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Cysteine cathepsins play an indispensable role in proteolytic processing of the major histocompatibility complex class II-associated invariant chain (Ii) and foreign antigens in a number of antigen presenting cells. Previously it was shown that a fragment of 64 residues present in the p41 form of the Ii (p41 fragment) selectively inhibits the endopeptidase cathepsin L, whereas the activity of cathepsin S remains unaffected. Comparison of structures indicated that the selectivity of interactions between cysteine cathepsins and the p41 fragment is far from being understood and requires further investigation. The p41 fragment has now been shown also to inhibit human cathepsins V, K, and F (also, presumably, O) and mouse cathepsin L with K i values in the low nanomolar range. These K i values are sufficiently low to ensure complex formation at physiological concentrations. In addition we have found that the p41 fragment can inhibit cathepsin S too. These findings suggest that regulation of the proteolytic activity of most of the cysteine cathepsins by the p41 fragment is an important and widespread control mechanism of antigen presentation.In the processes of adaptive immunity, antigenic proteins are cleaved to peptides, some of which are loaded into the binding cleft of MHC 2 class II molecules for presentation on the surface of professional antigen-presenting cells (APCs) (1, 2). The degradation of antigenic proteins takes place in the endocytic compartments (endosomes and lysosomes) rich in proteolytic activity. The current list of protein-degrading enzymes in these compartments includes the group of cysteine cathepsins, asparaginyl endoprotease, the aspartic proteases cathepsins D and E, and thiol reductase GILT (3-5). This work is focused on cysteine cathepsins. Studies on gene knock-out mice showed that the pattern of antigenic peptide generation is not affected by the absence of cathepsins L and S (6), indicating redundant and overlapping roles within the group of cysteine cathepsins, although in certain cases specific roles in the degradation of antigens have been assigned to particular proteases (7,8).It is thought that the activity of proteases in the endocytic mixture is also regulated by protein inhibitors (4). A number of different inhibitors of cysteine cathepsins, including cystatins C and F and stefins A and B, have so far been localized in different types of APCs (9); however, direct and precise evidence regarding their involvement in the regulation of endosomal protease activity in APCs is still lacking (10, 11). Even more intriguing and less well investigated is the role of the inhibitory fragment of the p41 form of Ii (p41 fragment).Ii associates with the ␣ and ␤ chains of MHC class II molecules in the endoplasmic reticulum and is responsible for their proper folding and trafficking to endosomes (12), where the MHC class II molecules are freed from Ii by proteolytic processing of Ii. Ii exists in mouse in two (and in human, four) alternately spliced forms, p31 and p41, distinguished by an additio...

Peptidoglycan is a giant molecule that forms the cell wall that surrounds bacterial cells. It is composed of alternating N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) residues connected by -(1,4)-glycosidic bonds and cross-linked with short polypeptide chains. Owing to the increasing antibiotic resistance against drugs targeting peptidoglycan synthesis, studies of enzymes involved in the degradation of peptidoglycan, such as N-acetylglucosaminidases, may expose new, valuable drug targets. The scientific challenge addressed here is how lysozymes, muramidases which are likely to be the most studied enzymes ever, and bacterial N-acetylglucosaminidases discriminate between two glycosidic bonds that are different in sequence yet chemically equivalent in the same NAG-NAM polymers. In spite of more than fifty years of structural studies of lysozyme, it is still not known how the enzyme selects the bond to be cleaved. Using macromolecular crystallography, chemical synthesis and molecular modelling, this study explains how these two groups of enzymes based on an equivalent structural core exhibit a difference in selectivity. The crystal structures of Staphylococcus aureus N-acetylglucosaminidase autolysin E (AtlE) alone and in complex with fragments of peptidoglycan revealed that N-acetylglucosaminidases and muramidases approach the substrate at alternate glycosidic bond positions from opposite sides. The recognition pocket for NAM residues in the active site of N-acetylglucosaminidases may make them a suitable drug target.

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