Crystal structure of tryptophanase

Abstract

The X-ray structure of tryptophanase (Tnase) reveals the interactions responsible for binding of the pyridoxal 5′-phosphate (PLP) and atomic details of the K + binding site essential for catalysis. The structure of holo Tnase from Proteus vulgaris (space group P2 12 12 1 with a = 115.0 Å, b = 118.2 Å, c = 153.7 Å) has been determined at 2.1 Å resolution by molecular replacement using tyrosine phenol-lyase (TPL) coordinates. The final model of Tnase, refined to an R-factor of 18.7%, ( R free = 22.8%) suggests that the PLP-enzyme form observed in the structure is a ketoenamine. PLP is bound in a cleft formed by both the small and large domains of one subunit and the large domain of the adjacent subunit in the so-called “catalytic” dimer. The K + cations are located on the interface of the subunits in the dimer. The structure of the catalytic dimer and mode of PLP binding in Tnase resemble those found in aspartate aminotransferase, TPL, ω-amino acid pyruvate aminotransferase, dialkylglycine decarboxylase (DGD), cystathionine β-lyase and ornithine decarboxylase. No structural similarity has been detected between Tnase and the β 2 dimer of tryptophan synthase which catalyses the same β-replacement reaction. The single monovalent cation binding site of Tnase is similar to that of TPL, but differs from either of those in DGD.