The nef gene of primate lentiviruses encodes a myristoylated protein that is important for pathogenicity and the maintenance of high virus loads. A deletion in nef leads to a significant reduction of the pathogenicity of simian immunodeficiency virus (SIV) in macaques. At the cellular and biochemical levels, Nef has been shown to down-regulate CD4 and major histocompatibility complex class I molecules and to interact with cellular protein kinases. The importance of these activities for Nef function remains uncertain. We have prepared vaccinia virus recombinants expressing different alleles of SIV nef. When grown on TK- 143 cells, recombinants constructed with the nef allele from SIVmac1A11 produced typical plaques while recombinants expressing the nef allele from SIVmac239-R1 gave rise to plaques with altered morphology. By using chimeric Nef proteins and site-directed mutagenesis, the amino acid responsible for altered plaque formation was mapped to a leucine at residue 211. In vitro phosphorylation of immunoprecipitates prepared from cells infected with the vaccinia virus recombinants resulted in labeled proteins of 62 and 90 kDa. The recombinants differed in the ability to stimulate phosphorylation, and the leucine at residue 211 was again found to be the determining amino acid. These results might help elucidate the role of nef in the pathogenesis of SIV.