Streptococcus pyogenes is responsible for over half a million deaths every year by causing diseases like necrotizing fasciitis and rheumatic heart disease. Streptococcal toxins that cause such diseases are encoded by prophages found in the S. pyogenes genome. The prophage encoded toxin genes are always found adjacent to a highly conserved gene termed paratox (prx). Past work by our lab discovered that Prx disrupts quorum sensing and natural competence in S. pyogenes by directly binding to the DNA binding domain (DBD) of quorum sensing receptor ComR. In doing so, Prx protects prophage DNA from being replaced by potential homologous recombination. To probe for additional Prx functions, we aimed to explore streptococcal biochemical pathways that may be regulated by Prx. Using a pull-down assay combined with mass-spectrometry, the lab previously identified SpyM3_0890 or EndoS1 and SpyM3_1246 or P1246 as potential Prx binding partners. To study the Prx partners, we purified both proteins to study their biochemical interactions with Prx. First, we show that both proteins form stable complexes with Prx in vitro. Next, an X-ray crystal structure of EndoS1 shows that it resembles the specificity (S) subunit of type I restriction modification (RM) enzymes. A cocrystal structure of an EndoS1:Prx complex revealed that Prx binds the EndoS1 at its potential DBD. P1246 is located in a cluster of phage genes that regulate DNA processing and Alpha Fold predicts that P1246 adopts a DBD-fold identical to ComR. Based on our structures we have identified a helical motif conserved in ComR, EndoS1, and P1246 that is critical for Prx interaction. This motif could serve as a different approach for pursuing more Prx interaction partners. Since both EndoS1 and P1246 are potential DNA binding proteins, Prx likely blocks their ability to interact with a specific promoter or repressor region in S. pyogenes. Overall, our study demonstrates how small phage proteins like Prx can regulate host biochemistry for the preservation of the phage.