The first enzyme in the microcystin (MC) degradation pathway identified in bacterial strains is coded by . mlrA gene and is referred to as microcystinase. To date, there has been no biochemical characterisation of this enzyme. The results presented herein show a successful heterologous expression of MlrA as well as mutational studies, partial purification and biochemical characterisation of the enzyme. The mutation and inhibition study confirmed previous ideas that MlrA is a metalloprotease and allowed to calculate the inhibition parameters. Moreover, the kinetic parameters of MC-LR linearization were measured showing that MlrA exhibits a positive cooperativity towards MC-LR. Furthermore, . in vitro experiments with . Escherichia coli cells expressing MlrA indicated the potency of the heterologous host to eliminate MCs with very high efficiency. This study reports a new approach to the analysis of a microcystin degrading enzyme, extends the knowledge about MC biodegradation and opens broad scope for future study.