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Information on EC 6.1.1.9 - valine-tRNA ligase and Organism(s) Thermus thermophilus and UniProt Accession P96142

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Thermus thermophilus
UNIPROT: P96142 not found.
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The taxonomic range for the selected organisms is: Thermus thermophilus
The enzyme appears in selected viruses and cellular organisms
Synonyms
valyl-trna synthetase, valrs, glp-4, val-trna synthetase, valyl-transfer rna synthetase, osvalrs2, valine-trna ligase, valyl-trna ligase, valyl transfer ribonucleic acid synthetase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Valyl-tRNA synthetase
-
Synthetase, valyl-transfer ribonucleate
Valine transfer ribonucleate ligase
Valine translase
Valine--tRNA ligase
ValRS
Valyl transfer ribonucleic acid synthetase
Valyl-transfer ribonucleate synthetase
Valyl-transfer RNA synthetase
Valyl-tRNA ligase
Valyl-tRNA synthetase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + L-valine + tRNAVal = AMP + diphosphate + L-valyl-tRNAVal
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
esterification
Aminoacylation
PATHWAY SOURCE
PATHWAYS
-
-
SYSTEMATIC NAME
IUBMB Comments
L-valine:tRNAVal ligase (AMP-forming)
-
CAS REGISTRY NUMBER
COMMENTARY hide
9023-47-6
-
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-valine + tRNAVal
AMP + diphosphate + L-valyl-tRNAVal
show the reaction diagram
-
-
-
?
ATP + L-valine + tRNAVal
AMP + diphosphate + L-valyl-tRNAVal
show the reaction diagram
additional information
?
-
-
loss of the electrostatically interactions between the coiled-coil domain of the enzyme and base A20 and tertiary bas pair G19.C56 increases the Km for the tRNA by 28fold and the kcat for aminoacylation by 19fold
-
?
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-valine + tRNAVal
AMP + diphosphate + L-valyl-tRNAVal
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Zn2+
-
2 Zn2+ tightly bound
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1,10-phenanthroline
-
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
-
loss of the electrostatically interactions between the coiled-coil domain of the enzyme and base A20 and tertiary bas pair G19.C56 increases the Km for the tRNA by 28fold and the kcat for aminoacylation by 19fold
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0015 - 0.042
tRNAVal
additional information
additional information
-
Km for tRNAVal mutants, loss of the electrostatically interactions between the coiled-coil domain of the enzyme and base A20 and tertiary bas pair G19.C56 increases the Km for the tRNA by 28fold
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.36 - 6.7
tRNAVal
additional information
additional information
-
kcat for tRNAVal mutants, loss of the electrostatically interactions between the coiled-coil domain of the enzyme and base A20 and tertiary bas pair G19.C56 increases the kcat for aminoacylation by 19fold
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
molecular trigger for pre-transfer editing pathway in valyl-tRNA synthetase, molecular dynamics simulations using ValRS structure, PDB ID 1GAX, overview. Structural models of the complexes ValRS-tRNAval-Val-AMP and ValRS-tRNAval-Thr-AMP
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
SYV_THETH
862
0
98775
Swiss-Prot
-
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
100000
-
HPLC gel filtration
108000
-
1 * 108000, SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
-
1 * 108000, SDS-PAGE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
1.7 A resolution crystal structure of the ValRS editing domain and 1.7 A resolution crystal structure of the editing domain bound with [N-(L-threonyl)-sulfamoyl]adenosine, hanging drop vapor diffusion method
molecular dynamics simulation studies based on PDB structure ID 1wk9. Noncognate substrates Thr-AMP and Thr-A76, bind more strongly than the cognate substrates Val-AMP and Val-A76 in both pre- and post-transfer editing, respectivel
