Structural and functional characterization of RNA dependent RNA polymerase of Macrobrachium rosenbergii nodavirus (MnRdRp)

Macrobrachium rosenbergii is a highly valued farmed freshwater species and its production has been affected globally by white tail disease caused by M. rosenbergii nodavirus (MrNV). MrNV is a single stranded positive sense RNA virus encoding RNA-dependent RNA polymerase (RdRp) for genome replication. Due to its essentiality for pathogenesis, it is an important drug target. The domain prediction of the complete sequence revealed the presence of two enzymatic regions namely methyl transferase and RdRp separated by transmembrane region. The predicted three-dimensional (3D) structure of MnRdRp using AlphaFold 2 shows that the structure is composed of three major sub-domains common for other polymerases namely fingers, palm and thumb. Structural similarity search revealed its similarity with other flaviviridea members especially with BVDV RdRp (BvdvRdRp). The structure of fingers and palm sub-domains is more conserved than the thumb sub-domain. A small alpha-helix named 'priming helix' having conserve Tyr was identified at position 829-833 with a potential role in de novo initiation. Analysis of electrostatic potential revealed that nucleotide and template channels are electropositive. Metal binding residues were identified as Asp599, Asp704 and Asp705. The alpha and beta phosphates of incoming nucleotide interact with two Mn2+, Arg455 and Arg537. For recognition of 2 '-OH of incoming rNTP, Asp604, Ser661 and Asn670 were identified which can form H-bond network with 2 '-OH group. Docking study revealed that Dasabuvir can potentially inhibit MnRdRp. The study concluded that the overall structure and function of MnRdRp are similar to Flaviviridae polymerases and their inhibitors can work against this enzyme.Communicated by Ramaswamy H. Sarma

Automated summary

Macrobrachium rosenbergii, a valuable farmed freshwater species, is globally affected by white tail disease caused by M. rosenbergii nodavirus (MrNV). MrNV is an important drug target for pathogenesis, encoding RNA-dependent RNA polymerase (RdRp) for genome replication. The predicted three-dimensional structure of MnRdRp shows similarity with other flaviviridae members. The study identified metal binding residues and potential inhibitors for MnRdRp.