Significance Tuberculosis, caused by Mycobacterium tuberculosis , remains a major global public health problem. Deciphering the complex biology of M. tuberculosis will aid in the development of new therapeutics to combat this pathogen. Encapsulins, naturally encapsulating specific cargo proteins, are a recently discovered class of smaller proteinaceous compartments found in bacteria and archaea and needed for essential physiological processes. Here, we report the structural and mechanistic characterization of a native DyP-packaging encapsulin from the Mycobacterium smegmatis , a model system for M. tuberculosis . Our results contribute to the understanding of the assembly and physiological role of the encapsulin systems and provide a rational framework for antituberculosis drug design.