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2.7.7.48: RNA-directed RNA polymerase

This is an abbreviated version!
For detailed information about RNA-directed RNA polymerase, go to the full flat file.

Word Map on EC 2.7.7.48

Reaction

nucleoside triphosphate
+
RNAn
=
diphosphate
+
RNAn+1

Synonyms

111 kDa protein, 180 kDa protein, 182 kDa protein, 183 kDa protein, 186 kDa protein, 216.5 kDa protein, 2A protein, 3CD protein, 3D pol, 3D polymerase, 3Dpol, 3Dpol-like protein, 3P complex, 69.6 kDa protein, core protein, core protein VP1, CVB3 RdRp, D-elp1, DENV 3 polymerase, DENV 3 RdRp, DENV RdRp, ego-1, ego-11, FluPol, FMDV 3D, GhRdRP, HC-J4 NS5BDELTA21, HCN NS5B protein, HCV NS5B, HCV NS5B polymerase, HCV RdRp, hepatitis C virus polymerase, HRV16 3Dpol, influenza polymerase PA, inner layer protein VP1, JEV NS5, JEV NS5 protein, JEV RdRp, jRdRp, L protein, L/P RdRP, large structural protein, M1 phosphoprotein, MOP1, More, NgRDR1, NIB, nonstructural phosphoprotein, nonstructural protein, nonstructural protein 12, nonstructural protein 5B, NS5, NS5 polymerase, NS5 protein, NS5 RdRp, NS5B, NS5B enzyme, NS5B polymerase, NS5B protein, NS5B RdRp, NS5B RNA-dependent RNA polymerase, NS5b-directed RNA polymerase, NS7, nsp12, nsp4, nucleocapsid phosphoprotein, nucleotidyltransferase, ribonucleate, RNA-dependent, ORF1, ORF1A, ORF1B, OsRDR6, P protein, P180, P3D, P66, P70, P88 protein, p92, PB1, PB1 proteins, PB2, PB2 proteins, Phage f2 replicase, phi6, phi6 polymerase, picornaviral 3D polymerase, plant-encoded RNA-dependent RNA polymerase 1, Pol, Pol IV, polymerase 3Dpol, polymerase acidic protein, polymerase basic 1 protein, polymerase L, protein 3Dpol, proteins PB1, proteins, PB 2, proteins, specific or class, lambda3, of reovirus, proteins, specific or class, PB 1, proteins, specific or class, PB 2, Q-beta replicase, Qbeta replicase, Qbeta-replicase, RDR, RDR1, RDR1a, RDR1b, RDR1c, RDR1c2, RDR2, RDR6, RDRP, replicase, phage f2, replicase, Qbeta, ribonucleic acid replicase, ribonucleic acid-dependent ribonucleate nucleotidyltransferase, ribonucleic acid-dependent ribonucleic acid polymerase, ribonucleic replicase, ribonucleic synthetase, RNA dependent RNA polymerase, RNA nucleotidyltransferase (RNA-directed), RNA polymerase, RNA polymerase IV, RNA replicase, RNA synthetase, RNA transcriptase, RNA-binding protein, RNA-dependent ribonucleate nucleotidyltransferase, RNA-dependent RNA polymerase, RNA-dependent RNA polymerase 1, RNA-Dependent RNA Polymerase 2, RNA-dependent RNA polymerase 6, RNA-dependent RNA polymerase NIb, RNA-dependent RNA polymerase NS5B, RNA-dependent RNA polymerases, RNA-dependent RNA replicase, RNA-dependent RNA-polymerase, RNA-directed RNA polymerase, RNA-directed RNA polymerase L, RNAdependent RNA polymerase, rrf-1, RRF-3, RrpC, RSV RdRp, SARS-CoV-2 RdRp, SARS-CoV-2 RNA polymerase, SARSCoV-2 polymerase, SARSCoV-2-core polymerase complex, self-priming RdRp, sigma NS protein, transcriptase, VP1, VP1 protein, WNV NS5

ECTree

     2 Transferases
         2.7 Transferring phosphorus-containing groups
             2.7.7 Nucleotidyltransferases
                2.7.7.48 RNA-directed RNA polymerase

