In Silico Structural Characterization of Arthrobacter Phage Alatato Immunity Cassette Reveals a Conserved Arginine-Mediated Repressor Motif

Understanding the regulatory mechanisms of viral lysogeny requires precise characterization of repressor-operator interactions. In this study, we investigated the unmapped immunity cassette of Arthrobacter phage Alatato (Cluster FB) utilizing silico structural modeling. We identified gp31 and gp33 as potential functional DNA-binding repressors, which are predicted to utilize a strictly conserved Helix-Turn-Helix (HTH) motif to engage the major groove of the operator DNA. Through structural mapping and computational mutagenesis via AlphaFold 3, computational analysis suggests Arginine 51 (R51) may serve as a candidate residue mediating electrostatic interactions with the DNA phosphate backbone; in silico substitution of R51 to Alanine (R51A) notably reduced the predicted structural confidence of the binding complex. Furthermore, structural alignment of Alatato gp31 with its homolog from the genetically divergent Cluster FA phage Bridgette (Pham 289627) yielded a 0.556 Å RMSD, consistent with a highly conserved structural architecture at the R51 interface. Conversely, the Cluster AZ1 phage Adolin (Pham 291150) exhibited no predictive binding affinity (ipTM 0.22) for the Alatato operator sequence, suggestive of functional divergence between these repressor families under the current model parameters. These predictive findings propose a conserved, Arginine-mediated binding mechanism that is modeled as structurally maintained across distinct viral clusters.