Thesis (Ph. D.)--University of Hong Kong, 2001. / Includes bibliographical references (leaves 203-238).

The catechol meta-fission pathway, a degradation pathway for simple aromatic compounds, is rich in enzyme chemistry and replete with structural and evolutionary diversity. Vinyl pyruvate hydratase (VPH) and MhpD catalyze the same reaction in this pathway, but in different bacterial species. These metal ion-dependent enzymes reportedly catalyze a 1,5-keto-enol tautomerization reaction followed by a Michael addition of water. MhpD, and most likely VPH, are members of the fumarylacetoacetate hydrolase (FAH) superfamily. The crystal structure of MhpD and the sequence of VPH identified four potential active site residues, Lys-60, Leu-72, Asp-78, and Ser-160 (Ser-161 in VPH). The K60A and D78N mutants of VPH and MhpD had the most damaging effects on catalysis. Moreover, the K60A mutant seemingly uncoupled tautomerization from hydration and provided evidence for an [alpha, beta]-unsaturated ketone in the reaction. The effects of the L72A and S160A (S161A in VPH) mutants were smaller, suggesting less important roles in the mechanism. 5-(carboxymethyl)-2-Oxo-3-hexene-1,6-dioate decarboxylase (COHED) is a metal ion-dependent enzyme in the homoprotocatechuate (HPC) pathway, a chromosomally encoded meta-fission pathway from Escherichia coli C that parallels the catechol meta-fission pathway. COHED is also a member of the FAH superfamily. It is a monomeric protein with two domains. It is postulated that the C-terminal domain catalyzes the decarboxylation reaction and the N-terminal domain carries out the 1,3-keto-enol tautomerization reaction. Site-directed mutagenesis, NMR, and kinetic analysis with different substrates and inhibitors have identified three potential active-site residues Glu-276, Glu-278 (in the C-terminal domain), and Lys-110 (in the N-terminal domain). Replacement of either glutamate with a glutamine eliminated both the decarboxylase and tautomerase activities. The K110A mutant also diminished both activities, but more importantly eliminated the C-3 proton/deuteron exchange reaction observed for substrate analogs. The enzymes of the catechol and homoprotocatechuate pathways provide examples of enzyme optimization toward a specific substrate even among related compounds, as reflected by the FAH superfamily. Hence, the results of these studies add to the growing body of information about how enzymes evolve and how pathways are assembled. / text

Thesis (Ph. D.)--University of Texas at Austin, 2008. / Vita. Includes bibliographical references.

This document only includes an excerpt of the corresponding thesis or dissertation. To request a digital scan of the full text, please contact the Ruth Lilly Medical Library's Interlibrary Loan Department (rlmlill@iu.edu).

Propionyl carboxylase purified from bovine liver mitochondria catalyzes the carboxylation of 992 micromoles of propionyl-CoA per hour per milligram of protein. Relative carboxylation rates for acetyl-, propionyl-, butyryl-, and valeryl-CoA remain constant during purification. The carboxylase is inhibited by PCMB, N-ethylmaleimide, and iodoacetamide; and the inhibition by PCMB can be almost completely reversed by GSH. The K_m values for acetyl-CoA, propionyl-CoA, butyryl-CoA, valeryh-CoA, propionyl pantetheine, ATP, and HCOj were determined. The K_m values for the aeyl-CoA derivatives are approximately the same while there is a 200-fold difference between the V_m values for propionyl-CoA and valeryl-CoA. Coenzyme A and valeryl-CoA, but not propionyl pantetheine were found to be competitive inhibitors of propionyl carboxylase. The apparent equilibrium constant for the enzymatic propionyl-CoA carboxylation reaction at pH 8.15 and 37°c is 8.1 x 10^-3 and the Δ F°₃₁₀ calculated from this constant is 2970 calories per mole. / Master of Science

published_or_final_version / Dentistry / Doctoral / Doctor of Philosophy

No description available.

