Crystal structure of MHC class II-associated p41 Ii fragment bound to cathepsin L reveals the structural basis for differentiation between cathepsinsL and S

The lysosomal cysteine proteases cathepsins S and L play crucial roles in t he degradation of the invariant chain during maturation of MHC class II mol ecules and antigen processing. The p41 form of the invariant chain includes a fragment which specifically inhibits cathepsin L but not S, The crystal structure of the p41 fragment, a homologue of the thyroglobulin type-1 doma ins, has been determined at 2.0 Angstrom resolution in complex with catheps in L, The structure of the p41 fragment demonstrates a novel fold, consisti ng of two subdomains, each stabilized by disulfide bridges. The first subdo main is an alpha-helix-beta-strand arrangement, whereas the second subdomai n has a predominantly beta-strand arrangement. The wedge shape and three-lo op arrangement of the p41 fragment bound to the active site cleft of cathep sin L are reminiscent of the inhibitory edge of cystatins, thus demonstrati ng the first example of convergent evolution observed in cysteine protease inhibitors. However, the different fold of the p41 fragment results in addi tional contacts with the top of the R-domain of the enzymes, which defines the specificity-determining S2 and S1' substrate-binding sites. This enable s inhibitors based on the thyroglobulin type-1 domain fold, in contrast to the rather non-selective cystatins, to exhibit specificity for their target enzymes.