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Isoaspartyl dipeptidase (IadA) is an enzyme that catalyzes the hydrolysis of an isoaspartyl dipeptide-like moiety, which can be inappropriately formed in proteins, between the β-carboxyl group side chain of Asp and the amino group of the following amino acid. Here, we have determined the structures of an isoaspartyl dipeptidase ( Cps IadA) from  Colwellia psychrerythraea , both ligand-free and that complexed with β-isoaspartyl lysine, at 1.85-Å and 2.33-Å resolution, respectively. In both structures,  Cps IadA formed an octamer with two Zn ions in the active site. A structural comparison with  Escherichia coli  isoaspartyl dipeptidase ( Eco IadA) revealed a major difference in the structure of the active site. For metal ion coordination,  Cps IadA has a Glu166 residue in the active site, whereas  Eco IadA has a post-translationally carbamylated-lysine 162 residue. Site-directed mutagenesis studies confirmed that the Glu166 residue is critical for  Cps IadA enzymatic activity. This residue substitution from lysine to glutamate induces the protrusion of the β12-α8 loop into the active site to compensate for the loss of length of the side chain. In addition, the α3-β9 loop of  Cps IadA adopts a different conformation compared to  Eco IadA, which induces a change in the structure of the substrate-binding pocket. Despite  Cps IadA having a different active-site residue composition and substrate-binding pocket, there is only a slight difference in  Cps IadA substrate specificity compared with  Eco IadA. Comparative sequence analysis classified IadA-containing bacteria and archaea into two groups based on the active-site residue composition, with Type I IadAs having a glutamate residue and Type II IadAs having a carbamylated-lysine residue.  Cps IadA has maximal activity at pH 8–8.5 and 45°C, and was completely inactivated at 60°C. Despite being isolated from a psychrophilic bacteria,  Cps IadA is thermostable probably owing to its octameric structure. This is the first conclusive description of the structure and properties of a Type I IadA.

Crystal structure and functional characterization of an isoaspartyl dipeptidase (CpsIadA) from Colwellia psychrerythraea strain 34H