Information on EC 3.6.4.13 - RNA helicase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
3.6.4.13
-
RECOMMENDED NAME
GeneOntology No.
RNA helicase
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
a nucleoside triphosphate + H2O = a nucleoside diphosphate + phosphate
show the reaction diagram
ATP + H2O = ADP + phosphate
show the reaction diagram
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
-
-
-
Manually annotated by BRENDA team
Borrelia burgdorferi
-
-
-
Manually annotated by BRENDA team
i.e. BMV
-
-
Manually annotated by BRENDA team
gene hel-1
UniProt
Manually annotated by BRENDA team
CSFV
SwissProt
Manually annotated by BRENDA team
-
UniProt
Manually annotated by BRENDA team
i.e. DEN2
-
-
Manually annotated by BRENDA team
serotype 2, PL046 strain
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
UniProt
Manually annotated by BRENDA team
gene lmo1722
UniProt
Manually annotated by BRENDA team
gene lmo1722
UniProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
RHBV
-
-
Manually annotated by BRENDA team
RHBV
-
-
Manually annotated by BRENDA team
-
UniProt
Manually annotated by BRENDA team
stress-responsive wheat
UniProt
Manually annotated by BRENDA team
WNV
-
-
Manually annotated by BRENDA team
-
UniProt
Manually annotated by BRENDA team
ZmRH3A
UniProt
Manually annotated by BRENDA team
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
2',3'-dideoxy-ATP + H2O
2',3'-dideoxy-ADP + phosphate
show the reaction diagram
-
53% of the phosphohydrolase activity with ATP
-
-
?
2',3'-dideoxy-GTP + H2O
2',3'-dideoxy-GDP + phosphate
show the reaction diagram
-
28% of the phosphohydrolase activity with ATP
-
-
?
2'-deoxy-ATP + H2O
2'-deoxy-ADP + phosphate
show the reaction diagram
-
62% of the phosphohydrolase activity with ATP
-
-
?
2'-deoxy-GTP + H2O
2'-deoxy-GDP + phosphate
show the reaction diagram
-
39% of the phosphohydrolase activity with ATP
-
-
?
2'-deoxy-L-GTP + H2O
2'-deoxy-L-GDP + phosphate
show the reaction diagram
-
11% of the phosphohydrolase activity with ATP
-
-
?
2'-fluoro-2'-deoxy-ATP + H2O
2'-fluoro-2'-deoxy-ADP + phosphate
show the reaction diagram
-
63% of the phosphohydrolase activity with ATP
-
-
?
2'-fluoro-2'-deoxy-GTP + H2O
2'-fluoro-2'-deoxy-GDP + phosphate
show the reaction diagram
-
22% of the phosphohydrolase activity with ATP
-
-
?
2'-O-methyl-GTP + H2O
2'-O-methyl-GDP + phosphate
show the reaction diagram
-
24% of the phosphohydrolase activity with ATP
-
-
?
2-amino-ATP + H2O
2-amino-ADP + phosphate
show the reaction diagram
-
103% of the phosphohydrolase activity with ATP
-
-
?
2-hydroxy-ATP + H2O
2-hydroxy-ADP + phosphate
show the reaction diagram
-
40% of the phosphohydrolase activity with ATP
-
-
?
3'-deoxy-ATP + H2O
3'-deoxy-ADP + phosphate
show the reaction diagram
-
60% of the phosphohydrolase activity with ATP
-
-
?
3'-deoxy-GTP + H2O
3'-deoxy-GDP + phosphate
show the reaction diagram
-
12% of the phosphohydrolase activity with ATP
-
-
?
3'-O-methyl-GTP + H2O
3'-O-methyl-GDP + phosphate
show the reaction diagram
-
35% of the phosphohydrolase activity with ATP
-
-
?
6-methyl-thio-GTP + H2O
6-methyl-thio-GDP + phosphate
show the reaction diagram
-
40% of the phosphohydrolase activity with ATP
-
-
?
6-methyl-thio-ITP + H2O
6-methyl-thio-IDP + phosphate
show the reaction diagram
-
16% of the phosphohydrolase activity with ATP
-
-
?
6-thio-GTP + H2O
6-thio-GDP + phosphate
show the reaction diagram
-
93% of the phosphohydrolase activity with ATP
-
-
?
7-methyl-GTP + H2O
7-methyl-GDP + phosphate
show the reaction diagram
-
14% of the phosphohydrolase activity with ATP
-
-
?
8-bromo-ATP + H2O
8-bromo-ADP + phosphate
show the reaction diagram
-
124% of the phosphohydrolase activity with ATP
-
-
?
8-bromo-GTP + H2O
8-bromo-GDP + phosphate
show the reaction diagram
-
19% of the phosphohydrolase activity with ATP
-
-
?
8-iodo-GTP + H2O
8-iodo-GDP + phosphate
show the reaction diagram
-
54% of the phosphohydrolase activity with ATP
-
-
?
