L-Carnosine is a bioactive dipeptide (-alanyl-L-histidine) present in mammalian tissues, including the central nervous system, and has potential neuroprotective and neurotransmitter functions. In mammals, two types of L-carnosine-hydrolyzing enzymes (CN1 and CN2) have been cloned thus far, and they have been classified as metallopeptidases of the M20 family. The enzymatic activity of CN2 requires Mn 2؉ , and CN2 is inhibited by a nonhydrolyzable substrate analog, bestatin. Here, we present the crystal structures of mouse CN2 complexed with bestatin together with Zn 2؉ at a resolution of 1.7 Å and that with Mn 2؉ at 2.3 Å . CN2 is a homodimer in a noncrystallographic asymmetric unit, and the Mn 2؉ and Zn 2؉ complexes closely resemble each other in the overall structure. Each subunit is composed of two domains: domain A, which is complexed with bestatin and two metal ions, and domain B, which provides the major interface for dimer formation. The bestatin molecule bound to domain A interacts with several residues of domain B of the other subunit, and these interactions are likely to be essential for enzyme activity. Since the bestatin molecule is not accessible to the bulk water, substrate binding would require conformational flexibility between domains A and B. The active site structure and substrate-binding model provide a structural basis for the enzymatic activity and substrate specificity of CN2 and related enzymes.L-Carnosine (-alanyl-L-histidine) and structurally related dipeptides, such as homocarnosine (␥-aminobutyryl-L-histidine) and anserine (-alanyl-L-1-methylhistidine) are distributed in a wide variety of vertebrate tissues (1). L-Carnosine is present at particularly high concentrations in mammalian skeletal muscles and the brain, and it has been implicated in neuroprotection (2), the olfactory system (1), and hypothalamic neuronal networks (3). Our recent observations suggest that central and peripheral administration of L-carnosine at low doses attenuates 2-deoxyglucose-induced hyperglycemia (4) and suppresses peripheral sympathetic nerve activity (5, 6). These effects of L-carnosine are suppressed by central administration of thioperamide, a histamine H3 blocker. This suggests that L-carnosine regulates the autonomic nervous system via the hypothalamic histaminergic neurons (4 -6). In addition, the dipeptide exhibits antioxidant and free radical scavenger properties via complexation of transition metals, such as zinc and copper, suggesting that it is also involved in neuroprotection from oxidative stress (2, 8, 9). L-Carnosine is synthesized from -alanine and L-histidine by carnosine synthetase and is degraded by intra-and extracellular dipeptidases known as carnosinases. Their enzymatic activities are regulated under various physiological conditions (10). Carnosinase was first isolated (11) from the porcine kidney in 1949 and was subsequently found to be widely distributed in tissues of rodents and higher mammals (12-15). Recently, two types of carnosinases were identified in humans and mice: h...