In the endocytic pathway of antigen-presenting cells, HLA-DM catalyzes the exchange between class II-associated invariant chain peptide (CLIP) and antigenic peptides onto major histocompatibility complex class II molecules. At low pH of lysosomal compartments, both HLA-DM and HLA-DR undergo conformational changes, and it was recently postulated that two partially exposed tryptophans on HLA-DM might be involved in the interaction between the two molecules. To define contact regions on HLA-DM, we have conducted site-directed mutagenesis on those two hydrophobic residues. The HLA-DM ␣W62A,W120A (DM W62A/W120A ) double mutant was expressed in HLA-DR ؉ HeLa cells expressing invariant chain, and the activity of this DM molecule was assessed. Flow cytometry analysis of cell surface DR-CLIP complexes revealed that DM W62A/W120A removes CLIP as efficiently as its wild-type counterpart. DM W62A/W120A was found in the endocytic pathway by immunofluorescence, and DM-DR complexes were immunoprecipitated from these cells at pH 5. Finally, mutations ␣W62A and W120A on HLA-DM did not affect the association with HLA-DO. The complex egresses the endoplasmic reticulum and accumulates in endocytic vesicles. Moreover, DO and DM W62A/W120A were co-immunoprecipitated at pH 7. We conclude that the ␣62 and 120 tryptophan residues are not required for the activity of DM, nor are they directly implicated in the interaction with DR or DO.Major histocompatibility complex class II molecules are primordial for activation of CD4ϩ T cells and for immunological response against pathogens (1). Three major histocompatibility complex II ␣/ heterodimers associate with a trimer of invariant chain (Ii) 1 to form a nanomeric complex in the endoplasmic reticulum (ER) (2). This association allows the proper folding and trafficking of the major histocompatibility complex II molecules (3-5). Gradual proteolysis of Ii occurs in the endocytic compartments by the sequential action of proteases including cathepsins (6). A residual peptide of Ii (CLIP) remains in the peptide groove of the class II molecule and stabilizes the heterodimer by preventing collapse of the groove (7,8). For most allotypes, CLIP must be actively removed to allow binding of antigenic peptides. HLA-DM, a nonclassical intracellular class II molecule, plays a central role in the efficiency of antigen presentation as it catalyzes CLIP release from HLA-DR and stabilizes the class II in a chaperone-like fashion (9 -14). In fact, mice lacking the H2-Ma gene express a high level of surface class II-CLIP complexes (15-17).The precise molecular mechanism of action of HLA-DM remains to be established. X-ray diffraction studies on HLA-DM crystals revealed a closed peptide-binding groove and an overall quaternary structure similar to classical class II molecules (18,19). Time-resolved fluorescence anisotropy and far-UV circular dichroism spectrum analysis using soluble HLA-DM revealed that its structure is quite rigid and that it is not subjected to gross pH-dependent conformational change. Ho...