Dihydroorotase (DHO) is a zinc metallo-enzyme that functions in the pathway for the biosynthesis of pyrimidine nucleotides by catalyzing the reversible interconversion of carbamoyl aspartate and dihydroorotate. The X-ray crystal structure of the enzyme was obtained at a resolution of 1.7 Å. The pH-rate profiles for the hydrolysis of dihydroorotate or thio-dihydroorotate demonstrated that a single group of DHO must be unprotonated for maximal catalytic activity. The pH-rate profiles for the condensation of carbamoyl aspartate to dihydroorotate showed that a single group from the enzyme must be protonated for maximal catalytic activity. The native zinc ions within the active site of DHO were substituted with cobalt or CADmium by reconstitution of the apo-enzyme with divalent cations. The ionizations observed in the pH-rate profiles were dependent on the specific metal ion bound to the active site. Mutation of Asp-250 resulted in the loss of catalytic activity. These results are consistent with the formation of a hydroxide bridge between the two divalent cations that functions as the nucleophile during the hydrolysis of dihydroorotate. In addition, Asp250 is postulated to shuttle the proton from the bridging hydroxide to the leaving group amide during dihydroorotate hydrolysis. The X-ray crystal structure of DHO showed that the side-chain carboxylate of dihydroorotate is electrostatically interacting with Arg20, Asn-44 and His-254. Mutation of these residues resulted in the loss of catalytic activity, indicating that these residues are critical for substrate recognition. The thioanalog of dihydroorotate, (TDO) was found to be a substrate of DHO. A comprehensive chemical mechanism for DHO was proposed based on the experimental data presented in this dissertation. Armed with this understanding of the structure-function relationship of DHO, a rational approach was used to alter the substrate specificity of the enzyme. The R20/N44/H254 mutant of DHO was obtained and found to have increased activity on dihydrouracil compared to the wild-type enzyme. The sequence of the gene PA5541 from Pseudomonas aeruginosa has a glutamine at a position where most active DHO proteins have a histidine residue. Results from the characterization of PA5541 indicate that it is a functional DHO.

Dihydroorotase (DHO) is a zinc metallo-enzyme that functions in the pathway for the biosynthesis of pyrimidine nucleotides by catalyzing the reversible interconversion of carbamoyl aspartate and dihydroorotate. The X-ray crystal structure of the enzyme was obtained at a resolution of 1.7 Ã . The pH-rate profiles for the hydrolysis of dihydroorotate or thio-dihydroorotate demonstrated that a single group of DHO must be unprotonated for maximal catalytic activity. The pH-rate profiles for the condensation of carbamoyl aspartate to dihydroorotate showed that a single group from the enzyme must be protonated for maximal catalytic activity. The native zinc ions within the active site of DHO were substituted with cobalt or CADmium by reconstitution of the apo-enzyme with divalent cations. The ionizations observed in the pH-rate profiles were dependent on the specific metal ion bound to the active site. Mutation of Asp-250 resulted in the loss of catalytic activity. These results are consistent with the formation of a hydroxide bridge between the two divalent cations that functions as the nucleophile during the hydrolysis of dihydroorotate. In addition, Asp250 is postulated to shuttle the proton from the bridging hydroxide to the leaving group amide during dihydroorotate hydrolysis. The X-ray crystal structure of DHO showed that the side-chain carboxylate of dihydroorotate is electrostatically interacting with Arg20, Asn-44 and His-254. Mutation of these residues resulted in the loss of catalytic activity, indicating that these residues are critical for substrate recognition. The thioanalog of dihydroorotate, (TDO) was found to be a substrate of DHO. A comprehensive chemical mechanism for DHO was proposed based on the experimental data presented in this dissertation. Armed with this understanding of the structure-function relationship of DHO, a rational approach was used to alter the substrate specificity of the enzyme. The R20/N44/H254 mutant of DHO was obtained and found to have increased activity on dihydrouracil compared to the wild-type enzyme. The sequence of the gene PA5541 from Pseudomonas aeruginosa has a glutamine at a position where most active DHO proteins have a histidine residue. Results from the characterization of PA5541 indicate that it is a functional DHO.

