3.6.4.13: RNA helicase
This is an abbreviated version!
For detailed information about RNA helicase, go to the full flat file.
Word Map on EC 3.6.4.13
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3.6.4.13
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single-stranded
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strand
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viruses
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duplex
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fork
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retinoic
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nucleic
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chromatin
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acid-inducible
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mda5
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dsrnas
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ssdna
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rna-binding
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stall
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werner
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nonstructural
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bloom
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polyproteins
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dna-dependent
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primase
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exonuclease
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replisome
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spliceosome
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hexameric
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minichromosome
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differentiation-associated
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dengue
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g-quadruplexes
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eif4g
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single-molecule
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unwound
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replicase
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restart
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ifn-stimulated
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nonsense-mediated
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rpa
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rad51
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holliday
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polyi:c
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flavivirus
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tfiih
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exoribonuclease
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ifn-beta
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d-loops
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pigmentosum
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cap-dependent
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xeroderma
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positive-stranded
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pre-rrnas
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overhang
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pharmacology
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medicine
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drug development
- 3.6.4.13
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single-stranded
- strand
- viruses
- duplex
- fork
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retinoic
- nucleic
- chromatin
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acid-inducible
- mda5
- dsrnas
- ssdna
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rna-binding
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stall
-
werner
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nonstructural
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bloom
- polyproteins
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dna-dependent
- primase
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exonuclease
- replisome
-
spliceosome
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hexameric
-
minichromosome
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differentiation-associated
- dengue
-
g-quadruplexes
- eif4g
-
single-molecule
-
unwound
-
replicase
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restart
-
ifn-stimulated
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nonsense-mediated
- rpa
- rad51
-
holliday
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polyi:c
- flavivirus
- tfiih
- exoribonuclease
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ifn-beta
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d-loops
- pigmentosum
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cap-dependent
- xeroderma
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positive-stranded
- pre-rrnas
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overhang
- pharmacology
- medicine
- drug development
Reaction
Synonyms
