The nef gene is required for optimal viral spread of human and simian immunodeficiency viruses. However, the molecular mechanisms underlying the action of the Nef proteins may not be identical for all viral families. Here we investigate the interaction between the Nef protein of human and simian immunodeficiency viruses and SH3 domains from Src family kinases. Using the yeast two-hybrid system and immunoblotting we show that, in contrast to HIV-1 Nef, SIV and HIV-2 Nef poorly interact with Hck SH3 but bind to Src and Fyn SH3 domains. The molecular basis of these differences in SH3 targeting was revealed by sequence analysis and homology modeling of the putative SH3-Nef structures. Three amino acids (Trp-113, Thr-117, and Gln-118) that localize in a "hydrophobic pocket" implicated in SH3 binding of HIV-1 Nef, are systematically substituted in SIV/HIV-2 alleles (by Tyr, Glu, and Glu, respectively). We demonstrate that site-directed mutagenesis of these residues in SIV mac239 Nef suffices to restore Hck SH3 binding and co-immunoprecipitation with full-length Hck from transfected cells. Our findings identify fundamental mechanistic differences in targeting of Src family kinases by HIV and SIV Nef. The herein described mechanism of SH3 selection by Nef via a "pocket" proximal to the canonical proline-rich motif may be a common feature for SH3 recognition by their natural ligands.The nef gene is conserved among all primate lentiviruses and has been implicated in optimal viral replication and disease induction by HIV-1 1 and SIV (1, 2). Substantial sequence polymorphism has been detected among nef alleles from various cloned isolates of HIV and SIV, suggesting that Nef proteins may have subtype-specific functions or possess different strategies to perform the same task. However, four stretches of residues have been identified that were highly conserved among sequences derived from AIDS patients but also from among sequences of HIV-2 and SIV (3). One of these stretches includes a Pro-Xaa-Xaa-Pro motif, the canonical Src homology (SH) 3 domain binding consensus, indicating that SH3 binding is a common feature of all types of Nef alleles.An intact PXXP motif is required for the potential of HIV-1 Nef to enhance viral growth and infectivity in cell cultures (4 -6). It has subsequently been shown that HIV-1 Nef binds with high affinity to the SH3 domains of the Src family kinases Hck and Lyn, whereas only with a modest affinity to SH3 domains of other members of the Src family (Lck, Fyn, and Src) (7,8). However, despite the PXXP motif being strictly conserved in all Nef proteins, an HIV-2 Nef allele has been reported to have lost the high affinity for Hck SH3 (9). Controversial data has further been collected for the requirement of the proline-rich motif for AIDS disease progression in infected macaques (10, 11). Especially, it was reported that a PXXP to AXXA mutated SIV mac239 protein could still bind to Src kinase (10), suggesting that SIV might have different strategies of interacting with the Src family of protein tyro...