Dihydroorotase (4,4—dihydroorotic acid amidolyase, EC 3.5.2.3.) which catalyzes the reversible cyclization of N-carbamyl-L-aspartate to L-dihydroorotate has been purified from orotate-grown Clostridium oroticum. The enzyme is stable in 0.3 M sodium chloride and 10 µ ZnSO4. Sodium dodecyl sulfate gel electrophoresis indicates the enzyme to be composed of two identical subunits each with a molecular weight of 58,000 + 6000. Dihydroorotase is shown to be a zinc-containing metalloenzyme with 2 g atoms of zinc per 58,000 g of protein. The role of zinc in dihydroorotase is discussed.

The ability to synthesize pyrimidine nucleotides is essential for most organisms. Pyrimidines are required for RNA and DNA synthesis, as well as cell wall synthesis and the metabolism of certain carbohydrates. Recent findings, however, indicate that the pyrimidine biosynthetic pathway and its intermediates maybe more important for bacterial metabolism than originally thought. Maksimova et al., 1994, reported that a P. putida M, pyrimidine auxotroph in the third step of the pathway, dihydroorotase (DHOase), failed to produce the siderophore pyoverdin. We created a PAO1 DHOase pyrimidine auxotroph to determine if this was also true for P. aeruginosa. Creation of this mutant was a two-step process, as P. aeruginosa has two pyrC genes (pyrC and pyrC2), both of which encode active DHOase enzymes. The pyrC gene was inactivated by gene replacement with a truncated form of the gene. Next, the pyrC2 gene was insertionally inactivated with the aacC1 gentamicin resistance gene, isolated from pCGMW. The resulting pyrimidine auxotroph produced significantly less pyoverdin than did the wild type. In addition, the mutant produced 40% less of the phenazine antibiotic, pyocyanin, than did the wild type. As both of these compounds have been reported to be vital to the virulence response of P. aeruginosa, we decided to test the ability of the DHOase mutant strain to produce other virulence factors as well. Here we report that a block in the conversion of carbamoyl aspartate (CAA) to dihydroorotate significantly impairs the ability of P. aeruginosa to affect virulence. We believe that the accumulation of CAA in the cell is the root cause of this observed defect. This research demonstrates a potential role for pyrimidine intermediates in the virulence response of P. aeruginosa and may lead to novel targets for chemotherapy against P. aeruginosa infections.

A doença de Chagas, que é causada pelo protozoário flagelado Trypanosoma cruzi, ocasiona grandes danos à saúde da população latino-americana e vem-se distribuindo para regiões não-endêmicas como os Estados Unidos, Europa e Japão. O tratamento é realizado pela administração de dois medicamentos (Nifurtimox e Benzonidazol) que apresentam sérios efeitos colaterais e baixa eficácia. A busca por novos compostos químicos bioativos com ação farmacológica sobre alvos bioquímicos constitui uma estratégia em desenvolvimento em nosso grupo de pesquisa. Neste trabalho, a principal cisteino protease - a cruzaína, e a enzima central na biossíntese de pirimidinas - a DHODH, ambas de T. cruzi, foram escolhidas como alvos para a identificação de novos inibidores com ação potencial contra o T. cruzi. A síntese de inibidores dessas duas enzimas foi realizada e os ensaios bioquímicos foram usados para identificar novos inibidores em concentrações micro- e nanomolar. Alguns desses inibidores enzimáticos foram ensaiados contra o T. cruzi em sua forma infectiva tripomastigota e foram ativos em concentrações micromolar. A enzima cruzaína (3.4.22.51) possui similaridade baixa na sequência de aminoácidos (18%) com a Catepsina-L (Cat-L, EC 3.4.22.15), mas suficiente para estabelecer a hipótese de que inibidores