Information on EC 3.6.4.13 - RNA helicase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY
3.6.4.13
-
RECOMMENDED NAME
GeneOntology No.
RNA helicase
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
a nucleoside triphosphate + H2O = a nucleoside diphosphate + phosphate
show the reaction diagram
-
-
-
-
a nucleoside triphosphate + H2O = a nucleoside diphosphate + phosphate
show the reaction diagram
catalytic mechanism involving a bound sulfate ion, NTPase active site structure, nucleic acid binding site
-
ATP + H2O = ADP + phosphate
show the reaction diagram
-
-
-
-
ATP + H2O = ADP + phosphate
show the reaction diagram
models: DbpA functions as an active monomer that possesses two distinct RNA binding sites, one in the helicase core domain and the other in the carboxyl-terminal domain that recognizes 23 S rRNA and interacts specifically with hairpin 92 of the peptidyl transferase center
-
ATP + H2O = ADP + phosphate
show the reaction diagram
quantitative kinetic and equilibrium characterization of the rRNA-activated ATPase cycle mechanism of DbpA
-
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).
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
1a NTPase/helicase
-
-
ATP/dATP-dependent RNA helicase
-, EF409381
-
ATPase
-
-
ATPase/helicase
-
-
ATPase/helicase
Dengue virus PL046
-
-
-
ATPase/RNA helicase
-, EF409381
-
BmL3-helicase
-, EF409381
-
BMV 1a protein
-
-
Brr2p
-
-
Cbu_0670
Q83DM8
-
CrhR
Synechocystis sp. PCC6803
-
-
-
DBP2
O60231
-
DDX17
Q501J6
-
DDX19
Q9UMR2
-
DDX25
Q9UHL0
-
DDX25
Q9QY15
-
DDX25
Q9QY16
-
DDX3
-
-
DDX3
O00571
-
DDX3X
O00571
the gene is localized to the X chromosome
DDX3Y
O15523
the gene is localized to the Y chromosome
DDX4
Q9NQI0
-
DDX5
P17844
-
DDX5
Q61656
-
DEAD box helicase
-
-
DEAD box RNA helicase
-
-
DEAD box RNA helicase
-
-
DEAD box RNA helicase
-
-
DEAD-box protein DED1
P06634
-
DEAD-box RNA helicase
-
-
DEAD-box RNA helicase
-
-
DEAD-box RNA helicase
P06634
-
DEAD-box RNA helicase
B9VSG1
-
DEAD-box RNA helicase
-
-
DEAD-box RNA helicase
Q7ZX48
-
DEAD-box rRNA helicase
-
-
DEAH-box protein 2
O60231
-
DEAH-box RNA helicase
O60231
-
DENV NS3H
-
-
DENV NS3H
Dengue virus PL046
-
-
-
DEx(H/D)RNA helicase
-
-
DEXD/H-box RNA helicase
Q9UMR2
-
DExH protein RNA helicase A
-
-
DHX36
-
-
DHX9
Q08211
-
Dhx9/RNA helicase A
-
-
EhDEAD1 RNA helicase
-
-
eIF4A
P29562
-
eIF4A helicase
P29562
-
eIF4AIII
P38919
-
eukaryotic initiation factor eIF 4A
P29562
-
FRH
Neurospora sp.
-
-
FRQ-interacting RNA helicase
Neurospora sp.