enzyme complexed with tRNAVal and valyl-adenylate, hanging-drop vapour diffusion method, 20°C, 1 month, equal volumes of protein and crystallization solution: 50 mM N-(2-acetoamide)iminodiacetic acid sodium salt buffer, pH 6.5, 2% 2-propanol, 0.1 M lithium sulfate, 12% PEG4000, equilibration against reservoir solution: 50 mM N-(2-acetoamide)iminodiacetic acid sodium salt buffer, pH 6.5, 2% propanol, 0.1 M lithium sulfate, and 14% PEG 4000, ligand-free crystals by macro-seeding, X-ray diffraction structure determination at 2.9 A resolution, and analysis
-
enzyme in complex with tRNAValCAC isoacceptor and an analogue of the Val-adenylate intermediate, hanging-drop vapour diffusion method, 2 months, 4°C, 7-10 mg/ml protein/tRNA/Val-AMS solution in a molar ration of 1:1.1:2, plus equal volume of crystallization solution containing 50 mM sodium cacodylate, pH 6.5, 1.0 ammonium sulfate, 10 mM MgSO4, 6% 1,8-diaminooctane, equilibration against a reservoir solution of 50 mM sodium cacodylate, pH 6.5, 2.8 M ammonium sulfate, 10 mM MgSO4, X-ray structure determination at 2.9 A resolution and analysis
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D276A
valylation activity is similar to that of wild-type enzyme
D279A
F264A
valylation activity is similar to that of wild-type enzyme, about 15% decrease in ATP consumption rate compared to wild-type enzyme, somewhat reduced deacylation activityith Thr-tRNAVal, mutation impairs editing activity of ValRS
K270A
R216A
valylation activity is similar to that of wild-type enzyme, about 15% decrease in ATP consumption rate compared to wild-type enzyme, somewhat reduced deacylation activity with Thr-tRNAVal
T272A
valylation activity is similar to that of wild-type enzyme, about 15% decrease in ATP consumption rate compared to wild-type enzyme, somewhat reduced deacylation activity with Thr-tRNAVal
R818A/R843A
-
slightly reduced activity compared to the wild-type enzyme with tRNAValCAC mutant substrate
additional information
-
a C-treminally truncated mutant enzyme shows highly reduced activity compared to the wild-type enzyme
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant from Escherichia coli strain JM109(DE3)
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
overexpression of wild-type and mutant emnzymes in Escherichia coli strain JM109(DE3)
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Kohda, D.; Yokoyama, S; Miyazawa, T.
Thermostable valyl-tRNA, isoleucyl-tRNA and methionyl-tRNA synthetases from an extreme thermophile Thermus thermophilus HB8. Protein structure and Zn2+ binding
FEBS Lett.
174
20-23
1984
Thermus thermophilus, Thermus thermophilus HB8 / ATCC 27634 / DSM 579
Manually annotated by BRENDA team
Fukai, S.; Nureki, O.; Sekine, S.; Shimada, A.; Tao, J.; Vassylyev, D.G.; Yokoyama, S.
Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase
Cell
103
793-803
2000
Thermus thermophilus
Manually annotated by BRENDA team
Fukai, S.; Nureki, O.; Sekine, S.; Shimada, A.; Vassylyev, D.G.; Yokoyama, S.
Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase
RNA
9
100-111
2003
Thermus thermophilus
Manually annotated by BRENDA team
Fukunaga, R.; Yokoyama, S.
Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain
J. Biol. Chem.
280
29937-29945
2005
Thermus thermophilus (P96142), Thermus thermophilus
Manually annotated by BRENDA team
Bharatham, N.; Bharatham, K.; Lee, Y.; Woo Lee, K.
Molecular dynamics simulation study of valyl-tRNA synthetase with its pre- and post-transfer editing substrates
Biophys. Chem.
143
34-43
2009
Thermus thermophilus (P96142)
Manually annotated by BRENDA team
Li, L.; Yu, L.; Huang, Q.
Molecular trigger for pre-transfer editing pathway in valyl-tRNA synthetase: a molecular dynamics simulation study
J. Mol. Model.
17
555-564
2011
Thermus thermophilus (P96142)
Manually annotated by BRENDA team