Aldolases are a group of enzymes that are able to catalyze in a reversible and stereoselective manner, one of the most fundamental reactions in organic chemistry, the formation of carbon-carbon bonds. Being key enzymes in many different metabolic processes, Class II pyruvate aldolases are metal dependent enzymes, specific for pyruvate as a donor substrate. Aiming at understanding the molecular basis of such enzymatic mechanism and substrate specificity, we did the structural characterization of a class II pyruvate aldolase (wild type and mutant forms) from Sphingomonas wittichii RW1 (SwHKA), that was shown to displayed an unusual promiscuity toward structural analogues of pyruvate. We were able to show how SwHKA is able to take hydroxypyruvate as donor substrate and to identify key residues involved in the enzymatic mechanism and in the stabilization of the hydroxypyruvate in the active site. Furthermore, we were able isolate and characterize for the first time the resting state of the enzyme, and to show that its metal cofactor undergoes a dynamic oscillation between two coordination spheres of distinct properties.