Capuramycin-related compounds, including A-500359s and A-503083s, are nucleoside antibiotics that inhibit the enzyme bacterial translocase I involved in peptidoglycan cell wall biosynthesis. Within the biosynthetic gene cluster for the A-500359s exists a gene encoding a putative aminoglycoside 3-phosphotransferase that was previously demonstrated to be highly expressed during the production of A-500359s and confers selective resistance to capuramycins when expressed in heterologous hosts. A similar gene (capP) was identified within the biosynthetic gene cluster for the A-503083s, and CapP is now shown to similarly confer selective resistance to capuramycins. Recombinant CapP was produced and purified from Escherichia coli, and the function of CapP is established as an ATP-dependent capuramycin phosphotransferase that regio-specifically transfers the ␥-phosphate to the 3؆-hydroxyl of the unsaturated hexuronic acid moiety of A-503083 B. Kinetic analysis with the three major A-503083 congeners suggests that CapP preferentially phosphorylates A-503083s containing an aminocaprolactam moiety attached to the hexuronic acid, and bi-substrate kinetic analysis was consistent with CapP employing a sequential kinetic mechanism similar to most known aminoglycoside 3-phosphotransferases. The purified CapP product lost its antibiotic activity against Mycobacterium smegmatis, and this loss in bioactivity is primarily due to a 272-fold increase in the IC 50 in the bacterial translocase I-catalyzed reaction. The results establish CapP-mediated phosphorylation as a mechanism of resistance to capuramycins and now set the stage to explore this strategy of resistance as a potential mechanism inherent to pathogens and provide the impetus for preparing second generation analogues as a preemptive strike to such resistance strategies.Infectious and parasitic diseases are the second leading cause of death worldwide, and this includes more than 1.6 million deaths by tuberculosis (TB) 4 in 2006 (1). Alarmingly, nearly 5% of all of the new cases of TB during this same year were caused by Mycobacterium tuberculosis, the primary causative agent of TB, that had resistance to at least one of the commonly used antibiotics to treat TB (2). To compound this problematic emergence of drug resistance, the discovery and development of new antibiotics have continued to decline with only a few new classes of antibiotics introduced into the clinic within the past few decades (3, 4). Thus, there is a great need for new antibiotics with novel modes of action and unique structures to combat multiple drug-resistant pathogens such as M. tuberculosis.Capuramycin was discovered from Streptomyces griseus 446-S3 based on gross antibacterial activity (5), and analogues termed A-500359s from S. griseus SANK 60196 (6 -8) and A-503083s from Streptomyces sp. SANK 62799 (9) were subsequently discovered using a specific screen aimed at identifying bacterial translocase I (MraY) inhibitors. MraY initiates the lipid cycle of peptidoglycan cell wall biosynthesis, a pathway ...