Stereochemistry of the formation of cysteine by O-acetylserine sulfhydrase

The multifaceted pyridoxal 5'-phosphate-dependent O-acetylserine sulfhydrylase

Cysteine is the final product of the reductive sulfate assimilation pathway in bacteria and plants and serves as the precursor for all sulfur-containing biological compounds, such as methionine, S-adenosyl methionine, iron-sulfur clusters and glutathione. Moreover, in several microorganisms cysteine plays a role as a reducing agent, eventually counteracting host oxidative defense strategies. Cysteine is synthesized by the PLP-dependent O-acetylserine sulfhydrylase, a dimeric enzyme belonging to the fold type II, catalyzing a beta-replacement reaction. In this review, the spectroscopic properties, catalytic mechanism, three-dimensional structure, conformational changes accompanying catalysis, determinants of enzyme stability, role of selected amino acids in catalysis, and the regulation of enzyme activity by ligands and interaction with serine acetyltransferase, the preceding enzyme in the biosynthetic pathway, are described. Given the key biological role played by O-acetylserine sulfhydrylase in bacteria, inhibitors with potential antibiotic activity have been developed. This article is part of a Special Issue entitled: Pyridoxal Phospate Enzymology.

Tartrate dehydrogenase reductive decarboxylation: stereochemical generation of diastereotopically deuterated hydroxymethylenes

Tartrate dehydrogenase catalyzes the reductive decarboxylation of meso-tartrate to glycerate. Concomitant with the ketonization of the intermediate enolate the C3 hydroxymethylene of glycerate necessarily acquires a proton from solvent. In D2O, the proton is shown to be added stereospecifically to form (2R,3R)-[3-2H]glycerate. The 1H-NMR assignments of the diastereotopic C3 protons of glycerate were confirmed by the enzymatic conversion of [1R-2H]fructose-6-phosphate to (2R,3R)-[3-2H]glycerate. The decarboxylation-protonation occurs with retention of configuration, implying that the general acid is positioned on the same face of the intermediate as the departing carboxylate. The stereochemically pure (2R,3R)-[3-2H]glycerate is readily synthesized and serves as a chiral hydroxymethylene synthon as demonstrated by the synthesis of (2S,3R)-[3-2H]serine.

Yeast cystathionine beta-synthase reacts with L-allothreonine, a non-natural substrate, and L-homocysteine to form a new amino acid, 3-methyl-L-cystathionine

Our studies of the reaction mechanism of cystathionine beta-synthase from yeast (Saccharomyces cerevisiae) are facilitated by the spectroscopic properties of the pyridoxal phosphate coenzyme. The enzyme catalyzes the reaction of L-serine with L-homocysteine to form L-cystathionine through a series of pyridoxal phosphate intermediates. In this work, we explore the substrate specificity of the enzyme by use of substrate analogues combined with kinetic measurements under pre-steady-state conditions and with circular dichroism and fluorescence spectroscopy under steady-state conditions. Our results show that L-allothreonine, but not L-threonine, serves as an effective substrate. L-Allothreonine reacts with the pyridoxal phosphate cofactor to form a stable 3-methyl aminoacrylate intermediate that absorbs maximally at 446 nm. The rapid-scanning stopped-flow results show that the binding of L-allothreonine as the external aldimine is faster than formation of the 3-methyl aminoacrylate intermediate. The 3-methyl aminoacrylate intermediate reacts with L-homocysteine to form a new amino acid, 3-methyl-L-cystathionine, which was characterized by nuclear magnetic resonance spectroscopy. This new amino acid may be a useful analogue of L-cystathionine.

Pyridoxal 5'-phosphate-dependent alpha,beta-elimination reactions: mechanism of O-acetylserine sulfhydrylase

O-Acetylserine sulfhydrylase catalyzes the replacement of the beta-acetoxy group of O-acetyl-L-serine with sulfide to generate L-cysteine. The reaction represents the final step in the biosynthesis of L-cysteine in enteric bacteria and plants. A quinonoid intermediate has not been detected using a variety of kinetic and spectroscopic probes for the wild-type or mutant enzymes, ruling out an E1 mechanism. The structure of the external Schiff base intermediate indicates an anti elimination. O-Acetylserine sulfhydrylase is the only known pyridoxal 5'-phosphate-dependent enzyme that catalyzes a beta-elimination reaction to have an anti E2 mechanism.

