Abstract: Bacterial flagella is crucial for motility, adhesion, pathogenesis, and biofilm formation. The assembly of functional flagella requires the coordinated expression of about 40 genes that express structural and regulatory components along with the associated chemosensory apparatus. The expression of flagellar genes occurs in a cascade-like fashion and is tightly regulated through dedicated transcription factors. For bacteria with a single polar flagella, FleQ, a master transcription regulator, is at the top of the hierarchy. The ATPase activity of FleQ is regulated via protein-protein interaction with FleN. The crystal structure of the hetero-tetrameric complex reveals that FleN allosterically prevents ATP binding to FleQ. Disruption of the conserved protein-protein interface by mutation shows motility and transcription defects in vivo and multi-flagellate phenotype. Our study provides a detailed mechanism mono-flagellate bacteria utilize to fine-tune the expression of flagellar genes to form and maintain a single flagellum.