1a NTPase/helicase, Aquarius, AtHELPS, ATP-dependent helicase, ATP-dependent RNA helicase, ATP-dependent RNA helicase DDX3X, ATP-dependent RNA helicase DDX5, ATP/dATP-dependent RNA helicase, ATPase, ATPase/helicase, ATPase/RNA helicase, AtRH3, AtRH7, bel, BmL3-helicase, BMV 1a protein, BRR2, Brr2 RNA helicase, Brr2p, Cbu_0670, ChlR1 helicase, cold-shock DEAD-box protein A, CrhR, CsdA, CshA, CTHT_0005780, CTHT_0009470, DBP2, DbpA, DDX17, DDX19, DDX19B, DDX21, DDX21 RNA helicase, DDX25, DDX27, DDX3, DDX3X, DDX3Y, DDX4, DDX5, DDX58, DeaD, DEAD box helicase, DEAD box RNA helicase, DEAD-box ATP-dependent RNA helicase CshA, DEAD-box helicase, DEAD-box protein DED1, DEAD-box RNA helicase, DEAD-box rRNA helicase, DEAH box protein 34, DEAH-box protein 2, DEAH-box RNA helicase, DEAH/RHA RNA helicase, DED1, DENV NS3H, DEx(H/D)RNA helicase, DExD/H box RNA helicase, DEXD/H-box RNA helicase, dexh helicase, DExH protein RNA helicase A, DExH/D-Box protein RNA helicase A, DExH/D-box RNA helicase, DHX34, DHX36, DHX8, DHX9, Dhx9/RNA helicase A, DNA/RNA-dependent ATPase, EhDEAD1, EhDEAD1 RNA helicase, eIF4A, eIF4A helicase, eIF4AIII, eukaryotic initiation factor eIF 4A, frequency-interacting RNA helicase, FRH, FRQ-interacting RNA helicase, gonadotropin-regulated testicular RNA helicase, GRTH, GRTH/DDX25, HCV NS3 helicase, HEL-1, helicase, helicase 1, helicase B, helicase/nucleoside triphosphatase, HRpA, IBP160, increased size exclusion limit2, intron-binding protein 160, ISE2, KOKV helicase, Lmo1722, mitochondrial DEAD-box RNA helicase, Mss116p, mtr4, Mtr4p, NA-helicase, non structural protein 3, non-structural 3, non-structural protein 3, non-structural protein 3 protein, nonstructural protein 3, NPH-II, NS3, NS3 ATPase/helicase, NS3 helicase, NS3 NTPase/helicase, NS3 protein, NTPase/helicase, nucleoside 5'-triphosphatase, nucleoside triphosphatase/helicase, nucleoside triphosphatase/RNA helicase and 5'-RNA triphosphatase, NWMN_1985, p54 RNA helicase, p68, p68 RNA helicase, P72, PH1280, pre-mRNA-splicing ATP-dependent RNA helicase 28, protein NS3, Prp28, Prp43, Prp5, RENT1, RH22, RHA, RhlB, RIG-I, Rm62, RNA DEAD-box helicase, RNA helicase, RNA helicase A, RNA helicase Aquarius, RNA helicase BELLE, RNA helicase CrhR, RNA helicase CsdA, RNA helicase CshA, RNA helicase DDX17, RNA helicase DDX27, RNA helicase DDX3, RNA helicase Ddx39, RNA helicase DDX3X, RNA helicase DDX5, RNA helicase DDX6, RNA helicase DeaD, RNA helicase DHX34, RNA helicase DHX8, RNA helicase DHX9, RNA helicase HEL-1, RNA helicase Hera, RNA helicase ISE2, RNA Helicase p68, RNA helicase RHAU, RNA helicase UPF1, RNA splicing effector, RNA-dependent ATPase, RNA-dependent NTPase/helicase, RNA-helicase, RTPase, SA1885, Ski2-like helicase, slr0083, SNRNP200, spliceosomal DEAH-box RNA helicase, spliceosomal RNA helicase, SpolvlgA, Supv3L1, TaRH1, TGBp1 NTPase/helicase domain, Tk-DeaD, Triticum aestivum RNA helicase, Upf1, UPF1_1, UPF1_2, Vasa, VRH1, YxiN, ZmRH3, ZmRH3A, ZmRH3B
ECTree
3.6.4.13 RNA helicaseAdvanced search results
results (
results (Inhibitors
Inhibitors on EC 3.6.4.13 - RNA helicase
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INHIBITOR 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
IMAGE
(6Z)-6-[[5-(3-chlorophenyl)furan-2-yl]methylidene]-5-imino-2-propyl-5,6-dihydro-7H-[1,3,4]thiadiazolo[3,2-a]pyrimidin-7-one
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2'-deoxythymidine 5'-phosphoryl-beta,gamma-hypophosphate
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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
3-[5-[(Z)-(2-cyclohexyl-5-imino-7-oxo-5H-[1,3,4]thiadiazolo[3,2-a]pyrimidin-6(7H)-ylidene)methyl]furan-2-yl]benzoic acid
binds an RNA-binding site inside the N-terminal cassette, mechanism of action, enzyme binding structure, overview
3-[5-[(Z)-(5-imino-7-oxo-2-propyl-5H-[1,3,4]thiadiazolo[3,2-a]pyrimidin-6(7H)-ylidene)methyl]furan-2-yl]benzoic acid
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4-(3,5-dimethoxyphenyl)-N-(7-fluoro-3-methoxyquinoxalin-2-yl)piperazine-1-carboxamide
i.e. supinoxin or RX-5902, intervenes in the phosphorylated p68-beta-catenin signaling pathway by interacting with Tyr593 in SK-MEL-28 (human melanoma), MDA-MB-231 (human metastatic breast cancer), and WI-38 (human normal fetal lung fibroblasts) cell lines
6-benzyl-3-[(2R)-2-(3-fluoropyridin-2-yl)-6-methyl-3,4-dihydro-2H-1-benzopyran-7-yl]-4,6-dihydropyrido[4,3-d]pyrimidine-2,7(1H,3H)-dione
binds to an unexpected allosteric site between the C-terminal and the N-terminal helicase cassettes, enzyme binding structure, overview
6-benzyl-3-[3-(benzyloxy)phenyl]-4,6-dihydropyrido[4,3-d]pyrimidine-2,7(1H,3H)-dione
enzyme binding structure, overview
AMP-PNP
structure of Aquarius in complex with AMP-PNP, modelling, overview
ATP-gamma-S
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5.4 mM, about 50% of the original helicase activity is inhibited, competitive inhibitor
benzoyl-Nle-Lys-Arg-Arg
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competitive inhibition, structure-activity relationship
beta,gamma-methylene-ATP
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efficient inhibitor, like the N1-oxides N1-O-ATP and N1-OH-ITP
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
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Hg2+
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inhibits ATPase activity, IC50: 49 nM, targets the cysteine residue in the DECH box, competitive, cysteine or DTT protect at large concentrations
Imidodiphosphate
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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
poly(X) RNA
DHX8 is an RNA-specific helicase by showing that a poly(dA)10 DNA strand cannot displace Cy5-poly(A)10 from DHX8 in the presence of ADP-AlFx. The displacement of the probe with poly(A)10, poly(C)10, poly(G)10 and poly(U)10 RNA indicates that DHX8 has a preference for binding adenine-rich sequences as the rank ascending order of IC50 values is poly (A)10, poly(U)10, poly(C)10, poly(G)10
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ADP
the affinity for RNA is over 90fold weaker in the absence of nucleotide and in the presence of ADP, the RNA affinity is too weak to determine. These results indicate that DHX8-mediated disruption of RNA interactions occurs through a series of alternating strong and weak RNA binding events controlled by ATP hydrolysis. Both full-length fl-DHX8 and truncated DHX8DELAT547 preferentially bind the purine nucleotides ADP and GDP, but are also able to bind CDP, TDP and UDP. RNA binding triggers DEAH and P-loop movement and stimulates ADP release
