Arginases and deacetylases are metallohydrolases that catalyze two distinct chemical transformations. The arginases catalyze the hydrolysis of the guanidinium group of arginine by using a hydroxide ion bridging the binuclear manganese cluster (Mn2+A-Mn2+B) for nucleophilic attack. The deacetylases catalyze the hydrolysis of amide bonds by using a mononuclear Zn2+-ion activated water molecule as the nucleophile. Despite the diverse functions, metallohydrolases of the arginase-deacetylase superfamily share the same characteristic α/β hydrolase core fold and a conserved metal binding site (the Mn2+B site in arginase corresponds to the catalytic Zn2+ site in deacetylase) which is essential for catalysis in both enzymes. We report crystal structure of formiminoglutamase from the parasitic protozoan Trypanosoma cruzi and confirm that formiminoglutamase is a Mn2+-requiring hydrolase that belongs to the arginase-deacetylase superfamily. We also report the crystal structure of an arginase-like protein from Trypanosoma brucei (TbARG) with unknown function. Although its biological role remains enigmatic, the evolutionarily more conserved Mn2+B site can be readily restored in TbARG through side-directed mutagenesis. We also report crystal structure of an arginase from the parasite Schistosoma mansoni (SmARG). Structural comparison of SmARG complexed with second-generation arginase inhibitors (α,α-disubstituted boronic acid inhibitors) with another parasitic arginase from Leishmania mexicana and human arginases reveal interesting differences in the binding modes of the additional α-substituents. Reversible lysine acetylation rivals phosphorylation in the regulation of protein structure and function, and inhibition of the “eraser” histone deacetylase (HDAC) is a validated approach for cancer chemotherapy. HDAC6, the sole HDAC that harbors a full duplication of catalytic domain (CD1 and CD2), is a cytosolic lysine deacetylase known to deacetylate α-tubulin, heat-shock protein 90, etc. Here, we report HDAC6 structures that provide new insights about mechanism, catalysis, and inhibitor binding. In light of biochemical studies, we reveal a “gate constriction” mechanism responsible for the strict substrate specificity of CD1 versus broad substrate specificity of CD2. Analysis of other isozymes indicates that the closest relative HDAC10 contains an alternative gatekeeper that favors catalysis with acetylpolyamines. Indeed, we provide structural evidence that HDAC10 is the long-sought mammalian N8-acetylspermidine deacetylase whose identity has remained elusive for 30 years.