Information on EC 3.6.4.13 - RNA helicase and Organism(s) Homo sapiens

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Homo sapiens


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The enzyme appears in selected viruses and cellular organisms

EC NUMBER
COMMENTARY hide
3.6.4.13
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RECOMMENDED NAME
GeneOntology No.
RNA helicase
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SYSTEMATIC NAME
IUBMB Comments
ATP phosphohydrolase (RNA helix unwinding)
RNA helicases utilize the energy from ATP hydrolysis to unwind RNA. Some of them unwind RNA with a 3' to 5' polarity [3], other show 5' to 3' polarity [8]. Some helicases unwind DNA as well as RNA [7,8]. May be identical with EC 3.6.4.12 (DNA helicase).
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
metabolism
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 + H2O
ADP + phosphate
show the reaction diagram
CTP + H2O
CDP + phosphate
show the reaction diagram
Q08211
-
-
-
?
dATP + H2O
dADP + phosphate
show the reaction diagram
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the enzyme displaces partial duplex RNA exclusively in a 5' to 3' direction. This reaction is supported by ATP and dATP at relatively high concentrations. The enzyme displays only ATPase and dATPase activity. RNA helicase catalyzes the unwinding of duplex RNA and RNA*DNA hybrids provided that single-stranded RNA is available for the helicase to bind
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-
?
GTP + H2O
GDP + phosphate
show the reaction diagram
Q08211
-
-
-
?
UTP + H2O
UDP + phosphate
show the reaction diagram
Q08211
-
-
-
?
additional information
?
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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 + H2O
ADP + phosphate
show the reaction diagram
additional information
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
KCl
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slight stimulation at 0.05-0.1 M, inhibition at 0.2 M
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
benzoquinoquinoxaline
BQQ, inhibits ChlR1 triplex DNA unwinding activity
EDTA
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EWS-FLI1
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the small molecule reduces RHA helicase activity in a dose-dependent and enantiomeric manner without affecting intrinsic ATPase activity, the RHA kinetics indicate a complex model. Only (S)-YK-4-279 reverses the EWS-FLI1 inhibition of RHA helicase activity. YK-4-279 inhibition of RHA binding to EWS-FLI1 alters the RNA binding profile of both proteins. EWS-FLI1 modulates RHA helicase activity causing changes in overall transcriptome processing
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additional information
enzyme ChlR1 fails to unwind the triplex substrate in the absence of ATP or in the presence of ADP or ATPgammaS
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
MLN51
stimulates the RNA-helicase activity of eIF4AIII
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poly(C)
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stimulates ATPase and dATPase activity
Single-stranded RNA
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RNA helicase catalyzes the unwinding of duplex RNA and RNA*DNA hybrids provided that single-stranded RNA is available for the helicase to bind
Upf2
interaction analysis. The two proteins Upf1 and Upf2 form a complex while unwinding RNA. The binding of Upf2 to CH domain activates Upf1-CH-HD unwinding and translocation
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0157 - 0.24
ATP
additional information
additional information
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Michaelis-Menten kinetics
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.4
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assay at
7.8
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assay at
8
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assay at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25
assay at
26
RNA assay at
30
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assay at
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
additional information
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
100000
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x * 100000, gel filtration
119037
x * 119037, calculated from sequence
130000
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glycerol gradient centrifugation
140000
246000
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calculated from sequence. Apart from an N-terminal domain of unknown function, Brr2p consists of two putative helicase domains, each connected at its C-terminus to a Sec63-like domain
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
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1 * 130000, SDS-PAGE
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phosphoprotein
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystal structure analysis of RIG-1, PDB ID 2YKG; crystal structure analysis, PDB ID 3G0H
crystals of DDX1954-475 in complex with RNA and Mg/adenosine 5'-(beta,gamma-imido)triphosphate are obtained by vapor diffusion in sitting drops incubated at 4°C by mixing 0.0001 ml of protein solution (20 mg/ml) including 10-molar excess of decauracil ssRNA, adenosine 5'-(beta,gamma-imido)triphosphate, and MgCl2 and 0.0002 ml of reservoir solution containing 14% polyethylene glycol monomethyl ether 2000, 0.25 M trimethylamine n-oxide, 0.1 M Tris, pH 8. The crystal structures of DDX19, in its RNA-bound prehydrolysis and free posthydrolysis state, reveal an alpha-helix that inserts between the conserved domains of the free protein to negatively regulate ATPase activity
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hanging-drop method, crystallization of recombinant DDX3 RNA helicase domain
