Latent LytM at 1.3 Å Resolution

LytM, an autolysin from Staphylococcus aureus, is a Zn2+-dependent glycyl-glycine endopeptidase with a characteristic HxH motif that belongs to the lysostaphin-type (MEROPS M23/37) of metallopeptidases. Here, we present the 1.3 Å crystal structure of LytM, the first structure of a lysostaphin-type peptidase. In the LytM structure, the Zn2+ is tetrahedrally coordinated by the side-chains of N117, H210, D214 and H293, the second histidine of the HxH motif. Although close to the active-site, H291, the first histidine of the HxH motif, is not directly involved in Zn2+-coordination, and there is no water molecule in the coordination sphere of the Zn2+, suggesting that the crystal structure shows a latent form of the enzyme. Although LytM has not previously been considered as a proenzyme, we show that a truncated version of LytM that lacks the N-terminal part with the poorly conserved Zn2+ ligand N117 has much higher specific activity than full-length enzyme. This observation is consistent with the known removal of profragments in other lysostaphin-type proteins and with a prior observation of an active LytM degradation fragment in S. aureus supernatant. The “asparagine switch” in LytM is analogous to the “cysteine switch” in pro-matrix metalloproteases.