Structure of mammalian ornithine decarboxylase at 1.6 angstrom resolution:stereochemical implications of PLP-dependent amino acid decarboxylases

Background: Pyridoxal-5'-phosphate (PLP) dependent enzymes catalyze a broad range of reactions, resulting in bond cleavage at C alpha, C beta, or C ga mma carbons of D and L amino acid substrates. Ornithine decarboxylase (ODC) is a PLP-dependent enzyme that controls a critical step in the biosynthesi s of polyamines, small organic polycations whose controlled levels are esse ntial for proper growth. ODC inhibition has applications for the treatment of certain cancers and parasitic ailments such as African sleeping sickness , Results: The structure of truncated mouse ODC (mODC') was determined by mul tiple isomorphous replacement methods and refined to 1.6 A resolution. This is the first structure of a Group IV decarboxylase. The monomer contains t wo domains: an alpha/beta barrel that binds the cofactor, and a second doma in consisting mostly of beta structure. Only the dimer is catalytically act ive, as the active sites are constructed of residues from both monomers. Th e interactions stabilizing the dimer shed light on its regulation by antizy me. The overall structure and the environment of the cofactor are compared with those of alanine racemase. Conclusions: The analysis of the mODC' structure and its comparison with al anine racemase, together with modeling studies of the external aldimine int ermediate, provide insight into the stereochemical characteristics of PLP-d ependent decarboxylation, The structure comparison reveals stereochemical d ifferences with other PLP-dependent enzymes and the bacterial ODC, These ch aracteristics may be exploited in the design of new inhibitors specific for eukaryotic and bacterial ODCs, and provide the basis for a detailed unders tanding of the mechanism by which these enzymes regulate reaction specifici ty.