The role of acidic dissociation of substrate's phenol group in the mechanism of tyrosine phenol-lyase

Design of a halogen bond catalyzed DNA endonuclease

In this study, we expand the repertoire of biological catalysts by showing that a halogen bond (X-bond) can functionally replace the magnesium (Mg2+) cofactor in mouse endonuclease G (mEndoG). We mutated the metal coordinating glutamate E136 in mEndoG to a meta-halotyrosine (mXY, X = chlorine or iodine) to form a mXY-mEndoG construct that is both acid and base catalyzed. Under basic conditions, the enzyme is inactivated by the metal chelator ethylene diamine tetraacetic acid (EDTA), indicating that the halogen substituent facilitates deprotonation of the tyrosyl hydroxyl group, allowing recruitment of Mg2+ to restore the metal-dependent catalytic center. At low pHs, we observe that the mXY-mEndoG is resistant to EDTA inactivation and that the iodinated constructed is significantly more active than the chlorinated analogue. These results implicate a hydrogen bond (H-bond) enhanced X-bond as the catalyst in the mXY-mEndoG, with asparagine N103 serving as the H-bond donor that communicates the protonation state of histidine H104 to the halogen. This model is supported by mutation studies and electrostatic potential (ESP) calculations on models for the protonated and unprotonated mXY···N103···H104 system compared to the Mg2+ coordination complex of the wild type. Thus, we have designed and engineered an enzyme that utilizes an unnatural catalyst in its active site-a catalytic X-bonding enzyme, or cX-Zyme-by controverting what constitutes a metal catalyst in biochemistry.

Purification and Biochemical Characterization of a Tyrosine Phenol-lyase from Morganella morganii

Tyrosine phenol-lyase (TPL) is a valuable and cost-effective biocatalyst for the biosynthesis of L-tyrosine and its derivatives, which are valuable intermediates in the pharmaceutical industry. A TPL from Morganella morganii (Mm-TPL) was overexpressed in Escherichia coli and characterized. Mm-TPL was determined as a homotetramer with molecular weight of 52 kDa per subunit. Its optimal temperature and pH for β-elimination of L-tyrosine were 45 °C and pH 8.5, respectively. Mm-TPL manifested strict substrate specificity for the reverse reaction of β-elimination and ortho- and meta-substituted phenols with small steric size were preferred substrates. The enzyme showed excellent catalytic performance for synthesis of L-tyrosine, 3-fluoro-L-tyrosine, and L-DOPA with a yield of 98.1%, 95.1%, and 87.2%, respectively. Furthermore, the fed-batch bioprocess displayed space-time yields of 9.6 g L^-1 h^-1 for L-tyrosine and 4.2 g L^-1 h^-1 for 3-fluoro-L-tyrosine with a yield of 67.4 g L^-1 and 29.5 g L^-1, respectively. These results demonstrated the great potential of Mm-TPL for industrial application.

Site-directed mutagenesis to improve the thermostability of tyrosine phenol-lyase

3,4-Dihydroxyphenyl-L-alanine (L-DOPA) is the most important antiparkinsonian drug, and tyrosine phenol-lyase (TPL)-based enzyme catalysis process is one of the most adopted methods on industrial scale production. TPL activity and stability represent the rate-limiting step in L-DOPA synthesis. Here, 25 TPL mutants were predicted, and two were confirmed as exhibiting the highest L-DOPA production and named E313W and E313M. The L-DOPA production from E313W and E313M was 47.5 g/L and 62.1 g/L, which was 110.2 % and 174.8 % higher, respectively, than that observed from wild-type (WT) TPL. The K_m of E313W and E313M showed no apparent decrease, whereas the k_cat of E313W and E313M improved by 45.5 % and 36.4 %, respectively, relative to WT TPL. Additionally, E313W and E313M displayed improved thermostability, a higher melting temperature, and enhanced affinity between for pyridoxal-5'-phosphate. Structural analysis of the mutants suggested increased stability of the N-terminal region via enhanced interactions between the mutated residues and H317. Application of these mutants in a substrate fed-batch strategy as whole-cell biocatalysts allows realization of a cost-efficient short fermentation period resulting in high L-DOPA yield.