-
-
gonadotropin-regulated testicular RNA helicase
-
-
GRTH
-
-
GRTH/DDX25
Q9UHL0
-
GRTH/DDX25
-
-
HCV NS3 helicase
-
-
helicase
-
-
helicase
Dengue virus PL046
-
-
-
helicase B
-
-
helicase/nucleoside triphosphatase
-
-
KOKV helicase
-
-
non structural protein 3
-
ambiguous
non-structural 3
-
-
non-structural protein 3
-
-
non-structural protein 3 protein
-
-
non-structural protein 3 protein
Rice hoja blanca virus RHBV
-
-
-
nonstructural protein 3
Q9YS30
-
nonstructural protein 3
Classical swine fever virus CSFV
Q9YS30
-
-
nonstructural protein 3
-
-
nonstructural protein 3
-
-
nonstructural protein 3
-
; ambiguous
nonstructural protein 3
-
ambiguous
nonstructural protein 3
Q9WPH5
ambiguous
nonstructural protein 3
P27395
ambiguous
nonstructural protein 3
-
ambiguous
NS3
Classical swine fever virus CSFV
Q9YS30
-
-
NS3
-
ambiguous
NS3
Q9WPH5
ambiguous
NS3
West Nile virus WNV
-
-
-
NS3 ATPase/helicase
-
-
NS3 ATPase/helicase
Dengue virus PL046
-
-
-
NS3 helicase
-
-
NS3 helicase
-
-
NS3 helicase
-
-
NS3 NTPase/helicase
-
; ambiguous
NS3 NTPase/helicase
West Nile virus WNV
-
; ambiguous
-
NS3 protein
-
-
NS3 protein
Dengue virus PL046
-
-
-
NS3 protein
-
ambiguous
NS3 protein
-
-
NS3 protein
Rice hoja blanca virus RHBV
-
-
-
NS3 protein
-
-
NTPase/helicase
-
-
NTPase/helicase
-
ambiguous
nucleoside 5'-triphosphatase
-
-
nucleoside triphosphatase/helicase
-
-
nucleoside triphosphatase/RNA helicase and 5'-RNA triphosphatase
-
-
p54 RNA helicase
P26196
-
p68 RNA helicase
-
-
p68 RNA helicase
-
-
protein NS3
-
ambiguous
RNA DEAD-box helicase
Q83DM8
-
RNA helicase
-
-
RNA helicase A
-
-
RNA helicase A
Q08211
-
RNA helicase CrhR
-
-
RNA helicase DDX3
O00571
-
RNA helicase Ddx39
Q7ZX48
-
RNA helicase Hera
-
-
RNA Helicase p68
P17844
-
RNA helicase RHAU
-
-
RNA-dependent ATPase
P38919
-
RNA-dependent NTPase/helicase
-
-
RTPase
-
-
slr0083
-
gene name
SpolvlgA
B9VSG1
-
Supv3L1
Q80YD1
-
TGBp1 NTPase/helicase domain
-
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
i.e. BMV
-
-
Manually annotated by BRENDA team
-
EF409381
GenBank
Manually annotated by BRENDA team
Classical swine fever virus CSFV
CSFV
SwissProt
Manually annotated by BRENDA team
; serotype 2, PL046 strain
-
-
Manually annotated by BRENDA team
; serotype 4
-
-
Manually annotated by BRENDA team
i.e. DNV
-
-
Manually annotated by BRENDA team
i.e. DEN2
-
-
Manually annotated by BRENDA team
Dengue virus PL046
serotype 2, PL046 strain
-
-
Manually annotated by BRENDA team
i.e. HCV
-
-
Manually annotated by BRENDA team
recombinant HCV helicase constructs, nonstructural protein 3
-
-
Manually annotated by BRENDA team
subtype 1b
SwissProt
Manually annotated by BRENDA team
viral genotype 1a, version H77
-
-
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
transgenic
-
-
Manually annotated by BRENDA team
Neurospora sp.
