The causative agent of tuberculosis, Mycobacterium tuberculosis is estimated to be present in roughly a third of the world’s population. One of the hallmarks of the pathogen is its reliance on lipids as a source of energy in order to survive in a non-replicating state and ultimately cause infection. A key player in lipid utilization by M. tuberculosis is the triglyceride lipase, LipY. LipY is the rate-limiting catalyst in the mobilization of free fatty acids from triglycerides acting on lipid bodies both within the tubercule bacillus and outside the bacterium. LipY also belongs to the PE/PPE family of proteins, a group of approximately 169 virulence-associated proteins characterized by a proline-glutamate or proline-proline-glutamate motif at their N-termini. It has been suggested that the PE domain of LipY may act as a regulator of enzymatic activity. Using several biochemical and activity-based approaches, we established a method for purifying LipY with improved resolution. We also introduced a rapid and reliable method for quantification of active sites for serine hydrolases using activity-based protein profiling (ABPP). Finally, by imploring these methodologies, we discovered that the PE domain of LipY acts as a non-competitive inhibitor of LipY enzymatic activity when it is attached to the mature lipase. The methodologies and evidence presented here may lead to discovery of additional PE/PPE family enzymes with roles in M. tuberculosis lipid metabolism and/or virulence. This work may also lead to expansion of our understanding of the roles of PE/PPE proteins and domains.