de Cat-L também poderiam inibir a cruzaína. Assim, com base no conhecimento prévio de vários inibidores da Cat-L, o dipeptídeo-nitrila Neq409 foi inicialmente sintetizado por outro membro do grupo para validar a hipótese de que nitrilas dipeptídicas poderiam inibir a cruzaína. O composto Neq409 inibiu a cruzaína com o valor de pIC50 igual a 5,7 que o qualificou não apenas como inibidor da cruzaína mas também como possível composto matriz para modificação molecular e estudos de relações estrutura-atividade (SAR). Cinco compostos foram então sintetizados através de uma rota de quatro etapas (proteção/desproteção de ácidos carboxílicos e duas formações de amida) e avaliados através de métodos fluorimétricos quanto às suas capacidades de inibir cruzaína. As modificações moleculares resultaram em aumento da potência de até 13 vezes em relação ao composto protótipo Neq409. A substituição do grupo benzoíla, presente em P3 no Neq409, pelo grupo 3-carboxi-5-terc-butil-2-metilpirazol (Neq414) e 5-bromopiridina (Neq419) resultou nos valores de pIC50 de 6,5 e 6,1, respectivamente. A substituição do átomo de hidrogênio por cloro na posição meta da fenila em P2 no composto Neq414 deu origem ao composto Neq415 com pIC50 de 6,8. Outras duas modificações envolveram a inserção do grupo ciclopropila na região P1 do composto Neq0414 gerando o Neq533 (pIC50 = 6,8) e do composto Neq533 resultando no composto Neq543 (pIC50 = 6,2). Os resultados mostraram que o grupo 3-carboxi-5-terc-butil-2-metilpirazol apresenta interações mais eficientes no sub-sítio S3 da cruzaína que o grupo 5-bromopiridina e que um átomo de cloro em P2 e um grupo ciclopropila em P1 possuem contribuições semelhantes para o aumento da potência de inibição da enzima. A busca de inibidores da enzima TcDHODH pelo grupo NEQUIMED levou à identificação de dois novos inibidores nanomolares, o Neq71 (pKi = 6,5) e o Neq130 (pKi = 6,4), ambos derivados de 5-arilpropilidenobarbitúricos. Com base nesses resultados, foi realizada a síntese do Neq71, Neq130 e de um novo inibidor - o Neq0393, biosóstero do composto Neq130, utilizando a condensação de Knoevenagel em meio aquoso sem catalisador, por adaptação de método já descrito anteriormente na literatura. Para avaliar a importância insaturação exocíclica ao anel barbitúrico desses derivados, o Neq71, Neq130 e o Neq393 foram submetidos à redução específica dessa insaturação utilizando-se NaBH4 que resultou nos compostos Neq395, Neq298 e Neq394, respectivamente. Os compostos Neq542, Neq421 e Neq420 derivados 5-metilidenobarbitúricos também foram sintetizados através do mesmo procedimento utilizado para obtenção de Neq71, Neq130 e Neq393, para avaliar a importância do comprimento da cadeia dos derivados 5-arilpropilidenobarbitúricos. A análise das constantes de inibição dos compostos obtidos mostrou que a redução da instauração resulta de até 280 vezes de potência, enquanto o encurtamento da cadeia lateral levou a diminuição de menor escala da potência (25 vezes), indicando a importância da instauração exocíclica para a afinidade dos compostos com a enzima. A característica eletrofílica desta instauração levou identificação de um novo esqueleto para futuros inibidores, o Neq411. / Chagas disease, which is caused by the flagellate protozoan Trypanosoma cruzi, causes severe damage to the health of the population in Latin American countries and comes up distributing to non-endemic regions such as the United States, Europe and Japan. The treatment is accomplished by administering two drugs (Benznidazole and Nifurtimox) that have serious side effects and low efficacy. The search for new bioactive chemical compounds with pharmacological action on biochemical targets is a strategy under development in our research