Crystallization

Crystallization on EC 2.7.7.48 - RNA-directed RNA polymerase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
vapour-diffusion with sitting drops, structure of a truncated enzyme form (residues 71-679 with a C-terminal His tag), structure of a truncated enzyme form (residues 71-679 with a C-terminal His tag) complexed with GTP, determined at 2.9 A resolution
crystallization using a nanolitre-drop crystallization robot, 2.1 A resolution
-
in complex with its protein primer VPg and diphosphate, hanging drop vapour diffusion method, in 20 mM Tris (pH 9.0), 300 mM NaCl, 15% glycerol, 0.5 mM Tris(2-carboxyethyl)phosphine
-
nanolitre-drop crystallization, with 2.0 M (NH4)2SO4, 100 mM CAPS pH 10.5, 200 mM Li2SO4
-
-
Cystovirus phi6
-
cocrystallization of RNA oligonucleotides with the polymerase
Cystovirus phi6
hanging drop vapour diffusion method, using 0.1 M Tris-HCl at pH 8.5, 0.8 M potassium-sodium tartrate, 0.5% (w/v) PEG monomethyl ether 5000
Q6DLV0
hanging drop vapour diffusion method, with 0.1 M Tris-HCl pH 8.5, 0.8 M potassium/sodium tartrate, and 0.5% (w/v) PEG monomethyl ether 5000
-
hanging-drop vapor diffusion method at 4°C, three-dimensional structure of a catalytically active DENV RdRp domain determined to 1.85 A resolution by X-ray crystallography
Q6DLV0
native and in complex with inhibitor 5-[[(4-chlorophenyl)sulfonyl]amino]-2-methyl-1-benzofuran-3-carboxylic acid, to 1.79 and 2.1 A resolution, respectively. The inhibitor binds to the protein as a dimer and causes conformational changes in the protein
Q6DLV0
purified enzyme in complex with NTP substrate, X-ray diffraction structure determination and analysis at 2.45-2.78 A resolution, analysis of multiple nucleotide-incorporation events and different NAC states
-
crystal structure of poliovirus 3CD protein, a virally encoded protease and precursor to the RNA-dependent RNA polymerase
-
hanging drop vapor diffusion at 16°C using 12 mg/ml protein. Full-length enzyme at 2.0 A resolution, enzyme in complex with GTP at 2.35 A resolution, mutant enzyme G1A and and DELTA68
-
hanging drop vapour diffusion method, with 2 M ammonium sulfate, 0.1 M HEPES (pH 7.0), and 0.3% Jeffamine M600 (pH 7.0)
-
sitting drop vapor diffusion method at 14°C, crystal structure of the enzyme (RdRp) in the apo state and in complex with the inhibitor NADPH
-
structure of Qbeta replicase complex, to 2.5 A resolution. Qbeta replicase is composed of the bacteriophage Qbeta catalytic beta-subunit as well as the Escherichia coli host translation elongation factors EF-Tu and EF-Ts. The basic catalytic machinery in the viral subunit appears similar to other RNA-dependent RNA polymerases, while a C-terminal region of the beta-subunit engages in extensive interactions with EF-Tu and may contribute to the separation of the transient duplex formed between the template and the nascent product to allow exponential amplification of the phage genome
-
hanging-drop vapour-diffusion method, structure of the enzyme in a free form at 1.9 A resolution and in complex with a template-primer RNA decanucleotide at 3.0 A resolution
-
HCV NS5B polymerase by hanging drop method at room temperature using a well buffer of 20% PEG 4000, 50 mM ammonium sulfate, 100 mM sodium acetate, pH 4.7, with 5 mM DTT, complexes are prepared by soaking the crystals for 3-24 h in solutions containing 15-20% DMSO, 20% glycerol, 20% PEG 4000, 0.1 M Hepes and 10 mM MgCl2 at pH 7.6 and an inhibitor concentration of 2-10 mM, X-ray diffraction structure determination and analysis at 2.6 A resolution for compound 29 and 2.15 A for compound 49
a large fragment of subunit PA bound to a fragment of subunit PB1, hanging dropn vapour diffusion method, 20°C, mixing of 0.001 ml of protein solution, containing 10 mg/ml protein in 20 mM Tris-HCl, pH 8.0, and 100 mM sodium chloride, and 0.001 ml of reservoir solution consisting of 100 mM Tris-HCl, pH 7.5, and 2.4 M sodium formate, X-ray diffraction structure determination and analysis at 2.3 A resolution