-
-
-
Manually annotated by BRENDA team
Rice hoja blanca virus RHBV
RHBV
-
-
Manually annotated by BRENDA team
Synechocystis sp. PCC6803
-
-
-
Manually annotated by BRENDA team
West Nile virus WNV
WNV
-
-
Manually annotated by BRENDA team
kcat/KM VALUE [1/mMs-1]
kcat/KM VALUE [1/mMs-1] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
1.7
-
ATP
-
pH 7.5, 37C, mutant enzyme E180A
22040
2.3
-
ATP
-
pH 7.5, 37C, mutant enzyme K187A
22040
3.22
-
ATP
-
pH 7.5, 37C, mutant enzyme D172A
22040
4.6
-
ATP
-
pH 7.5, 37C, mutant enzyme E173A
22040
5
-
ATP
-
pH 7.5, 37C, mutant enzyme R170A
22040
5.2
-
ATP
-
pH 7.5, 37C, mutant enzyme Q188A
22040
5.68
-
ATP
-
pH 7.5, 37C, mutant enzyme E169A
22040
6.7
-
ATP
-
pH 7.5, 37C, mutant enzyme F179A
22040
6.9
-
ATP
-
pH 7.5, 37C, mutant enzyme K186A
22040
12.2
-
ATP
-
pH 7.5, 37C, mutant enzyme E182A
22040
21.43
-
ATP
-
pH 7.5, 37C, wild-type enzyme
22040
2.79
-
GTP
-
pH 7.5, 37C, mutant enzyme D172A
11186
4.8
-
GTP
-
pH 7.5, 37C, mutant enzyme E180A
11186
5.38
-
GTP
-
pH 7.5, 37C, mutant enzyme E169A
11186
5.9
-
GTP
-
pH 7.5, 37C, mutant enzyme Q188A
11186
6.3
-
GTP
-
pH 7.5, 37C, mutant enzyme R170A
11186
10
-
GTP
-
pH 7.5, 37C, mutant enzyme E173A
11186
11
-
GTP
-
pH 7.5, 37C, mutant enzyme K187A
11186
12
-
GTP
-
pH 7.5, 37C, mutant enzyme F179A
11186
15.7
-
GTP
-
pH 7.5, 37C, mutant enzyme E182A
11186
17
-
GTP
-
pH 7.5, 37C, mutant enzyme K186A
11186
22.26
-
GTP
-
pH 7.5, 37C, wild-type enzyme
11186
IC50 VALUE [mM]
IC50 VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.8
-
2',3'-dideoxy-ATP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
0.5
-
2',3'-dideoxy-GTP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
0.9
-
2'-Deoxy-ATP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
1.8
-
2'-deoxy-L-GTP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
-
0.5
-
2'-fluoro-2'-deoxy-ATP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
-
0.3
-
2-amino-ATP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
3.3
-
2-hydroxy-ATP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
-
0.7
-
3'-deoxy-ATP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
0.8
-
6-methyl-thio-ITP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
-
2.7
-
6-thio-GTP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
1.4
-
7-methyl-GTP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
0.9
-
8-bromo-ATP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
0.7
-
Ara-ATP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
0.4
-
ATP
-
pH 7.5, 37C, wild-type enzyme
0.13
-
Cu2+
-
inhibits ATPase activity, IC50: 0.13 mM
0.75
-
Fe2+
-
inhibits ATPase activity, IC50: 0.75 mM
-
11
-
GTP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
0.000049
-
Hg2+
-
inhibits ATPase activity, IC50: 49 nM, targets the cysteine residue in the DECH box, competitive, cysteine or DTT protect at large concentrations
2
-
N1-methyl-ATP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
3.5
-
N1-methyl-GTP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
-
0.7
-
N6-methyl-ATP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
0.000088
-
PCMB
-
inhibits ATPase activity, IC50: 88 nM
3.1
-
ribavirin triphosphate
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
0.06
-
tetrabromobenzotriazole
-
-
1.2
-
ITP
-
pH 7.5, 37C, wild-type enzyme, inhibition of the ATPase reaction
additional information
-
additional information
-
sequences of NTPase/helicase motifs VI derived peptides and their deleted derivatives analyzed, NTPase activity not affected
-
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
0.00000001
-
-
about, wild-type enzyme, RNA helicase activity
additional information
-
-
specificities and activities of wild-type and mutant enzymes
additional information
-
-
RNA replication, RNA protection, spherule formation size, relative ATPase activity, RNA accumulation and stabilization, of wild-type and mutant enzymes, overview
additional information
-
P27395
structural characterization of catalytic domain, mutation analysis of residue substitution in the Walker A motif (Gly199, Lys200 and Thr201), within the NTP-binding pocket (Gln457, Arg461 and Arg464) and of Arg458 in the outside of the pocket in the motif IV, residues crucial for ATPase and RNA helicase activities and virus replication, Lys200 cannot be substituted by other residues to establish sufficient activities, structure of the NTP-binding pocket well conserved among the viruses of the Flaviviridae
