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

by Selleckchem | May 03 2023

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 α-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 α and β 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.

Comments：

It is interesting to learn about the presence of two enzymatic regions, methyl transferase and RdRp, separated by a transmembrane region, as well as the three major sub-domains (fingers, palm, and thumb) that are common for other polymerases.

The identification of a small alpha-helix named 'priming helix' at position 829-833 with a potential role in de novo initiation is also intriguing, as is the analysis of electrostatic potential, metal binding residues, and nucleotide and template channels. The identification of potential metal binding and H-bonding residues for recognition of incoming nucleotides and rNTPs is particularly noteworthy.

It is also interesting to learn about the structural similarity of MnRdRp with other flaviviridea members, especially BVDV RdRp, and the conservation of the fingers and palm sub-domains over the thumb sub-domain. The identification of Dasabuvir as a potential inhibitor of MnRdRp through docking studies is a promising finding, as it suggests that existing inhibitors for other flaviviridea polymerases may also be effective against MnRdRp.

Overall, this information provides valuable insights into the structure and function of MnRdRp, and may have important implications for the development of effective treatments for white tail disease in farmed Macrobrachium rosenbergii.