O-acetylserine sulfhydrylase

The 31P NMR data suggest slight differences in the structures around the 5'-P for the internal Schiff base and the lanthionine external Schiff base (both largely ketoeneamine) and a large difference for enolimine portion of the serine external Schiff base. Addition of cysteine or serine increase delayed fluorescence and triplet to singlet energy transfer. Addition of OAS exhibits a splitting of the 0,0 vibronic, the result of two distinct conformations, likely enolimine and ketoeneamine tautomers. Nonetheless, the alpha-amino-acrylate Schiff base conformation differs from either the internal or external Schiff base conformations. All of the time-resolved fluorescence data are consistent with conformation changes reflecting redistribution of ketoeneamine and enolimine tautomers as catalysis occurs. It is important to remember that the structural changes are substantial. The native structure (internal Schiff base) is active site open, while the K41A mutant enzyme (ketoeneamine external Schiff base) is active site closed. The trigger for the conformational change from open to closed as one goes from the internal to external Schiff base is the occupancy of the alpha-carboxyl subsite of the active site (Burkhard et al., 1999). Associated with this, as observed in pH-rate profiles, pH-dependent changes in phosphorescence, and pH-dependent changes in fluorescence enhancement upon binding acetate or cysteine is an enzyme group with a pK in the range 7-8. Dependent on the protonation state of the enzyme group, structural changes likely occur that also reflect a redistribution of the tautomeric equilibrium. Finally, the minimal catalytic cycle can likely be pictured as shown in Fig. 20. The changes may be pH dependent, and the open conformations for the internal Schiff base and the alpha-aminoacrylate Schiff base are not identical structurally, as expected because of the increased stability of the latter.

Catalytic competence of O-acetylserine sulfhydrylase in the crystal probed by polarized absorption microspectrophotometry

The reactions of the pyridoxal 5'-phosphate-dependent enzyme O-acetylserine sulfhydrylase with the substrate O-acetyl-L-serine and substrate analogs have been investigated in the crystalline state by single-crystal polarized absorption microspectrophotometry. This approach has allowed us to examine the catalytic competence of the enzyme in different crystalline states, one of which was used to determine the three-dimensional structure; experimental conditions were defined for the accumulation of catalytic intermediates in the crystal suitable for crystallographic analyses.O-Acetyl-L-serine reacts with the enzyme in one of the crystal forms leading via a beta-elimination reaction to the accumulation of the alpha-aminoacrylate Schiff base, absorbing maximally at 320 and 470 nm, as in solution. The dissociation constant for the alpha-aminoacrylate Schiff base is in the millimolar range, 500-fold higher than in solution, suggesting that crystal lattice interactions may oppose functionally relevant conformational changes. The dissociation constant exhibits a bell-shaped dependence on pH centered at pH 7. At this pH the alpha-aminoacrylate species slowly decays with time (30% decrease in 24 hours). The alpha-aminoacrylate intermediate readily reacts with sodium azide, an analog of sulfide, the natural nucleophilic agent, to give a new amino acid and the native enzyme, indicating that the crystalline enzyme catalyzes the overall beta-replacement reaction as in solution. In other crystal forms, including that used for the X-ray investigation, O-acetyl-L-serine either has an even higher dissociation constant or causes crystal damage upon binding. When the crystalline enzyme reacts with either L-cysteine or L-serine, the external aldimine intermediate is formed. The dissociation constants for both substrate analogs are closer to those observed in solution and are modulated by pH as in solution. Findings demonstrate that O-acetylserine sulfhydrylase is catalytically competent in the crystal although some regions of the molecule, likely involved in an open-closed transition induced by O-acetyl-L-serine binding, may have a limited flexibility. The accumulation in the crystal of both the external aldimine and the alpha-aminoacrylate intermediate makes feasible their structural determination and, therefore, the elucidation of the catalytic pathway at the molecular level.

Deuterium labelling in NMR structural analysis of larger proteins

In the last few years since the early NMR structural studies of small proteins such as glucagon (Braunet al.1983) andlacrepresser headpiece (Zuiderweget al.1984) the quality of the structure determinations have improved considerably. Of major importance has been the introduction of phase sensitive detection in the Tl dimension (Stateset al.1982; Marion & Wüthrich, 1983) which has allowed for absorption presentation of 2D data with the resulting enhancement in resolution, accuracy of coupling constant measurements and accuracy of peak volume integrations. Introduction of new pulse sequences, advances in instrumentation and further developments in the structure calculation algorithms have also helped improve the quality of NMR structural analyses of proteins.

On the synthesis of serine and homoserine samples asymmetrically labelled with tritium and deuterium in the hydroxymethylene group

(1R) [1-3H, 2H1] 3-Phenylpropanol, the key intermediate in the synthesis of (4R) [4-3H, 2H1] D,L-homoserine and of the (4S)-isomer, is obtained from (1S) [1-2H1] 3-phenylpropanol and (1RS) [1-3H] ethanol upon incubation with yeast alcohol dehydrogenase and NAD+; under similar conditions 2-phenylethanol undergoes very small exchange with [1-2H2] ethanol.