KCl
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RNA-dependent ATPase activity is sensitive to high salt concentrations. Maximal activity is obtained in the absence of KCl, and it is inhibited 50% at 0.1 M KC1, completely inhibited at 0.3 M KCl
Prp8 protein
the Jab1 domain of the Prp8 proten can inhibit Brr2 by intermittently inserting a C-terminal tail in the enzyme's RNA-binding tunnel or activate the helicase after removal of this tail. Binding of the Prp8 Jab1 C-terminal tail at the Brr2 RNA binding tunnel is evolutionarily conserved, Brr2-Jab1 binding structure and analysis, overview. Jab1-based inhibition of Brr2 presumably takes effect in all eukaryotes but is implemented via organism-specific molecular contacts. Brr2 autoinhibition can act in concert with Jab1-mediated inhibition. The NTR and the Jab1 tail cooperate in inhibiting RNA binding by Brr2; the Jab1 domain of the Prp8 proten can inhibit Brr2 by intermittently inserting a C-terminal tail in the enzyme's RNA-binding tunnel or activate the helicase after removal of this tail. Binding of the Prp8 Jab1 C-terminal tail at the Brr2 RNA binding tunnel is evolutionarily conserved, Brr2-Jab1 binding structure and analysis, overview. Jab1-based inhibition of Brr2 presumably takes effect in all eukaryotes but is implemented via organism-specific molecular contacts. Brr2 autoinhibition can act in concert with Jab1-mediated inhibition.The NTR and the Jab1 tail cooperate in inhibiting RNA binding by Brr2
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Prp8 protein
Thermochaetoides thermophila
the Jab1 domain of the Prp8 proten can inhibit Brr2 by intermittently inserting a C-terminal tail in the enzyme's RNA-binding tunnel or activate the helicase after removal of this tail. Binding of the Prp8 Jab1 C-terminal tail at the Brr2 RNA binding tunnel is evolutionarily conserved, Brr2-Jab1 binding structure and analysis, overview. Jab1-based inhibition of Brr2 presumably takes effect in all eukaryotes but is implemented via organism-specific molecular contacts. Brr2 autoinhibition can act in concert with Jab1-mediated inhibition.The NTR and the Jab1 tail cooperate in inhibiting RNA binding by Brr2
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additional information
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no or poor inhibition by Mn2+, Zn2+, Co2+, Ca2+, and Ni2+
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additional information
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inhibitory potential of sequences of NTPase/helicase motifs VI derived peptides and their deleted derivatives analyzed, NTP-binding and hydrolyzing site not involved
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additional information
domain 2 of wild-type NS3 protein and domain 2 devoid of the loop structure used for inhibition studies on functions of protein kinase C (PKC), inhibitory potential towards the majority of protein kinase C isoforms shown
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additional information
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domain 2 of wild-type NS3 protein and domain 2 devoid of the loop structure used for inhibition studies on functions of protein kinase C (PKC), inhibitory potential towards the majority of protein kinase C isoforms shown
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additional information
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several extracts of marine organisms exhibit different inhibitory effects on the RNA and DNA helicase activities of HCV NS3
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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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additional information
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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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additional information
Brr2 can be autoinhibited via a large N-terminal region folding back onto its helicase core and autoactivated by a catalytically inactive C-terminal helicase cassette
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additional information
selectivity profiling indicated the allosteric inhibitor 6-benzyl-3-[(2R)-2-(3-fluoropyridin-2-yl)-6-methyl-3,4-dihydro-2H-1-benzopyran-7-yl]-4,6-dihydropyrido[4,3-d]pyrimidine-2,7(1H,3H)-dione is more Brr2-selective than the RNA site binder 3-[5-[(Z)-(2-cyclohexyl-5-imino-7-oxo-5H-[1,3,4]thiadiazolo[3,2-a]pyrimidin-6(7H)-ylidene)methyl]furan-2-yl]benzoic acid
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additional information
Comparison of the ATPase activities of UPF1_1 and UPF1_2 shows that a longer regulatory loop does not inhibit the catalytic activity of the helicase. In fact, UPF1_1 shows a marginally higher ATPase activity than UPF1_2. ATP-dependent helicase assays with UPF11 and UPF12 also show that the unwinding activity of UPF1 is not inhibited by a longer regulatory loop
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additional information
Thermochaetoides thermophila
Brr2 can be autoinhibited via a large N-terminal region folding back onto its helicase core and autoactivated by a catalytically inactive C-terminal helicase cassette. Effects of NTR truncations on Chaetomium thermophilum Brr2NC variants. Binding of N-terminal Brr2NC truncations to U4/U6 di-snRNA monitored by electrophoretic mobility shift assays and time courses of U4/U6 unwinding by Brr2NC variants, overview
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