group. In this study, the major cysteine protease - cruzain, and the central enzyme in the biosynthesis of pyrimidines - DHODH, both from T. cruzi, were chosen as targets for the identification of new inhibitors with potential activity against T. cruzi. The synthesis of inhibitors of these two enzymes was performed and biochemical assays were used to identify new inhibitors at micro- and nanomolar concentrations. Some of these enzyme inhibitors were tested against T. cruzi infective trypomastigote form and were active at micromolar concentrations. The cruzain enzyme (EC 3.4.22.51) has low similarity in amino acid sequence (18 %) towards Cathepsin L (Cat-L, EC 3.4.22.15 ), but sufficient to establish the hypothesis that Cat-L inhibitors could also inhibit cruzain. Thus, based on prior knowledge of various Cat-L inhibitors, a dipeptide nitrile - Neq409 was initially synthesized by another group member in order to validate the hypothesis that dipeptide nitriles could really inhibit cruzain. The compound Neq409 inhibited cruzain with a pIC50 value of 5.7, which qualified it not only as an inhibitor of cruzain but also as a possible lead compound for molecular modification and structure-activity relationships (SAR) studies. Five compounds were then designed and synthesized through a route of four steps (protection/deprotection of carboxylic acids and two formations of amides) and evaluated using fluorimetric methods to evaluate their ability to inhibit cruzain. The molecular changes for most potent compound resulted in 13-fold potency increase as compared to the prototype compound Neq0409. The replacement of the P3 benzoyl group present in the Neq409 by 3-carboxy-5-tert- butyl-2-methylpyrazole (Neq0414) and 5- bromopyridine (Neq0419) resulted in the pIC50 values of 6.5 and 6.1, respectively. The replacement of the hydrogen atom by chlorine in the meta position of the phenyl at P2 in the compound neq0414 yielded compound Neq415 with a pIC50 of 6.8. Two other modifications involved the insertion of the cyclopropyl group in the P1 region of Neq0414 generating compound Neq0533 (pIC50 = 6.8) and compounds Neq0533 resulting in compound neq0543 with a pIC50 of 6.2. The results showed that the 3-carboxy-5-tert-butyl-2-methylpyrazole provides more efficient interactions in the cruzain S3 sub-site than 5- bromopyridine group and a chlorine atom at P2 and a cyclopropyl group at P1. The search for inhibitors of the enzyme TcDHODH led to the identification of two new nanomolar inhibitors, the Neq0071 (pKi = 6.5) and Neq0130 (pKi = 6.4), both derived from 5-aril-propiliden-barbituric acid. The Neq393, a bioisostere compound of Neq0130, was synthesized using the Knoevenagel condensation in aqueous media without catalyst, by adaptation of the method previously described in the literature. Based on these results, the synthesis of Neq71, Neq130 and a new inhibitor was performed. To assess the importance of exocyclic barbiturate ring unsaturation, Neq71, Neq130 and Neq393 underwent specific reduction of such unsaturation using NABH4 that resulted in compounds Neq395, Neq298 and Neq0394, respectively. Neq542, Neq421 and Neq420 derived compounds of 5-metilidenobarbiturate were also synthesized by the same procedure used to obtain Neq71 and Neq393 to evaluate the importance of the length of the 5-arilpropilidenobarbiturate derivatives. The inhibition constant of these compounds showed that de lack of the exocyclic double bond decreased the potency 200 times and the shrinkage of the side chain to a decrease of 25 times, showing the importance of the exocyclic bond for the inhibitors affinity for the enzyme. The electrophilicity of this bond lead to an identification of a new scaffold for novel inhibitors, the Neq411.

