The Mycobacterium tuberculosis serine/threonine protein kinases are attractive potential drug targets, and protein kinase D (PknD) is particularly interesting, as it is autophosphorylated on 11 residues, binds proteins containing forkhead associated domains, and contains a beta-propeller motif that likely functions as an anchoring sensor domain. We created a pknD knockout of a clinical M. tuberculosis isolate, and found that on in vitro phosphorylation of cell wall fractions it lacked a family of phosphorylated polypeptides seen in the WT. Mass spectrometry identified the phosphorylated polypeptides as MmpL7, a transporter of the RND family. MmpL7 is essential for virulence, presumably because it transports polyketide virulence factors such as phthiocerol dimycocerosate (PDIM) to the cell wall. Phosphorylation of the MmpL family of transporters has not been previously described, but these results suggest that PknD, and perhaps other serine/threonine kinases, could regulate their critical role in the formation of the M. tuberculosis envelope.