proteolytic modification
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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
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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 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
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
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
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
-
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
-
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
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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
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
hars-1 RNAi-dependent downregulation of hars-1 decreases brood size in both wild-type and ced-4(n1162) mutants, but less severely in ced-4(n1162) mutants
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C88V/C196S/C241L
-
denoted as clHisRS, can not be labeled with maleimide probes
E83A
-
15fold increase in Km-value, decrease in kcat-value
E83Q
-
2fold decrease in Km-value, decrease in kcat-value
L276C clHisRS
-
an additional cysteine is introduced at a solvent-accessible position proximal to substrate binding sites
L402C clHisRS
-
an additional cysteine is introduced at a solvent-accessible position proximal to substrate binding sites
MDCC-HisRS
-
fluorescently labeled version of HisRS, conjugated with 7-diethylamino-3-((((2-maleimidyl)ethyl)amino)carbonyl)-coumarin, MDCC, to a cysteine introduced at residue 212, located in the insertion domain
N212C clHisRS
-
an additional cysteine is introduced at a solvent-accessible position proximal to substrate binding sites
N368C clHisRS
-
an additional cysteine is introduced at a solvent-accessible position proximal to substrate binding sites
NcatHisRS
-
320-residue fragment, NcatHisRS, truncated immediately following motif 3 catalyzes both the the specific aminoacylation of tRNA and ATP-diphosphate exchange, albeit less efficiently than the full length enzyme. NcatHisRs shows no mischarging of noncognate tRNAs but exhibits reduced selectivity for the C73 discriminator base. NcatHisRs is monomeric, indicating that the C-terminal domain is essential for maintaining the dimeric structure of the enzyme
Q118E
-
site-directed point mutagenesis of an active site residue, reduced kcat but unaltered Km with wild-type tRNAHis G-1
Q127A
-
decrease in kcat-value
R116A
-
site-directed mutagenesis, reduced activity, increased specificity for the wild-type full length tRNAHis G-1
R123A
-
site-directed point mutagenesis of an active site residue, reduced activity, increased specificity for the wild-type full length tRNAHis G-1
R9H
-
site-directed point mutangenesis, increased activity with wild-type full length tRNAHis G-1, reduced activity with the synthetic tRNAHis G-1 and A-1 substrates, increased specificity for the wild-type full length tRNAHis G-1
V-HisRS-R259K
-
mutants: V-HisRS-R259K, V-HisRS-R259Q, des(A2-G10)-HisRS, des(A2-Q6)-HisRS, V-His-RS with N-terminal addition of valine, and M-HisRS with N-terminal addition of methionine. N-terminal addition of either methionine or valine, or the deletion of 6 amino terminal amino acids deceases the specific aminoacylation activity 2fold to 7fold. Further N-terminal deletions of 10 or 17 amino acids causes 100fold reduced aminoacylation and 10fold reduced ATP-diphosphate exchange. Removal of 18 or more amino acids from the N-terminus results in an inactive enzyme mutants. The two point mutations R259Q and R259K, show blocked histidyl-tRNA synthetase activity without affecting histidine or ATP binding
D48A
-
site-directed mutagenesis, the mutant is cleaved by caspase-6, but not by granzyme B
L200V
-
naturally occuring mutations in HARS2 involved in the Perrault syndrome, the mutant shows reduced activity compared to wild-type enzyme
V368L
-
naturally occuring mutations in HARS2 involved in the Perrault syndrome, the mutant shows reduced activity compared to wild-type enzyme
additional information
Renatured/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
denaturation with SDS, renatured enzyme shows 10% recovery of activity
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
analysis
-
alternating catalysis requires a mechanism for coupling events between active sites, presumably through conformational changes propagated between these active sites, a version of HisRS is developed that features the site-specific incorporation of extrinsic environmentally sensitive fluorescent probes, allowing the adenylation reaction to be followed by stopped-flow fluorometry
medicine
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