In a previous study [Bulté, L. & Wollman, F.-A. (1992) Eur. J. Biochem. 204, 327-336], we identified a novel gamete-specific polypeptide of Chlamydomonas reinhardtii, M alpha. This 66-kDa polypeptide reacts with antibodies to cytochrome f and accumulates in gametes only in conditions that promote destabilisation of the cytochrome b6/f complex. Here, we show that M alpha is not a modification product of cytochrome f, but is part of protein M, a high-molecular-mass L-amino-acid oxidase located in the periplasm. It catalyzes oxidation of all L-amino acids tested, except cysteine. Using phenylalanine as a substrate, saturation of the enzymatic rate is reached at 2 microM. These characteristics suggest that protein M may operate in vivo as an efficient scavanger of ammonium from extracellular amino acids. The enzyme contains non-covalently bound FAD. It exists in two forms with essentially similar enzymatic properties, of 1.2-1.3 MDa and 0.9-1.0 MDa, respectively. The lighter form is an oligomer of M alpha, while the heavier form contains, in addition to M alpha, a second polypeptide of 135 kDa, M beta, in a molar ratio of 3-4 M alpha/M beta. Both polypeptides are glycosylated.