Ara-ATP + H2O
Ara-ADP + phosphate
show the reaction diagram
-
18% of the phosphohydrolase activity with ATP
-
-
?
ATP + H2O
ADP + phosphate
show the reaction diagram
CTP + H2O
CDP + phosphate
show the reaction diagram
dATP + H2O
dADP + phosphate
show the reaction diagram
dCTP + H2O
dCDP + phosphate
show the reaction diagram
helicase activity is about 25% of the activity with ATP
-
-
?
dGTP + H2O
dGDP + phosphate
show the reaction diagram
helicase activity is about 10% of the activity with ATP
-
-
?
dTTP + H2O
dTDP + phosphate
show the reaction diagram
helicase activity is about 55% of the activity with ATP
-
-
?
GTP + H2O
GDP + phosphate
show the reaction diagram
ITP + H2O
IDP + phosphate
show the reaction diagram
-
49% of the phosphohydrolase activity with ATP
-
-
?
N1-methyl-ATP + H2O
N1-methyl-ADP + phosphate
show the reaction diagram
-
66% of the phosphohydrolase activity with ATP
-
-
?
N1-methyl-GTP + H2O
N1-methyl-GDP + phosphate
show the reaction diagram
-
49% of the phosphohydrolase activity with ATP
-
-
?
N6-methyl-ATP + H2O
N6-methyl-ADP + phosphate
show the reaction diagram
-
43% of the phosphohydrolase activity with ATP
-
-
?
O6-methyl-GTP + H2O
O6-methyl-GDP + phosphate
show the reaction diagram
-
17% of the phosphohydrolase activity with ATP
-
-
?
ribavirin triphosphate + H2O
ribavirin diphosphate + phosphate
show the reaction diagram
-
36% of the phosphohydrolase activity with ATP
-
-
?
RNA + H2O
?
show the reaction diagram
UTP + H2O
UDP + phosphate
show the reaction diagram
XTP + H2O
XDP + phosphate
show the reaction diagram
-
40% of the phosphohydrolase activity with ATP
-
-
?
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 + H2O
ADP + phosphate
show the reaction diagram
RNA + H2O
?
show the reaction diagram
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
-
activity 3-5-fold lower when magnesium ions are replaced by
KCl
-
slight stimulation at 0.05-0.1 M, inhibition at 0.2 M
Ni2+
-
activity 3-5-fold lower when magnesium ions are replaced by
sulfate
-
bound, required for the metal-dependent NTPase reaction mechanism
Zn2+
-
activity 3-5-fold lower when magnesium ions are replaced by
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2',3'-ddATP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
2',3'-ddGTP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
2',3'-ddTTP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
2',3'-dideoxy-ATP
-
-
2',3'-dideoxy-GTP
-
-
2'-dATP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
2'-deoxy-ATP
-
-
2'-deoxy-GTP
-
-
2'-deoxy-L-GTP
-
-
2'-deoxythymidine 5'-phosphoryl-beta,gamma-hypophosphate
-
i.e. ppopT, dTTP analogue, most efficient inhibitor of NTPase activity among nucleotide derivaties, inhibits the ATP-dependent helicase reaction and also the ATP-independent duplex unwinding, structure of nucleic base and ribose fragment of NTP molecule have a slight effects on inhibitory properties
2'-dGTP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
2'-dTTP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
2'-fluoro-2'-deoxy-ATP
-
-
2-amino-ATP
-
-
2-hydroxy-ATP
-
-
3'-dATP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
3'-deoxy-ATP
-
-
3'-dGTP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
3'-dUTP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
6-methyl-thio-ITP
-
-
6-thio-GTP
-
-
7-methyl-GTP
-
-
8-bromo-ATP
-
-
AMP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
Ara-ATP
-
-
ATP-gamma-S
-
5.4 mM, about 50% of the original helicase activity is inhibited, competitive inhibitor
benzoquinoquinoxaline
BQQ, inhibits ChlR1 triplex DNA unwinding activity
benzoyl-Nle-Lys-Arg-Arg
-
competitive inhibition, structure-activity relationship
beta,gamma-methylene-ATP
-
efficient inhibitor, like the N1-oxides N1-O-ATP and N1-OH-ITP
Cu2+
-
inhibits ATPase activity, IC50: 0.13 mM
dATP
-
inhibits unwinding
EDTA
-
-
EWS-FLI1
-
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
-
Fe2+
-
inhibits ATPase activity, IC50: 0.75 mM
Hg2+
-
inhibits ATPase activity, IC50: 49 nM, targets the cysteine residue in the DECH box, competitive, cysteine or DTT protect at large concentrations
Imidodiphosphate
-
maximal inhibitory activity among diphosphate analogues, non-catalytic and catalytic conditions, inhibits the ATP-dependent helicase reaction but no effect on the ATP-independent duplex unwinding, structure of nucleic base and ribose fragment of NTP molecule have a slight effects on inhibitory properties
N1-methyl-ATP
-
-
N1-methyl-GTP
-
-
N1-O-ATP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
N1-OH-ITP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
N6-methyl-ATP
-
-
PCMB
-
inhibits ATPase activity, IC50: 88 nM
ribavirin triphosphate
-
-
tetrabromobenzotriazole
-
inhibits unwinding, no inhibition of ATP hydrolysis
UTP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
additional information
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Deoxyribonucleotides
EF409381
