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PROSITE documentation PDOC50507 [for PROSITE entry PS50507]

RNA-directed RNA polymerase catalytic domain profiles





Description

RNA-directed RNA polymerase (RdRp) (EC 2.7.7.48) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [1,2]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear. The postulated 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) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (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 [3].

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 (see <PDB:1RDR>) [4]. Only the palm subdomain, composed of a four-stranded antiparallel β-sheet with two α-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 is synthesized rather than DNA [5].

RNA viruses with no DNA stage can be placed in three main categories based on their replication and coding strategies: positive single-stranded RNA (ssRNA), negative ssRNA and double-stranded RNA (dsRNA) viruses. To recognize RNA-directed RNA polymerase we have developed six profiles that roughly follow this classification (see below). They are all directed against the catalytic region (palm subdomain).

Note:

The GDD motif lacks in Birnaviridae RNA-directed RNA polymerases [6].

Last update:

November 2005 / First entry.

Technical section

PROSITE methods (with tools and information) covered by this documentation:

RDRP_SSRNA_POS, PS50507; RdRp of positive ssRNA viruses catalytic domain profile  (MATRIX)

RDRP_DSRNA_BIR, PS50524; RdRp of Birnaviridae dsRNA viruses catalytic domain profile  (MATRIX)

RDRP_DSRNA_REO, PS50523; RdRp of Reoviridae dsRNA viruses catalytic domain profile  (MATRIX)

RDRP_PHAGE, PS50522; RdRp of RNA-containing bacteriophages catalytic domain profile  (MATRIX)

RDRP_SSRNA_NEG_NONSEG, PS50526; RdRp of negative ssRNA viruses with non-segmented genomes catalytic domain profile  (MATRIX)

RDRP_SSRNA_NEG_SEG, PS50525; RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile  (MATRIX)


References

1AuthorsKoonin E.V., Gorbalenya A.E., Chumakov K.M.
TitleTentative identification of RNA-dependent RNA polymerases of dsRNA viruses and their relationship to positive strand RNA viral polymerases.
SourceFEBS Lett. 252:42-46(1989).
PubMed ID2759231

2AuthorsZanotto P.M., Gibbs M.J., Gould E.A., Holmes E.C.
TitleA reevaluation of the higher taxonomy of viruses based on RNA polymerases.
SourceJ. Virol. 70:6083-6096(1996).
PubMed ID8709232

3AuthorsKao C.C., Singh P., Ecker D.J.
TitleDe novo initiation of viral RNA-dependent RNA synthesis.
SourceVirology 287:251-260(2001).
PubMed ID11531403
DOI10.1006/viro.2001.1039

4AuthorsHansen J.L., Long A.M., Schultz S.C.
TitleStructure of the RNA-dependent RNA polymerase of poliovirus.
SourceStructure 5:1109-1122(1997).
PubMed ID9309225

5AuthorsGohara D.W., Crotty S., Arnold J.J., Yoder J.D., Andino R., Cameron C.E.
TitlePoliovirus RNA-dependent RNA polymerase (3Dpol): structural, biochemical, and biological analysis of conserved structural motifs A and B.
SourceJ. Biol. Chem. 275:25523-25532(2000).
PubMed ID10827187
DOI10.1074/jbc.M002671200

6AuthorsShwed P.S., Dobos P., Cameron L.A., Vakharia V.N., Duncan R.
TitleBirnavirus VP1 proteins form a distinct subgroup of RNA-dependent RNA polymerases lacking a GDD motif.
SourceVirology 296:241-250(2002).
PubMed ID12069523
DOI10.1006/viro.2001.1334



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