DNA transposons are mobile genetic elements that translocate from one site to another within a host chromosome. Although most transposons exhibit practically no target sequence specificity, some elements have mechanisms to distinguish between their own DNA and the host genome and avoid self-destructive autointegration. Phage Mu is among the most complex and efficient DNA transposons. The protein MuB plays a central role in the target DNA selection in the transposition of bacteriophage Mu. Mechanistic understanding of MuB function has previously been hindered by its poor solubility and tendency to aggregate. Recently, we demonstrated that MuB is an AAA+ ATPase composed of an N-terminal appendage (NTA) and an AAA+ ATPase module. Within AAA+ module we identified critical residues for its ATPase, DNA binding, polymerization and MuA interaction activities. Using single-particle electron microscopy, we show that MuB assembles into helical filaments that coat the DNA without deforming it, resulting in a unique symmetry mismatch. This lead to a model in which MuB-imposed symmetry deforms the DNA and results in a bent DNA favored by MuA for transposition. However, the role of the NTA remains unknown. We set to study the structure and function of the NTA to further understand the MuB-DNA recognition mechanism. We prove that the NTA is an independent, well-folded, globular domain that behaves as a monomer in solution. The structure, determined by NMR spectroscopy, reveals a four α-helical bundle containing a characteristic helix-turn-helix motif. The overall arrangement of the helixes highly resembles the λ repressor-like DNA-binding domains. Although the interaction of the isolated domain with the DNA could not be observed, by negative staining electron microscopy we demonstrate that this domain mediates the interaction between MuB filaments. We propose a model on how the N-terminal sequence could aid in binding, condensing and protecting the DNA from autointegration.