IDRs, or Intrinsically Disordered Regions, are segments of proteins that lack a well-defined three-dimensional structure under physiological conditions. Sigma-A (σA) protein is a bacterial transcription factor that plays a vital role in the initiation of transcription by association with RNA polymerase (RNAP) driving transcription initiation. σA responds to environmental signals to regulate the expression of genes crucial for bacterial growth, survival, and adaptation. Through an unbiased search for interacting partners of M. smegmatis σA, a number of proteins were discovered, with MoaB2 being the most prominent. Molybdenum cofactor biosynthesis protein B (MoaB2) is a member of a universally conserved protein family involved in catalyzing complex oxygen transfer reactions in the Molybdenum incorporation pathway, a trace element essential in bacteria. Recent studies have shown MoaB2 is catalytically inactive structural homolog in prokaryotes. In this study, we explored several functional experiments which demonstrated that MoaB2 inhibits σA-dependent transcription and increases the biological stability of σA. Several approaches were used to validate and characterize the σA-MoaB2 interaction which demonstrated that the binding was specific and independent of RNAP, as other sigma factors did not show binding to MoaB2. The structural analysis of MoaB2 revealed that the Intrinsically disordered N-terminal domain of σA plays a role in the σA-MoaB2 interaction. In summary, this study uncovers MoaB2 as a novel binding partner of mycobacterial σA, which suggests it may have adopted an alternate function in prokaryotes.