Increasing consumer demand for fresh fishery products with minimized loss of their nutritional properties is forcing food industry to look for alternative technologies to maintain the fresh attributes, stability and safety of foods. Demand for fresh tuna fish is no exception, being a valuable source of nutrients with immense health benefits. However, this product is highly perishable and has been commonly implicated in scombroid (histamine) poisoning caused by microbial decarboxylation of histidine contained in high levels in the tissues of scombroid fishes. Current techniques are inadequate for the prevention of histamine formation in fresh fishery products and high pressure processing is a potential alternative for it can inactivate microorganisms and enzymes, without affecting (or only minimally altering) the quality characteristics of foodstuffs. Previous studies have shown a decrease in histamine formation after a high pressure treatment and this study focuses on the effect of high pressure on the histidine decarboxylase enzyme and selected histamine forming microorganisms involved in histamine formation. / Commercial histidine decarboxylase suspended in different media (buffer solution and fish slurry with and without added histidine) was submitted to different high pressure treatments (200--400 MPa) with distinct time durations (0--60 min) at room temperature (20°C--25°C). Enzymatic activity of pressure treated and control samples were then compared by measuring histamine formation. Results were similar in all media; a 200 MPa treatment increased the enzymatic activity a little more than 20% as time increased; a 300 MPa treatment increased activity over 20% at first, followed by a decrease in activity as time increased only to reach a level of residual activity similar or only slightly lower than control samples; and a 400 MPa treatment reduced enzyme activity as time increased to a level of 55% residual activity in a buffer solution where the greatest inactivation was observed. / Enzyme activation and inactivation were affected by a dual effect attributed to a pulse effect, which caused a shift in activity and was independent of the length of the treatment, and a pressure-hold effect, during which activation or inactivation followed first order kinetics. The enzyme appeared highly resistant to pressure in all media as observed from D-values (>2700 min) and pressure sensitivity of destruction rate (zp) values (>500 MPa). / Inactivation of non-pathogen histamine forming bacteria (HFB) Escherichia coli K12 and Bacillus megaterium was evaluated by inoculating cultures in a fish tissue homogenate. Surviving colonies were enumerated after the treatments observing inactivation described by the same dual effect described earlier. Pressures above 300 MPa achieved a significant destruction of E. coli K12 (> 4 log-cycles) while B. megaterium appeared highly resistant for only a 2 log-cycle reduction was observed after at the highest pressure treatment conditions (400 MPa, 20 min). / D-values for both microorganisms decreased as pressure increased being significantly smaller for E. coli K 12, which also appeared to be more sensitive to pressure changes as observed from the zp values (zp = 151.51 MPa and zp = 909.10 MPa for E. coli and B. megaterium respectively. Inactivation caused by the pulse effect appeared very effective for both microorganisms as pressure increased, particularly at 400 MPa (PE > 1.25).

Thesis (Ph.D.)--York University, 2003. Graduate Programme in Chemistry. / Typescript. Includes bibliographical references. Also available on the Internet. MODE OF ACCESS via web browser by entering the following URL: http://wwwlib.umi.com/cr/yorku/fullcit?pNQ99165

Indiana University-Purdue University Indianapolis (IUPUI) / Oxalate decarboxylase (EC 4. 1. 1. 2 OxDC) from Bacillus subtilis is a manganese-dependent enzyme that catalyzes the cleavage of the chemically inactive C-C bond in oxalate to yield formate and carbon dioxide. A mechanism involving Mn(III) has been proposed for OxDC, however no clear spectroscopic evidence to support this mechanism has yet been obtained. In addition, a recent study has shown that N-terminal metal binding site loop variants of OxDC were able to catalyze the oxidation of oxalate to yield hydrogen peroxide and carbon dioxide, which makes OxDc function as another oxalate degradation protein in the cupin superfamily, oxalate oxidase (EC 1.2.3.4 OxOx). In this work, wild-type (WT) Bacillus subtilis OxDC and a series of variants with mutations on conserved residues were characterized to investigate the catalytic mechanism of OxDC. The application of membrane inlet mass spectrometry (MIMS), electronic paramagnetic resonance (EPR) spectroscopy and kinetic isotope effects (KIEs) provided information about the mechanism. The Mn(III) was identified and characterized under acidic conditions in the presence of dioxygen and oxalate. Mutations on the second shell residues in the N-terminal metal binding site affected the enzyme activity properties of the metal. In the N-terminal domain, the functional importance of the residues in the active site loop region, especially Glu162, was confirmed, and evidence for the previously proposed mechanism in which OxDC and the OxDC/OxOx chimeric variant share the initial steps has been found. In addition, the mono-dentate coordination of oxalate in the N-terminal metal binding site was confirmed by X-ray crystallography. A proteinase cleavable OxDC was constructed and characterized, revealing the interaction between the N-terminal and C-terminal domains.