Functional assignment of enzymes encoded by the Mycobacterium tuberculosis genome is largely incomplete despite recent advances in genomics and bioinformatics. Here, we applied an activitybased metabolomic profiling method to assign function to a unique phosphatase, Rv1692. In contrast to its annotation as a nucleotide phosphatase, metabolomic profiling and kinetic characterization indicate that Rv1692 is a D,L-glycerol 3-phosphate phosphatase. Crystal structures of Rv1692 reveal a unique architecture, a fusion of a predicted haloacid dehalogenase fold with a previously unidentified GCN5-related N-acetyltransferase region.Although not directly involved in acetyl transfer, or regulation of enzymatic activity in vitro, this GCN5-related N-acetyltransferase region is critical for the solubility of the phosphatase. Structural and biochemical analysis shows that the active site features are adapted for recognition of small polyol phosphates, and not nucleotide substrates. Functional assignment and metabolomic studies of M. tuberculosis lacking rv1692 demonstrate that Rv1692 is the final enzyme involved in glycerophospholipid recycling/catabolism, a pathway not previously described in M. tuberculosis.haloacid dehalogenase superfamily | enzyme function | pathway discovery E ach year, 1.4 million people succumb to tuberculosis, making Mycobacterium tuberculosis the deadliest bacterium affecting mankind (1). In addition, the dissemination of strains resistant to several antibiotics underscores the need for better understanding of this pathogen and for the development of novel vaccines and therapeutics (2, 3). Our approach to elucidating the unique pervasiveness of M. tuberculosis is through comprehensive discovery and characterization of metabolic pathways, as metabolism underlies survival of the bacteria both inside and outside the host and can contribute to phenotypic and genetic drug resistance.The M. tuberculosis genome encodes for 4,043 genes, of which 3,933 encode proteins (4, 5). Many genes with essential functions, such as DNA replication, protein and RNA synthesis, and cell-division, have close homologs in other bacteria, and their functions are annotated largely on the basis of analysis of their counterparts. However, functions of at least one-third of the genes are unknown or putative (4). In particular, little is known about genes that are not conserved or conditionally important. Characterization of such genes presents a daunting task. M. tuberculosis is thought to be subjected to a myriad of conditions during its life cycle in the host, such as low pH, reactive oxygen and nitrogen species, and so on (6, 7). Understanding how M. tuberculosis adapts to and even thrives in such diverse environments is critical to our understanding of the pathology itself and for the discovery of novel therapeutics to treat tuberculosis.We applied an innovative, activity-based metabolomic profiling (ABMP) approach to assign function to orphan (without a priori known substrates/products) mycobacterial enzymes and to discover unk...