additional information
-
-
helicase capable of unwinding duplex RNA or DNA, ambiguous
additional information
-
-
overview of sequences of NTPase/helicase motifs VI derived peptides and their deleted derivatives, kinetic analyses reveals that binding of the peptides do not interfere with the NTPase activity, peptides do not interact with the ATP binding site
additional information
-
-
structure of nucleic base and ribose fragment of NTP molecule has a slight effect on inhibitory properties
additional information
-
P27958
surface of domain 2 of the NS3 NTPase/helicase in direct vicinity to a flexible loop that is localized between Val1458 and Thr1476, accessibility of the Arg-rich amino acid motif by this loop for protein kinase C inhibition analyzed, two variants of domain 2 generated, in vitro protein kinase C (PKC) phosphorylation studies, binding and competition assays, modelling of ribbon diagrams, presence of the intact loop abolishes the binding of domain 2 to a tailed duplex RNA, binding of dsDNA not affected, loop structure reduces the extent of inhibition of protein kinase C (PKC) by domain 2 and regulates the binding of dsRNA, various mechanisms by which the NS3 protein perturb signal transduction in infected cells
additional information
-
-
biochemical properties and enzymatic activity of the RNA-helicase domain, functional characterization to get information about the flavivirus replication mechanism, NTPase-deficient mutant generated, RNA binding features, electrostatic interaction with RNA, basal ATPase activity insensitive to high ionic strength
additional information
-
-
the nonstructural protein 4A (NS4A) stimulates NS3 serine protease activity, truncated and full-length complexes between nonstructural protein 3 (NS3) and nonstructural protein 4A (NS4) purified, serine protease activities analyzed, NS3 protease domain enhances the RNA binding, ATPase, and RNA unwinding activities of the C-terminal NS3 helicase domain, isolated protease domain is much less reactive than full-length NS3, NS3 protease activity is enhanced by the presence of the NS3 helicase domain, indicating that the two domains have evolved to become completely interdependent
additional information
-
Q9WPH5
the nonstructural protein 4A (NS4A) enhances the ability of the N-terminal domain of NS3 protein to bind RNA in the presence of ATP, stimulates helicase activity, interaction between nonstructural protein 3 (NS3) and nonstructural protein 4A (NS4) mediated by amino acids of the C-terminus of NS4, mutation of the C-terminus of NS4 reduces ATP-coupled RNA binding, RNA binding studies, RNA-stimulated ATPase activity of N3-4a variants
additional information
-
-
structural characterization of the C-terminal portion containing the ATPase/helicase domain, encompasses residues 181-619, monomer structure determined by analytical centrifugation and gel filtration, SDS-PAGE and immunoblotting, structure determined by circular dichroism and fluorescence spectroscopy, ATPase activity stimulated by RNA and ssDNA, no RNA helicase activity at protein concentrations up to 500 nM, linker region between the protease and the helicase domains predicted as a prerequisite for protein-protein interactions leading to the formation of the active oligomer
additional information
-
-
development of continuous fluorescence assay based on fluorescence resonance energy transfer for the monitoring of RNA helicase activity in vitro. This assay will be useful for monitoring the detailed kinetics of RNA unwinding mechanisms and screening RNA helicase inhibitors at high throughput
pH RANGE
pH RANGE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
6
9
-
activity range, ATPase activity
6.5
-
-, Q9YS30
pH 6.5: about 50% of maximal activity, pH 8: about 80% of maximal activity
TEMPERATURE RANGE
TEMPERATURE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
40
50
-
40C: about 40% of maximal activity, 50C: optimum, 60C: less than 10% of maximal activity
PDB
SCOP
CATH
ORGANISM
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Escherichia coli (strain K12)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Reovirus type 1 (strain Lang)
Reovirus type 3 (strain Dearing)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)
Vaccinia virus (strain Western Reserve)
TEMPERATURE STABILITY
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
20
70
-
the enzyme starts to unfold at 20C and fully unfolds at 70C