purified recombinant enzyme, at 20°C by the hanging drop method using a protein solution of 5-10 mg/ml protein in 20 mM Tris-HCl, pH 8.0, 100 mM NaCl and 2.5 mM MnCl2 and a reservoir composition of 1.2 M Li2SO4, 100 mM MES, pH 6.0, 10 mM Mg acetate and 3% ethylene glycol
purified apo-FluPol in closed conformation, sitting-drop vapour-diffusion, protein:precipitant ratio of 2:1, mixing of 5 mg/ml protein with either 70% v/v Morpheus G2, supplemented with 0%-1% 1 M NaOH, to generate P43212 crystals, or with crystal-seeds and 0.2 M NaCl, 0.1 M Na-HEPES, pH 7.5, and 25% w/v PEG 4000 for P212121 crystals, 20°C, heavy atom derivatization by P43212 crystals soaking in a solution of gold(I) potassium cyanide dissolved in mother liquor, for 2-3 h at 20°C, X-ray diffraction structure determination and analysis at 3.9 A resolution
-
purified recombinant enzyme in apo-form or in complex with ATP or GTP, jRdRp (0.08 mM) is incubated with GTP/ATP (5 mM) for 30 min before setting crystallization trials, screening and method optimization, hanging drop vapour diffusion method, mixing of protein-ATP/GTP with 10-18% w/v PEG 4000, 100 mM Tris-Cl buffer, pH 8.0, and 7% v/v 1-propanol, 25°C, for the apo-enzyme mixing of 0.096 mM protein with 10-15% PEG 5000 mono methyl ether, 100 mM Tris-Cl, pH 8.0, and 200mM NaSCN, 25°C, X-ray diffraction structure determination and analysis at 2.28-3.65 A resolution, molecular replacement using the apo-enzyme structures of WNV and DENV, PDB IDs 2HFZ and 2J7W, as search models
in-silico docking search of inhibitors. The location of inhibitors 8,8'-[carbonylbis(iminobenzene-3,1-diylcarbonylimino)]dinaphthalene-1,3,5-trisulfonic acid and Suramin inner head is stabilized by offset-tilted aromatic/aromatic interaction with residue Trp42
-
in-silico docking search of inhibitors. The location of inhibitors 8,8'-[carbonylbis(iminobenzene-3,1-diylcarbonylimino)]dinaphthalene-1,3,5-trisulfonic acid and Suramin inner head is stabilized by offset-tilted aromatic/aromatic interaction with residue Trp41
-
a complex of Norovirus RNA-dependent RNA polymerase bound to Mn2+ and an RNA primer-template duplex is investigated using X-ray crystallography and hybrid quantum chemical/molecular mechanical simulations. The complex crystallizes in a tetragonal crystal form. The nature of the primer/template duplex binding in the resulting structure indicates that the complex is a closed back-tracked state of the enzyme, in which the 3'-end of the primer occupies the position expected for the postincorporated nucleotide before translocation. Computationally, it is found that the complex can accept a range of divalent metal cations without marked distortions in the active site structure. The highest binding energy is for copper, followed closely by manganese and iron, and then by zinc, nickel, and cobalt
-
enzyme in two crystal forms A and B, method screening, 300 nl of 6-20 mg/ml protein in 50 mM Tris, 100 mM NaCl, and 2 mM DTT, pH 8.0, are mixed with reservoir solution containing 4.0 M sodium formate, 0.2 M magnesium formate, and 20% w/v PEG 3350, in hanging drops at 20°C, or with 4.3 M NaCl, 0.1 M HEPES, and 30 mM tri-glycine in sitting drops at room temperature, X-ray diffraction structure determination and analysis at resolutions of 1.7 A and 2.1 A, respectively. Form A contains Mg2+ bound at a site that deviates from the canonical non-catalytic position seen in form B
structure of Qbeta replicase complex, to 2.5 A resolution. Qbeta replicase is composed of the bacteriophage Qbeta catalytic beta-subunit as well as the Escherichia coli host translation elongation factors EF-Tu and EF-Ts. The basic catalytic machinery in the viral subunit appears similar to other RNA-dependent RNA polymerases, while a C-terminal region of the beta-subunit engages in extensive interactions with EF-Tu and may contribute to the separation of the transient duplex formed between the template and the nascent product to allow exponential amplification of the phage genome
Q8LTE0
sitting-drop vapour-diffusion method, 2.4 A resolution
overall structure of the sapovirus 3Dpol is determined by X-ray crystallography to 2.32 A resolution
-