A doença de Chagas, que é causada pelo protozoário flagelado Trypanosoma cruzi, ocasiona grandes danos à saúde da população latino-americana e vem-se distribuindo para regiões não-endêmicas como os Estados Unidos, Europa e Japão. O tratamento é realizado pela administração de dois medicamentos (Nifurtimox e Benzonidazol) que apresentam sérios efeitos colaterais e baixa eficácia. A busca por novos compostos químicos bioativos com ação farmacológica sobre alvos bioquímicos constitui uma estratégia em desenvolvimento em nosso grupo de pesquisa. Neste trabalho, a principal cisteino protease - a cruzaína, e a enzima central na biossíntese de pirimidinas - a DHODH, ambas de T. cruzi, foram escolhidas como alvos para a identificação de novos inibidores com ação potencial contra o T. cruzi. A síntese de inibidores dessas duas enzimas foi realizada e os ensaios bioquímicos foram usados para identificar novos inibidores em concentrações micro- e nanomolar. Alguns desses inibidores enzimáticos foram ensaiados contra o T. cruzi em sua forma infectiva tripomastigota e foram ativos em concentrações micromolar. A enzima cruzaína (3.4.22.51) possui similaridade baixa na sequência de aminoácidos (18%) com a Catepsina-L (Cat-L, EC 3.4.22.15), mas suficiente para estabelecer a hipótese de que inibidores de Cat-L também poderiam inibir a cruzaína. Assim, com base no conhecimento prévio de vários inibidores da Cat-L, o dipeptídeo-nitrila Neq409 foi inicialmente sintetizado por outro membro do grupo para validar a hipótese de que nitrilas dipeptídicas poderiam inibir a cruzaína. O composto Neq409 inibiu a cruzaína com o valor de pIC50 igual a 5,7 que o qualificou não apenas como inibidor da cruzaína mas também como possível composto matriz para modificação molecular e estudos de relações estrutura-atividade (SAR). Cinco compostos foram então sintetizados através de uma rota de quatro etapas (proteção/desproteção de ácidos carboxílicos e duas formações de amida) e avaliados através de métodos fluorimétricos quanto às suas capacidades de inibir cruzaína. As modificações moleculares resultaram em aumento da potência de até 13 vezes em relação ao composto protótipo Neq409. A substituição do grupo benzoíla, presente em P3 no Neq409, pelo grupo 3-carboxi-5-terc-butil-2-metilpirazol (Neq414) e 5-bromopiridina (Neq419) resultou nos valores de pIC50 de 6,5 e 6,1, respectivamente. A substituição do átomo de hidrogênio por cloro na posição meta da fenila em P2 no composto Neq414 deu origem ao composto Neq415 com pIC50 de 6,8. Outras duas modificações envolveram a inserção do grupo ciclopropila na região P1 do composto Neq0414 gerando o Neq533 (pIC50 = 6,8) e do composto Neq533 resultando no composto Neq543 (pIC50 = 6,2). Os resultados mostraram que o grupo 3-carboxi-5-terc-butil-2-metilpirazol apresenta interações mais eficientes no sub-sítio S3 da cruzaína que o grupo 5-bromopiridina e que um átomo de cloro em P2 e um grupo ciclopropila em P1 possuem contribuições semelhantes para o aumento da potência de inibição da enzima. A busca de inibidores da enzima TcDHODH pelo grupo NEQUIMED levou à identificação de dois novos inibidores nanomolares, o Neq71 (pKi = 6,5) e o Neq130 (pKi = 6,4), ambos derivados de 5-arilpropilidenobarbitúricos. Com base nesses resultados, foi realizada a síntese do Neq71, Neq130 e de um novo inibidor - o Neq0393, biosóstero do composto Neq130, utilizando a condensação de Knoevenagel em meio aquoso sem catalisador, por adaptação de método já descrito anteriormente na literatura. Para avaliar a importância insaturação exocíclica ao anel barbitúrico desses derivados, o Neq71, Neq130 e o Neq393 foram submetidos à redução específica dessa insaturação utilizando-se NaBH4 que resultou nos compostos Neq395, Neq298 e Neq394, respectivamente. Os compostos Neq542, Neq421 e Neq420 derivados 5-metilidenobarbitúricos também foram sintetizados através do mesmo procedimento utilizado para obtenção de Neq71, Neq130 e Neq393, para avaliar a importância do comprimento da cadeia dos derivados 5-arilpropilidenobarbitúricos. A análise das constantes de inibição dos compostos obtidos mostrou que a redução da instauração resulta de até 280 vezes de potência, enquanto o encurtamento da cadeia lateral