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sitting-drop vapor diffusion method at 4 °C. Crystal structures of the conserved domain 1 of the DEIH-motif-containing helicase DHX9 and of the DEAD-box helicase DDX20. Both contain a RecA-like core, but DHX9 differs from DEAD-box proteins in the arrangement of secondary structural elements and is more similar to viral helicases such as NS3. The N-terminus of the DHX9 core contains two long alpha-helices that reside on the surface of the core without contributing to nucleotide binding
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
recombinant C-terminally His-tagged and N-terminally calmodulin-binding-protein-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) Rosetta by nickel and calmodulin affinity chromatography
recombinant His-tagged enzyme from Spodoptera frugiperda Sf9 cells by nickel affinity and heparin affinity chromatography
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recombinant N-terminally His6-tagged mutant enzymes from HEK293E cells by nickel affinity chromatography
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using affinity chromatography
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using Ni-NTA chromatography; using Ni-NTA chromatography
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL-21
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expression in Escherichia coli
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overexpression in Escherichia coli
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recombinant expression of C-terminally His-tagged and N-terminally calmodulin-binding-protein-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3) Rosetta
recombinant expression of FLAG-tagged DHX34 in HEK-293T cells, co-expression with recombinant UPF1 protein, DHX34 and UPF1 interact directly, but weak interaction with UPF2 and UPF3b
recombinant expression of FLAG3-tagged wild-type and mutant enzymes in HEK293T cells
recombinant expression of N-terminally His6-tagged wild-type and mutant enzymes in HEK293e cells
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recombinant His-tagged enzyme expression in Spodoptera frugiperda Sf9 cells using the baculovirus expression system
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recombinantly expressed as a His-tagged fusion protein; recombinantly expressed as a His-tagged fusion protein
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
an alpha-helix that inserts between the conserved domains of the free protein negatively regulate ATPase activity
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polymerase II can interact with beta-actin, and this interaction is enhanced due to the overexpression of RNA helicase A
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D279A
site-directed mutagenesis, the mutation affects ATP hydrolysis
DELTA53-105
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a region within the N-terminus of RHAU, referred to as the RSM, interacts with human telomerase RNA
F192E
site-directed mutagenesis, the mutant shows slightly reduced activity compared with the wild-type enzyme. Upf1F192E definitely prefers to unwind a dsDNA than to translocate it, strand switching
K191S
site-directed mutagenesis, the mutation affects ATP binding
K235A
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site-directed mutagenesis of a conserved Lys residue in RNA binding domain dsRBD2, the mutation does not prevent purified full-length RNA helicase A from binding and unwinding duplex RNA in vitro, but efficiently inhibits RNA helicase A-stimulated HIV-1 RNA metabolism including the accumulation of viral mRNA and tRNALys3 annealing to viral RNA
K236A
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site-directed mutagenesis of a conserved Lys residue in RNA binding domain dsRBD2, the mutation does not prevent purified full-length RNA helicase A from binding and unwinding duplex RNA in vitro, but efficiently inhibits RNA helicase A-stimulated HIV-1 RNA metabolism including the accumulation of viral mRNA and tRNALys3 annealing to viral RNA
K236E
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mutant exhibits relatively minor reduction in interaction with SNV PCE
K50R
site-directed mutagenesis, ATPase dead mutant, fails completely to unwind triplex substrates
K54A
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site-directed mutagenesis of a conserved Lys residue in RNA binding domain dsRBD1, the mutation does not prevent purified full-length RNA helicase A from binding and unwinding duplex RNA in vitro, but efficiently inhibits RNA helicase A-stimulated HIV-1 RNA metabolism including the accumulation of viral mRNA and tRNALys3 annealing to viral RNA
K54A/K55A
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mutant exhibits relatively minor reduction in interaction with SNV PCE
K54A/K55A/K236E
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triple mutant shows a severe reduction in interaction with junD post-transcriptional control element (PCE) or SNV PCE compared with wild-type
K55A
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site-directed mutagenesis of a conserved Lys residue in RNA binding domain dsRBD1, the mutation does not prevent purified full-length RNA helicase A from binding and unwinding duplex RNA in vitro, but efficiently inhibits RNA helicase A-stimulated HIV-1 RNA metabolism including the accumulation of viral mRNA and tRNALys3 annealing to viral RNA
K897del
site-directed mutagenesis, the mutant fails in unwinding the DNA substrates
Y593F
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expression of the mutant enzyme in SW620 cells leads to Snail repression, E-cadherin upregulation and vimentin repression
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine