The RNA-dependent RNA polymerase (RdRp) of SARS-Coronavirus plays a crucial action in the processes of viral replication and discontinuous transcription.Because of its important function and its highest conservation among the Coronaviruses,SARS-RdRp will be a potential drug target for anti-SARS therapy.Here we map the conserved motifs in SARS-RdRp by multiple sequence alignment,combined with structural information,in groups of virus RdRps proteins which are evolutionarily related,but share significantly low sequence similarity(10%-20%).Besides six known motifs,three novel ones are identified.Secondary structure and three dimensional structure indicate that conserved motifs tend to be situated in the junction regions of conserved beta sheets or alpha helices,whose location and length are conserved,but the primary amino acid sequences do not display conservation.SARS-RdRp shows similar structure to other viral RdRps and this implies that the current available antiviral agents for other RdRps might have important implications for anti-SARS therapy.