2-Fluorotyrosine is a valuable but understudied amino acid for protein-observed 19F NMR

Incorporation of ¹⁹F into proteins allows for the study of their molecular interactions via NMR. The study of ¹⁹F labeled aromatic amino acids has largely focused on 4-,5-, or 6-fluorotryptophan, 4-fluorophenylalanine, (4,5, or 6FW) or 3-fluorotyrosine (3FY), whereas 2-fluorotyrosine (2FY) has remained largely understudied. Here we report a comparative analysis with different fluorinated amino acids. We first report the NMR chemical shift responsiveness of five aromatic amino acid mimics to changes in solvent polarity and find that the most responsive, a mimic of 3FY, has a 2.9-fold greater change in chemical shift compared to the other amino acid mimics in aprotic solvents including the 2FY mimic. We also probed the utility of 2FY for ¹⁹F NMR by measuring its NMR relaxation properties in solution and the chemical shift anisotropy (CSA) of a polycrystalline sample of the amino acid by magic angle spinning. Using protein-observed fluorine NMR (PrOF NMR), we compared the influence of 2FY and 3FY incorporation on stability and pK_a perturbation when incorporated into the KIX domain of CBP/p300. Lastly, we investigated the ¹⁹F NMR response of both 2FY and 3FY-labeled proteins to a protein-protein interaction partner, MLL, and discovered that 2FY can report on allosteric interactions that are not observed with 3FY-labeling in this protein complex. The reduced perturbation to pK_a and similar but reduced CSA of 2FY to 3FY supports 2FY as a suitable alternative amino acid for incorporation into large proteins for ¹⁹F NMR analysis.

Crystal Structures of Wild-Type and F448A Mutant Citrobacter freundii Tyrosine Phenol-Lyase Complexed with a Substrate and Inhibitors: Implications for the Reaction Mechanism

Tyrosine phenol-lyase (TPL; EC 4.1.99.2) is a pyridoxal 5'-phosphate-dependent enzyme that catalyzes the reversible hydrolytic cleavage of l-tyrosine to phenol and ammonium pyruvate. We have shown previously that F448A TPL has k_cat and k_cat/ K_m values for l-tyrosine reduced by ∼10⁴-fold [Phillips, R. S., Vita, A., Spivey, J. B., Rudloff, A. P., Driscoll, M. D., and Hay, S. (2016) ACS Catal. 6, 6770-6779]. We have now obtained crystal structures of F448A TPL and complexes with l-alanine, l-methionine, l-phenylalanine, and 3-F-l-tyrosine at 2.05-2.27 Å and the complex of wild-type TPL with l-phenylalanine at 1.8 Å. The small domain of F448A TPL, where Phe-448 is located, is more disordered in chain A than in wild-type TPL. The complexes of F448A TPL with l-alanine and l-phenylalanine are in an open conformation in both chains, while the complex with l-methionine is a 52:48 open:closed equilibrium mixture in chain A. Wild-type TPL with l-alanine is closed in chain A and open in chain B, and the complex with l-phenylalanine is a 56:44 open:closed mixture in chain A. Thus, the Phe-448 to alanine mutation affects the conformational equilibrium of open and closed active sites. The structure of the 3-F-l-tyrosine quinonoid complex of F448A TPL is unstrained and in an open conformation, with a hydrogen bond from the phenolic OH to Thr-124. These results support our previous conclusion that ground-state strain plays a critical role in the mechanism of TPL.

The Metabolism and Dechlorination of Chlorotyrosine in Vivo

During inflammation, neutrophil- and monocyte-derived myeloperoxidase catalyzes the formation of hypochlorous acid, which can chlorinate tyrosine residues in proteins to form chlorotyrosine. However, little is known of the metabolism and disposition of chlorotyrosine in vivo. Following infusion of deuterium-labeled [D(4)]chlorotyrosine into Sprague-Dawley rats, the major urinary metabolites were identified by mass spectrometry. 3-Chloro-4-hydroxyphenylacetic acid was identified as the major chlorinated metabolite of chlorotyrosine and accounted for 3.6 +/- 0.3% of infused [D(4)]chlorotyrosine. The striking observation was that approximately 40% (39 +/- 1%) of infused [D(4)]chlorotyrosine was dechlorinated and excreted in the urine as deuterated 4-hydroxyphenylacetic acid, a major metabolite of tyrosine. 1.1 +/- 0.1% of infused [D(4)]chlorotyrosine was excreted as [D(4)]tyrosine. To determine whether protein-bound chlorotyrosine could undergo dechlorination, chlorinated albumin was incubated with liver homogenate from mutant rats, which did not synthesize albumin. There was approximately 20% decrease in the chlorotyrosine content over 1 h. This study is the first to describe the dechlorination of chlorotyrosine as the major metabolic pathway to eliminate this modified amino acid in vivo.

A twisted base? The role of arginine in enzyme-catalyzed proton abstractions

Arginine residues are generally considered poor candidates for the role of general bases because they are predominantly protonated at physiological pH. Nonetheless, Arg residues have recently emerged as general bases in several enzymes: IMP dehydrogenase, pectate/pectin lyases, fumarate reductase, and l-aspartate oxidase. The experimental evidence suggesting this mechanistic function is reviewed. Although these enzymes have several different folds and distinct evolutionary origins, a common structural motif is found where the critical Arg residue is solvent accessible and adjacent to carboxylate groups. The chemistry of the guanidine group suggests unique strategies to lower the pK(a) of Arg. Lastly, the presumption that general bases must be predominantly deprotonated is revisited.