Summary: RNA dependent RNA polymerase
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RNA-dependent RNA polymerase Edit Wikipedia article
|RNA-directed RNA polymerase|
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / EGO|
|RNA dependent RNA polymerase|
|RNA-directed RNA polymerase, flaviviral|
RNA-dependent RNA polymerase (RdRp), (RDR), or RNA replicase, is an enzyme that catalyzes the replication of RNA from an RNA template. This is in contrast to a typical DNA-dependent RNA polymerase, which catalyzes the transcription of RNA from a DNA template.
RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the genomes of all RNA-containing viruses with no DNA stage that have sense negative RNA. It catalyses synthesis of the RNA strand complementary to a given RNA template. The RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo), or a primer-dependent mechanism that utilizes a viral protein genome-linked (VPg) primer. The de novo initiation consists in the addition of a nucleoside triphosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product.
Viral RdRPs were discovered in the early 1960s from studies on mengovirus and polio virus when it was observed that these viruses were not sensitive to actinomycin D, a drug that inhibits cellular DNA-directed RNA synthesis. This lack of sensitivity suggested that there is a virus-specific enzyme that could copy RNA from an RNA template and not from a DNA template.
The most famous example of RdRP is that of the polio virus. The viral genome is composed of RNA, which enters the cell through receptor-mediated endocytosis. From there, the RNA is able to act as a template for complementary RNA synthesis, immediately. The complementary strand is then, itself, able to act as a template for the production of new viral genomes that are further packaged and released from the cell ready to infect more host cells. The advantage of this method of replication is that there is no DNA stage; replication is quick and easy. The disadvantage is that there is no 'back-up' DNA copy.
Many eukaryotes also have RdRPs involved in an amplification of RNA interference. In them RdRP transcribes secondary- siRNAs, which in turn are bound by class 3 Argonauts (SAGO) to repress target RNA. In fact these same RdRPs that are used in the defense mechanisms can be usurped by RNA viruses for their benefit.
RdRps are highly conserved throughout viruses and is even related to telomerase, though the reason for such high conservation in such diverse organisms is an ongoing question as of 2009. The similarity has led to speculation that viral RdRps are ancestral to human telomerase.
All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organization has been likened to the shape of a right hand with three subdomains termed fingers, palm, and thumb. Only the palm subdomain, composed of a four-stranded antiparallel beta-sheet with two alpha-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well-conserved motifs (A, B, and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and, thus, determines whether RNA rather than DNA is synthesized. The domain organization and the 3D structure of the catalytic centre of a wide range of RdPps, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues.
There are 4 superfamilies of viruses that cover all RNA-containing viruses with no DNA stage:
- Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families
- Mononegavirales (negative-strand RNA viruses with non-segmented genomes)
- Negative-strand RNA viruses with segmented genomes, i.e., Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses
- Birnaviridae family of dsRNA viruses.
The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups:
- All positive-strand RNA eukaryotic viruses with no DNA stage
- All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages)
- Reoviridae family of dsRNA viruses.
Flaviviruses produce a polyprotein from the ssRNA genome. The polyprotein is cleaved to a number of products, one of which is NS5. Recombinant dengue type 1 virus NS5 protein expressed in Escherichia coli exhibits RNA-dependent RNA polymerase activity. This RNA-directed RNA polymerase possesses a number of short regions and motifs homologous to other RNA-directed RNA polymerases.
- Akutsu, M; Ye, Y; Virdee, S; Chin, JW; Komander, D (February 2011). "Molecular basis for ubiquitin and ISG15 cross-reactivity in viral ovarian tumor domains". Proc. Natl. Acad. Sci. U.S.A. 108 (6): 2228â€“33. doi:10.1073/pnas.1015287108. PMC 3038727. PMID 21266548.
- Koonin EV, Gorbalenya AE, Chumakov KM (July 1989). "Tentative identification of RNA-dependent RNA polymerases of dsRNA viruses and their relationship to positive strand RNA viral polymerases". FEBS Lett. 252 (1â€“2): 42â€“6. doi:10.1016/0014-5793(89)80886-5. PMID 2759231.
