Preliminary X-ray crystallographic analysis of tryptophanase from Escherichia coli

The chemo- enzymatic synthesis of labeled l-amino acids and some of their derivatives

This review compiles the combined chemical and enzymatic synthesis of aromatic l-amino acids (l-phenylalanine, l-tyrosine, l-DOPA, l-tryptophan, and their derivatives and precursors) specifically labeled with carbon and hydrogen isotopes, which were elaborated in our research group by the past 20 years. These compounds could be then employed to characterize the mechanisms of enzymatic reactions via kinetic and solvent isotope effects methods.

Structure of Escherichia coli tryptophanase purified from an alkaline-stressed bacterial culture

Tryptophanase is a bacterial enzyme involved in the degradation of tryptophan to indole, pyruvate and ammonia, which are compounds that are essential for bacterial survival. Tryptophanase is often overexpressed in stressed cultures. Large amounts of endogenous tryptophanase were purified from Escherichia coli BL21 strain overexpressing another recombinant protein. Tryptophanase was crystallized in space group P6522 in the apo form without pyridoxal 5'-phosphate bound in the active site.

Structures of Escherichia coli tryptophanase in holo and 'semi-holo' forms

Two crystal forms of Escherichia coli tryptophanase (tryptophan indole-lyase, Trpase) were obtained under the same crystallization conditions. Both forms belonged to the same space group P43212 but had slightly different unit-cell parameters. The holo crystal form, with pyridoxal phosphate (PLP) bound to Lys270 of both polypeptide chains in the asymmetric unit, diffracted to 2.9 Å resolution. The second crystal form diffracted to 3.2 Å resolution. Of the two subunits in the asymmetric unit, one was found in the holo form, while the other appeared to be in the apo form in a wide-open conformation with two sulfate ions bound in the vicinity of the active site. The conformation of all holo subunits is the same in both crystal forms. The structures suggest that Trpase is flexible in the apo form. Its conformation partially closes upon binding of PLP. The closed conformation might correspond to the enzyme in its active state with both cofactor and substrate bound in a similar way as in tyrosine phenol-lyase.

Tryptophan metabolism and brain function: focus on kynurenine and other indole metabolites

The synthesis of NAD (or NADP) from tryptophan involves a series of enzymes and the formation of a number of intermediates which are collectively called 'kynurenines.' In the late 1970s and early 1980s, it became clear that intraventricular administration of several 'kynurenines' could cause convulsions and that one of the 'kynurenines,' quinolinic acid, was an agonist of a sub-population of NMDA receptors and caused excitotoxic neuronal death. A related metabolite, kynurenic acid, could, on the other hand, reduce excitotoxin-induced neuronal death by antagonising ionotropic glutamate receptors. Since then, modifications in quinolinic and kynurenic acid synthesis have been proposed as a pathogenetic mechanism in Huntington's chorea and epilepsy. It was subsequently shown that a robust activation of the kynurenine pathway and a large accumulation of quinolinic acid in the central nervous system occurred in several inflammatory neurological disorders. More recently, it has been shown that 3OH-kynurenine or 3OH-anthranilic acid, two other kynurenine metabolites, may cause either apoptotic or necrotic neuronal death in cultures and that inhibitors of kynurenine hydroxylase may reduce neuronal death in in vitro and in vivo models of brain ischaemia or excitotoxicity. Finally, it has been reported that indole metabolites, indirectly linked to the kynurenine pathway, are able to modify neuronal function and animal behaviour by interacting with voltage-dependent Na+ channels. Oxindole, one of these metabolites, has sedative and anticonvulsant properties and accumulates in the blood and brain when liver function is impaired. In conclusion, a number of metabolites affecting brain function originate from tryptophan metabolism. Selective inhibitors of their forming enzymes may be useful to understand their role in physiology or as therapeutic agents in pathology.

Analysis of the pH- and ligand-induced spectral transitions of tryptophanase: activation of the coenzyme at the early steps of the catalytic cycle

Tryptophanase has an absorption maximum at 338 nm at high pH and 422 nm at low pH. The 422-nm absorption species has been considered to be the catalytically competent ketoenamine form of the Schiff base of pyridoxal 5'-phosphate with a lysine residue. The 338-nm absorption band showed an intense fluorescence band at 390 nm and not around 500 nm, indicating that the 338-nm absorption species is the substituted aldamine rather than an enolimine form of the Schiff base which has been suggested previously. To explore the mechanism of the enzyme that can exert its catalytic ability at high pH where most of its coenzyme exists as the catalytically incompetent aldamine structure, the reaction of tryptophanase with 3-indolepropionate, a substrate analogue that stops the reaction at the step of the Michaelis complex, was studied at various pH values and analogue concentrations. Kinetic analysis was done based on a scheme involving eight forms of the enzyme, i.e., the liganded and unliganded forms of the ketoenamine, the substituted aldamine structures, and their protonated and deprotonated forms. Kinetic parameters were obtained for each interconversion step. The results showed that the binding of 3-indolepropionate to tryptophanase shifts the equilibrium from the substituted aldamine to the ketoenamine structure over the entire pH region studied. This implies that in the reaction of tryptophanase with tryptophan at high pH, where the enzyme shows maximum activity, the binding of the substrate to the enzyme converts the inactive aldamine form of the coenzyme to the active ketoenamine form. Mechanisms for the activation process, in which a nucleophile is expelled from the aldamine either by steric hindrance of the nucleophile with the ligand or by the negative charge of the ligand alpha-carboxylate group that stabilizes the aldimine structure, were discussed.

Crystal structure of tryptophanase

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(1)2(1)2(1) with a = 115.0 A, b = 118.2 A, c = 153.7 A) has been determined at 2.1 A resolution by molecular replacement using tyrosine phenol-lyase (TPL) coordinates. The final model of Tnase, refined to an R-factor of 18.7%, (Rfree = 22.8%) suggests that the PLP-enzyme from 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 amino-transferase, TPL, omega-amino acid pyruvate aminotransferase, dialkylglycine decarboxylase (DGD), cystathionine beta-lyase and ornithine decarboxylase. No structural similarity has been detected between Tnase and the beta 2 dimer of tryptophan synthase which catalyses the same beta-replacement reaction. The single monovalent cation binding site of Tnase is similar to that of TPL, but differs from either of those in DGD.