ATPase activity of the bacterially expressed BmL3-helicase is triggered by both the ssRNA and the dsRNA and, to a much lesser extent, by the ssDNA and dsDNA
-
Double-stranded DNA
EF409381
weak stimulation
Double-stranded RNA
EF409381
ATPase activity of the recombinant BmL3-helicase is strongly stimulated by dsRNA
-
MLN51
stimulates the RNA-helicase activity of eIF4AIII
-
nonstructural protein 4A
nonstructural protein 5
-
interaction with NS5, the viral RNA-dependent RNA polymerase, stimulates NS3 NTPAse and RTPase activities as well as thr RNA helicase activity
-
poly(C)
poly(dA)
strong stimulation of ATPase activity
Poly(dT)
strong stimulation of ATPase activity
Poly(rU)
-
stimulates the ATPase activity of NS3
Poly(U)
strong stimulation of ATPase activity
polyU
-
stimulatory effect of polyU on ATP hydrolysis is significantly attenuated when NaCl concentration is 50 mM or higher, functional binding of polyU mainly through electrostatic interaction, binding triggers a conformational rearrangement that activates the catalytic core of the enzyme for ATP hydrolysis
ribonucleotides
EF409381
ATPase activity of the bacterially expressed BmL3-helicase is triggered by both the ssRNA and the dsRNA and, to a much lesser extent, by the ssDNA and dsDNA, recombinant BmL3-helicase is strongly stimulated by dsRNA
-
RNase E
-
is required for ATPase and RNA unwinding activities of the enzyme, forms a complex with the enzyme, interaction analysis, overview. Avid, enthalpy-favored interaction between the helicase and RNase E 696-762 with an equilibrium binding constant Kaof at least 1 x 108 M-1 determined by isothermal titration calorimetry. Protein-protein and RNA-binding surfaces both communicate allosterically with the ATPase catalytic center
-
rRNA
-
activates the ATPase activity of DbpA by promoting a conformational change after ATP binding that is associated with hydrolysis
single-stranded DNA
Single-stranded RNA
single-strandede DNA
-
stimulates
-
tRNA
-
stimulates
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
-
additional information
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.000001 - 33
ATP
0.09 - 0.35
GTP
0.000114 - 0.000496
RNA
additional information
additional information
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.043 - 22.2
ATP
0.92 - 3.6
GTP
0.64 - 1.48
RNA
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.7 - 21.43
ATP
2.79 - 22.26
GTP
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.116
2',3'-ddATP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
0.721
2',3'-ddGTP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
0.298
2',3'-ddTTP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
0.6
2',3'-dideoxy-ATP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
0.3
2',3'-dideoxy-GTP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
0.291
2'-dATP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
0.6
2'-deoxy-ATP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
3.4
2'-deoxy-GTP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
1.3
2'-deoxy-L-GTP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
0.097
2'-deoxythymidine 5'-phosphoryl-beta,gamma-hypophosphate
-
i.e. ppopT, dTTP analogue, inhibition of NTPase activity of NS3 protein by NTP derivatives
0.277
2'-dGTP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
0.116
2'-dTTP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
0.4
2'-fluoro-2'-deoxy-ATP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
0.2
2-amino-ATP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
2.4
2-hydroxy-ATP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
0.141
3'-dATP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
0.5
3'-deoxy-ATP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
0.443
3'-dGTP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
0.26
3'-dUTP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
0.6
6-methyl-thio-ITP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
1
7-methyl-GTP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
0.7
8-bromo-ATP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
0.34 - 3
ADP
5
AMP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
0.5
Ara-ATP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
0.3
ATP
-
pH 7.5, 37C, wild-type enzyme
0.007
benzoyl-Nle-Lys-Arg-Arg
-
full-length enzyme in presence of cofactor CF40-Gly4-Ser-Gly4-NS3FL
0.145
beta,gamma-methylene-ATP
-
efficient inhibitor, like the N1-oxides N1-O-ATP and N1-OH-ITP
0.576 - 8.1
GTP
0.9
ITP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
1.5
N1-methyl-ATP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
2.6
N1-methyl-GTP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
0.205
N1-O-ATP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
0.109
N1-OH-ITP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
0.5
N6-methyl-ATP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
2.3
ribavirin triphosphate
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
1.46
UTP
-
inhibition of NTPase activity of NS3 protein by NTP derivatives
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE