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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

Reaction

a nucleoside triphosphate
+
H2O
=
a nucleoside diphosphate
 +
phosphate

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 Hydrolases
         3.6 Acting on acid anhydrides
             3.6.4 Acting on acid anhydrides to facilitate cellular and subcellular movement
                3.6.4.13 RNA helicase

Crystallization

Crystallization on EC 3.6.4.13 - RNA helicase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure analysis of full length helicase-protease apo-enzyme, PDB ID 2JLQ, of helicase core complex with AMPPNP, PDB ID 2JLR, of helicase core complex with ADP, PDB ID 2JLS, of helicase core complex with ssRNA, PDB ID 2JLU, and of helicase core complex with ssRNA and ADP, PDB ID 2JLZ
-
hanging drop vapour diffusion method, crystallization of native enzyme, enzyme in complex with adenylyl imidodiphosphate, enzyme in complex with ADP, enzyme in complex with single-stranded RNA and enzyme in complex with single-stranded RNA and ADP
-
purified catalytic domain fragment, hanging drop vapour diffusion method, 0.002 ml of 10 mg/ml protein in 0.1 M MES, pH 6.5, 0.2 M ammonium sulfate, 14% PEG 8000, mixed with an equal volume of precipitation solution, 18°C, macroseeding, cryoprotection by 25% glycerol, X-ray diffraction structure determination and analysis at 2.4 A resolution, modeling
-
purified recombinant His-tagged catalytic domain of the NS3, hanging drop vapour diffusion method, at 13°C over a well solution containing 0.1M MES, pH 6.5, and 20% PEG 3350, X-ray diffraction structure determination and analysis. Crystals for the AMPPNP complex are obtained by cocrystallization of NS3h at 5 mg/ml with 5 mM MnCl2 and 5 mM AMPPNP using a precipitating solution containing 0.1M MES, pH 6.5, and 10% PEG 3350, at 13°C. Crystals with ADP are obtained by cocrystallization at a concentration of 2.5 mg/ml with 5 mM MnCl2 and 5 mM ADP in 0.1 M Tris-HCl, pH 7.0, and 7.5% PEG 3350 at 23°C, further preparation of ternary complexes,overview
-
structure of CsdA_218-445 is determined by X-ray diffraction and refined to an R factor of 0.225, with an Rfree of 0.268 at a resolution of 2.3 A by molecular replacement using Hera (PDB ID 3EAQ) as the model. The structure of CsdA_218-445 includes two RecA-like domains (RecA2) and two DDs, which form a V-shape dimer. The V-shape conformation of the CsdA_218-445 dimer in solution is further confirmed by SAXS experiments. Conformational flexibilities of CsdA_1-445 and CsdA_FL are revealed by SAXS
crystal structure analysis of NS3, PDB ID 1A1V, of full length helicase-protease apo-enzyme, PDB ID 3O8C, of full length helicase-protease complex with ssRNA, PDB ID 3O8R, of full length helicase-protease complex with a protease inhibitor, PDB ID 4A92, and of helicase core complex with ssRNA, PDB ID 3KQU
-
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
hanging-drop method, crystallization of recombinant DDX3 RNA helicase domain
purified recombinant Brr2-Jab1 complex, for complex 1: yBrr2FL and yJab1 are mixed in a 1:2 molar ratio in 10 mM Tris-HCl, pH 7.5, 150 mM NaCl, 2 mM DTT, and separated by gel filtration and and concentrated to 2 mg/ml, followed by sitting drop vapor diffusion technique, mixing of 0.0013 ml of protein solution with 0.0013 ml of reservoir solution containing 0.1 M Tris-HCl, pH 7.5, 10.5% w/v PEG 3350, and 0.2 M MgCl2, 18°C. For complex 2: yBrr2T2, yJab1 and yNtr2 are mixed in a 1:5:5 molar ratio in 10 mM Tris-HCl, pH 7.5, 150 mM NaCl, 2 mM DTT, and separated by gel filtration and and concentrated to 4 mg/ml, followed by hanging drop vapor diffusion technique, mixing of 0.0005 ml of protein solution with 0.00025 ml of reservoit solution containing 0.1 M MES-NaOH, pH 6.5, 9.2% w/v PEG 4000, 0.4 M MgCl2, and with 0.00025 ml 0.33% w/v 1,5-naphthalenedisulfonic acid, 18°C. X-ray diffraction structure determination and analysis at 3.4-4.2 A resolution, molecular replacement using the yBrr2T4-Jab1 structure coordinates as the search model (PDB ID 4BGD)
purified recombinant Brr2-Jab1 complex, X-ray diffraction structure determination and analysis at 3.4-4.2 A resolution
