RNA-directed RNA polymerase

Best example is PDB entry 4dcd and is shown in the viewer.

Molecule RNA-directed RNA polymerase, also known as Protein P2, RNA-directed RNA polymerase, p8, NS3P, Hepacivirin, gp70, gp32, Protease NS2-3, p21, p27, NS4A, Core protein p21, Non-structural protein 4B, p23, Core protein p19, NS5A, p70, p68, NS5B, Serine protease NS3, NS1, Non-structural protein 4A, gp68, gp35, Envelope glycoprotein E1, Genome polyprotein, p56, Capsid protein C, Non-structural protein 5A, NS4B, p7, Envelope glycoprotein E2, gp55, N-pro, N-terminal protease, Non-structural protein 3, gp33, Non-structural protein 2-3, E(rns) glycoprotein, Autoprotease p20, Non-structural protein 2, gp44/48, Cysteine protease NS2, Picornain 2A, P1B, P3B, Protease 3C, 3D polymerase, Capsid protein VP1, P1D, Protein 3B, P1C, VP4-VP2, Capsid protein VP4, Protein 2B, Virion protein 3, P3A, Capsid protein VP0, 3Dpol, Virion protein 1, VPg, Protein 2C, Capsid protein VP3, P3C, Protein 2A, P1A, Virion protein 2, Viral protein genome-linked, Protein 3D, P2A, Virion protein 4, Protein 3A, 3D, Protein 3AB, Protein 3CD, P2B, P2C, RdRp, P1, Capsid protein VP2, P2, Protease 2A, P3, Protein VP1, p13, Viral genome-linked protein, Protein p18, Capsid protein VP60, NTPase, Precursor p41, p15, 3CLpro, 3C-like protease, Protein p29, Protein p16, Calicivirin, p37, Protein p23/2, Protein p23, p58, 2C-like protein, Thiol protease P3C, p254, RDRP, nsp3, p65 homolog, nsp5, 2'-O-methyltransferase, 3CLp, Uridylate-specific endoribonuclease, nsp12, pp1ab, Non-structural protein 8, Hel, Leader protein, GFL, nsp2, Host translation inhibitor nsp1, NendoU, nsp14, PL-PRO, Growth factor-like peptide, nsp16, SARS coronavirus main proteinase, Pol, ExoN, ORF1ab polyprotein, Papain-like proteinase, Non-structural protein 9, nsp4, Non-structural protein 6, Non-structural protein 10, nsp1, nsp15, nsp7, Non-structural protein 4, nsp13, nsp6, 3CL-PRO, 3C-like proteinase, Non-structural protein 7, Replicase polyprotein 1ab, nsp8, Helicase, nsp10, nsp9, PL2-PRO, Guanine-N7 methyltransferase, NS2-3, HEL, 42 kDa protein, Methyltransferase/Protease, RNA replicase polyprotein, 66 kDa protein, MET/PRO, Putative helicase, 98 kDa protein, 206 kDa polyprotein, POL, Protein L, Transcriptase, Large structural protein, Replicase, mRNA (guanine-N(7)-)-methyltransferase, mRNA guanylyltransferase, RNA-directed RNA polymerase L, PL1-PRO/PL2-PRO, Peptide HD2, p12, p66-HEL, p5, Putative 2'-O-methyl transferase, p14, p66, Non-structural protein 1, Exoribonuclease, p195, Papain-like proteinases 1/2, p34, p41, p9, M-PRO, PLP1/PLP2, p100, p87, Ubiquitin thioesterase, nsp11, Non-structural protein 11, VPG, Protein p48, Protein p22, p10, p33, p39, p16, p35, p24, 3CLSP, Non-structural protein 5-6-7, 3C-like serine proteinase, Nsp6, Nsp3, Nsp5, Non-structural protein 7-beta, Nsp4, Nsp5-6-7, Nsp9, Nsp8, Non-structural protein 12, CP2, Non-structural protein 7-alpha, Nsp7-alpha, Nsp12, CP, Nsp10, PCP, Nsp2 cysteine proteinase, Nsp7-beta, Nsp11, Nsp1 papain-like cysteine proteinase, Non-structural protein 5, Core protein, p6, Nuclear inclusion protein B, Helper component proteinase, 6 kDa protein 1, Nuclear inclusion protein A, NI-a, P1 proteinase, 49 kDa proteinase, Capsid protein, NIa-pro, CI, 6K1, NI-b, NIb, 6K2, 49 kDa-Pro, Cytoplasmic inclusion protein, 6 kDa protein 2, HC-pro, Protein P3, N-terminal protein, Coat protein, NIa, 183 kDa protein, 126 kDa protein, MT/HEL, Methyltransferase/RNA helicase, Replicase small subunit, Replicase large subunit, p22, p67, p28, p65, p44 and p210.

Function

NS5B is an RNA-dependent RNA polymerase that plays an essential role in the virus replication.Data source: Uniprot P26663

Catalytic Activity

ATP + H(2)O = ADP + phosphate.Data source: Uniprot P26663

Disease

Relevance

Structural highlights

Biological process

Is involved in the following biological processes:
viral RNA genome replication
proteolysis
viral genome replication
transcription, DNA-templated
transformation of host cell by virus
viral protein processing
transcription, RNA-templated
RNA-protein covalent cross-linking
viral process

In structures

RNA-directed RNA polymerase is found in 623 PDB entries

• Viruses (602 PDB entries):
  
  • Hepatitis C virus (78 PDB entries):
    
    • 4dgv
    • Title: Structure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the broadly neutralizing antibody HCV1, P2(1) form
    • 1.805 A resolution
    • Other macromolecules also in this entry: HCV1 Heavy Chain, HCV1 Light Chain.
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  • SARS coronavirus (57 PDB entries):
    