- Zanotto PM, Gibbs MJ, Gould EA, Holmes EC (September 1996). "A reevaluation of the higher taxonomy of viruses based on RNA polymerases". J. Virol. 70 (9): 6083â€“96. PMC 190630. PMID 8709232.
- Jin, Z; Leveque, V; Ma, H; Johnson, K. A.; Klumpp, K (2012). "Assembly, purification, and pre-steady-state kinetic analysis of active RNA-dependent RNA polymerase elongation complex". Journal of Biological Chemistry 287 (13): 10674â€“83. doi:10.1074/jbc.M111.325530. PMC 3323022. PMID 22303022.
- Kao CC, Singh P, Ecker DJ (September 2001). "De novo initiation of viral RNA-dependent RNA synthesis". Virology 287 (2): 251â€“60. doi:10.1006/viro.2001.1039. PMID 11531403.
- Iyer LM, Koonin EV, Aravind L (January 2003). "Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases". BMC Struct. Biol. 3: 1. doi:10.1186/1472-6807-3-1. PMC 151600. PMID 12553882.
- Suttle CA (September 2005). "Viruses in the sea". Nature 437 (7057): 356â€“61. doi:10.1038/nature04160. PMID 16163346.
- Hansen JL, Long AM, Schultz SC (August 1997). "Structure of the RNA-dependent RNA polymerase of poliovirus". Structure 5 (8): 1109â€“22. doi:10.1016/S0969-2126(97)00261-X. PMID 9309225.
- Gohara DW, Crotty S, Arnold JJ, Yoder JD, Andino R, Cameron CE (August 2000). "Poliovirus RNA-dependent RNA polymerase (3Dpol): structural, biochemical, and biological analysis of conserved structural motifs A and B". J. Biol. Chem. 275 (33): 25523â€“32. doi:10.1074/jbc.M002671200. PMID 10827187.
- O'Reilly EK, Kao CC (December 1998). "Analysis of RNA-dependent RNA polymerase structure and function as guided by known polymerase structures and computer predictions of secondary structure". Virology 252 (2): 287â€“303. doi:10.1006/viro.1998.9463. PMID 9878607.
- Tan BH, Fu J, Sugrue RJ, Yap EH, Chan YC, Tan YH (February 1996). "Recombinant dengue type 1 virus NS5 protein expressed in Escherichia coli exhibits RNA-dependent RNA polymerase activity". Virology 216 (2): 317â€“25. doi:10.1006/viro.1996.0067. PMID 8607261.
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Internal database links
|SCOOP:||RdRP_2 RdRP_3 RdRP_4 DUF832 DUF2719 DUF5000|
|Similarity to PfamA using HHSearch:||RdRP_3 RdRP_4 Birna_RdRp|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001205
This entry represents the C-terminal domain of the RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses viruses. It is part of the genome polyprotein that contains other polypeptides such as coat proteins VP1 to VP4, core proteins P2A to P2C and P3A, genome-linked protein VPG and picornain 3C (EC).
Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases [PUBMED:15306852, PUBMED:15296746].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||RNA binding (GO:0003723)|
|RNA-directed RNA polymerase activity (GO:0003968)|
|Biological process||transcription, DNA-templated (GO:0006351)|
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This clan represents the replicative RNA dependent RNA polymerase. from a variety of RNA viruses .
The clan contains the following 9 members:Birna_RdRp Flavi_NS5 Mitovir_RNA_pol RdRP_1 RdRP_2 RdRP_3 RdRP_4 RVT_1 RVT_2
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Curation and family details
|Seed source:||Pfam-B_32 (release 2.1)|
|Number in seed:||12|
|Number in full:||20248|
|Average length of the domain:||240.90 aa|
|Average identity of full alignment:||23 %|
|Average coverage of the sequence by the domain:||26.91 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||16|
|Download:||download the raw HMM for this family|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the RdRP_1 domain has been found. There are 249 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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