purified recombinant detagged enzyme in complex with inhibitors 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, 6-benzyl-3-[3-(benzyloxy)phenyl]-4,6-dihydropyrido[4,3-d]pyrimidine-2,7(1H,3H)-dione, and 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, X-ray diffraction structure determination and analysis at 2.75 A, 2.95 A, and 2.80 A resolution, respectivly
purified recombinant enzyme Aquanrius, X-ray diffraction structure determination and analysis at 2.3 A resolution
purified recombinant helicase core of UPF1_1 in its apo-state, X-ray diffraction structure determination and analysis at 3.34 A resolution. Analysis of the X-ray crystal structures of the different states of UPF1_2DELTACH mutant
recombinant catalytic core fragment DHX8DELTA547 bound to ADP and to poly(A)6 single-strand RNA, hanging-drop vapour-diffusion, mixing of 500 nl of protein solution consisting of 3 mg/ml DHX8DELTA547, 1 mM ADP, and 1 mM MgCl2, with 0.00015 ml of reservoir solution comprising 15% v/v 2-methyl-2,4-pentanediol, 100 mM sodium acetate, pH 5.5 and 6% v/v DMSO, and equilibration over 0.25 ml reservoir solution. For the DHX8DELTA547 structure bound to poly(A)6 RNA, a DHX8DELTA547 crystal grown in the presence of ADP is soaked with 1 mM poly(A)6 ssRNA at 4°C for 48 h, X-ray diffraction structure determination and analysis at 2.3-3.2 A resolution, molecular replacement using the structures of RecA1 and RecA2 domains of Saccharomyces cerevisiae Prp43 (PDB ID 2XAU) and of helicase-associated domain of DHX8 (PDB ID 3I4U) as two independent search models
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
crystal structure analysis of helicase core, PDB ID 2Z83
enzymatically active fragment of the JEV NTPase/helicase catalytic domain, recombinant protein, crystal structure determined at 1.8 A resolution, data collection and refinement statistics
crystals of the recombinant C-terminal helicase domain are obtained by the hanging-drop vapour-diffusion method
-
crystal structure analysis of helicase core, PDB ID 2QEQ
crystal structure analysis of helicase core, PDB ID 2WV9
crystal structure analysis, PDB ID 2XGJ
-
purified N-terminally truncated enzyme mutants (FRH-DELTA100 or FRHDELTA114) free or in complex with ADP and/or a single-stranded 13-nucleotide RNA in several conformations, X-ray diffraction structure determination and analysis st 3.1-3.8 A resolution
crystallization is carried out at 20°C by hanging-drop vapor diffusion. The crystal structure of the enzyme has been solved at a resolution of 3.5 A using single wavelength anomalous dispersion and selenomethionyl-substituted protein. Structural comparison reveals a unique arrangement of domains, a feature implicated in the specific function of the Ski2p-like RNA helicase in 3' to 5' mRNA degradation
crystal structure analysis
crystal structure analysis, PDB ID 2XGJ
crystal structure analysis, PDB ID 4LJY
purified recombinant N-terminal RecA-like domain 1 of DEAD-box RNA helicase CshA free and in complex with AMP or AMP-PNP, sitting drop vapor diffusion method, mixing of 0.001 ml of 5 mg/ml protein in 50 mM Tris-HCl, pH 7.5, 500 mM NaCl, with AMP or AMP-PNP in a molar ratio of 1:5 for the complexes, is mixed with 0.001 ml of reservoir solution containing 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 30% v/v PEG 4000, at 16°C, X-ray diffraction structure determination and analysis at 1.5 and 1.8 A resolution, respectively, molecular replacement modelling
enzyme in complex with ADP, using 200 mM NaCl, 20% (w/v) PEG 4000, 100 mM Tris pH 8.0
Thermochaetoides thermophila
purified recombinant Brr2-Jab1 complex, X-ray diffraction structure determination and analysis at 3.2 A resolution
Thermochaetoides thermophila
purified recombinant Prp43 with bound RNA in an active state, i.e. ctPrp43DELTAN-U7-ADP-BeF3-, ctPrp43DELTAN-ADP-BeF3-(HR), and ctPrp43DELTAN-ADP-BeF3-(LR), X-ray diffraction structure determination and analysis at 1.78-3.24 A resolution
Thermochaetoides thermophila
RNA helicase Hera C-terminal domain, vapour diffusion, microbatch under oil
-
crystal structure analysis of helicase core, PDB ID 1YKS, and of helicase core complex with ADP, PDB ID 1YMF
-
hanging-drop vapor diffusion method, the 1.8 A crystal structure of the helicase region of the YFV NS3 protein (includes residues 187 to 623) and the 2.5 A structure of its complex with ADP