    • 2v6n
    • Title: CRYSTAL STRUCTURES OF THE SARS-CORONAVIRUS MAIN PROTEINASE INACTIVATED BY BENZOTRIAZOLE COMPOUNDS
    • 1.98 A resolution
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  • Human poliovirus 1 Mahoney (47 PDB entries):
    
    • 4dcd
    • Title: 1.6A resolution structure of PolioVirus 3C Protease Containing a covalently bound dipeptidyl inhibitor
    • 1.69 A resolution
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  • Hepatitis C virus (isolate BK) (45 PDB entries):
    
    • 4eo8
    • Title: HCV NS5B polymerase inhibitors: Tri-substituted acylhydrazines as tertiary amide bioisosteres
    • 1.798 A resolution
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  • Hepatitis C virus isolate HC-J4 (44 PDB entries):
    
    • 3u4o
    • Title: Novel HCV NS5B polymerase Inhibitors: Discovery of Indole C2 Acyl sulfonamides
    • 1.77 A resolution
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  • Human rhinovirus B14 (33 PDB entries):
    
    • 4pdw
    • Title: A benzonitrile analogue inhibits rhinovirus replication
    • 3.0 A resolution
    • Other macromolecules also in this entry: Capsid protein VP4/VP2, Capsid protein VP2, Capsid protein VP3, .
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  • Hepatitis C virus subtype 1b (25 PDB entries):
    
    • 3ciz
    • Title: Crystal structure of hepatitis c virus rna-dependent rna polymerase ns5b in complex with small molecule fragments
    • 1.87 A resolution
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  • Hepatitis C virus JFH-1 (20 PDB entries):
    
    • 4wtm
    • Title: CRYSTAL STRUCTURE OF HCV NS5B GENOTYPE 2A JFH-1 ISOLATE WITH S15G E86Q E87Q C223H V321I MUTATIONS IN COMPLEX WITH RNA TEMPLATE 5'-UAGG, RNA PRIMER 5'-PCC, MN2+, AND UDP
    • 2.15 A resolution
    • Other macromolecules also in this entry: RNA PRIMER CC, RNA TEMPLATE UAGG.
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  • Pseudomonas phage phi6 (19 PDB entries):
    
    • 4a8o
    • Title: Non-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial dsRNA virus phi6 from De Novo Initiation to Elongation
    • 2.67 A resolution
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  • Norovirus Hu/1968/US (11 PDB entries):
    
    • 4xbb
    • Title: 1.85A resolution structure of Norovirus 3CL protease complex with a covalently bound dipeptidyl inhibitor diethyl [(1R,2S)-2-[(N-{[(3-chlorobenzyl)oxy]carbonyl}-3-cyclohexyl-L-alanyl)amino]-1-hydroxy-3-(2-oxo-2H-pyrrol-3-yl)propyl]phosphonate
    • 1.85 A resolution
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  • Human rhinovirus A16 (10 PDB entries):
    
    • 1qjy
    • Title: HUMAN RHINOVIRUS 16 COAT PROTEIN IN COMPLEX WITH ANTIVIRAL COMPOUND VP65099
    • 2.8 A resolution
    • Other macromolecules also in this entry: Capsid protein VP3, Capsid protein VP4, Capsid protein VP2, .
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  • Human rhinovirus A2 (9 PDB entries):
    
    • 1a3r
    • Title: FAB FRAGMENT (ANTIBODY 8F5) COMPLEXED WITH PEPTIDE FROM HUMAN RHINOVIRUS (SEROTYPE 2) VIRAL CAPSID PROTEIN VP2 (RESIDUES 156-170)
    • 2.1 A resolution
    • Other macromolecules also in this entry: Igh protein, ENSMUSG00000076577 protein.
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  • Hepatitis C virus subtype 1a (7 PDB entries):
    
    • 3hkw
    • Title: HCV NS5B genotype 1a in complex with 1,5 benzodiazepine inhibitor 6
    • 1.55 A resolution
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  • Human rhinovirus sp. (6 PDB entries):
    
    • 1aym
    • Title: HUMAN RHINOVIRUS 16 COAT PROTEIN AT HIGH RESOLUTION
    • 2.15 A resolution
    • Other macromolecules also in this entry: Capsid protein VP3, Capsid protein VP4, Capsid protein VP1, .
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  • BACTERIOPHAGE PHI-6 (5 PDB entries):
    
    • 1uvj
    • Title: THE STRUCTURAL BASIS FOR RNA SPECIFICITY AND CA2 INHIBITION OF AN RNA-DEPENDENT RNA POLYMERASE PHI6P2 WITH 7NT RNA
    • 1.9 A resolution
    • Other macromolecules also in this entry: 5'-R(*UP*UP*CP*CP)-3', .
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  • Crimean-Congo hemorrhagic fever virus strain IbAr10200 (4 PDB entries):
    
    • 3phx
    • Title: OTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex with ISG15
    • 1.6 A resolution
    • Other macromolecules also in this entry: Ubiquitin-like protein ISG15, .
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  • Transmissible gastroenteritis virus (3 PDB entries):
    
    • 1lvo
    • Title: Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain
    • 1.96 A resolution
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  • Hepatitis C virus isolate HC-J8 (2 PDB entries):
    
    • 3gsz
    • Title: Structure of the genotype 2B HCV polymerase
    • 1.9 A resolution
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  • Hepatitis B virus (1 PDB entries):
    
    • 4tn2
    • Title: NS5b in complex with lactam-thiophene carboxylic acids
    • 2.7 A resolution