levou a diminuição de menor escala da potência (25 vezes), indicando a importância da instauração exocíclica para a afinidade dos compostos com a enzima. A característica eletrofílica desta instauração levou identificação de um novo esqueleto para futuros inibidores, o Neq411. / Chagas disease, which is caused by the flagellate protozoan Trypanosoma cruzi, causes severe damage to the health of the population in Latin American countries and comes up distributing to non-endemic regions such as the United States, Europe and Japan. The treatment is accomplished by administering two drugs (Benznidazole and Nifurtimox) that have serious side effects and low efficacy. The search for new bioactive chemical compounds with pharmacological action on biochemical targets is a strategy under development in our research group. In this study, the major cysteine protease - cruzain, and the central enzyme in the biosynthesis of pyrimidines - DHODH, both from T. cruzi, were chosen as targets for the identification of new inhibitors with potential activity against T. cruzi. The synthesis of inhibitors of these two enzymes was performed and biochemical assays were used to identify new inhibitors at micro- and nanomolar concentrations. Some of these enzyme inhibitors were tested against T. cruzi infective trypomastigote form and were active at micromolar concentrations. The cruzain enzyme (EC 3.4.22.51) has low similarity in amino acid sequence (18 %) towards Cathepsin L (Cat-L, EC 3.4.22.15 ), but sufficient to establish the hypothesis that Cat-L inhibitors could also inhibit cruzain. Thus, based on prior knowledge of various Cat-L inhibitors, a dipeptide nitrile - Neq409 was initially synthesized by another group member in order to validate the hypothesis that dipeptide nitriles could really inhibit cruzain. The compound Neq409 inhibited cruzain with a pIC50 value of 5.7, which qualified it not only as an inhibitor of cruzain but also as a possible lead compound for molecular modification and structure-activity relationships (SAR) studies. Five compounds were then designed and synthesized through a route of four steps (protection/deprotection of carboxylic acids and two formations of amides) and evaluated using fluorimetric methods to evaluate their ability to inhibit cruzain. The molecular changes for most potent compound resulted in 13-fold potency increase as compared to the prototype compound Neq0409. The replacement of the P3 benzoyl group present in the Neq409 by 3-carboxy-5-tert- butyl-2-methylpyrazole (Neq0414) and 5- bromopyridine (Neq0419) resulted in the pIC50 values of 6.5 and 6.1, respectively. The replacement of the hydrogen atom by chlorine in the meta position of the phenyl at P2 in the compound neq0414 yielded compound Neq415 with a pIC50 of 6.8. Two other modifications involved the insertion of the cyclopropyl group in the P1 region of Neq0414 generating compound Neq0533 (pIC50 = 6.8) and compounds Neq0533 resulting in compound neq0543 with a pIC50 of 6.2. The results showed that the 3-carboxy-5-tert-butyl-2-methylpyrazole provides more efficient interactions in the cruzain S3 sub-site than 5- bromopyridine group and a chlorine atom at P2 and a cyclopropyl group at P1. The search for inhibitors of the enzyme TcDHODH led to the identification of two new nanomolar inhibitors, the Neq0071 (pKi = 6.5) and Neq0130 (pKi = 6.4), both derived from 5-aril-propiliden-barbituric acid. The Neq393, a bioisostere compound of Neq0130, was synthesized using the Knoevenagel condensation in aqueous media without catalyst, by adaptation of the method previously described in the literature. Based on these results, the synthesis of Neq71, Neq130 and a new inhibitor was performed. To assess the importance of exocyclic barbiturate ring unsaturation, Neq71, Neq130 and Neq393 underwent specific reduction of such unsaturation using NABH4 that resulted in compounds Neq395, Neq298 and Neq0394, respectively. Neq542, Neq421 and Neq420 derived compounds of 5-metilidenobarbiturate were also synthesized by the same procedure used to obtain Neq71 and Neq393 to evaluate the importance of the length of the 5-arilpropilidenobarbiturate derivatives. The inhibition constant of these compounds showed that de lack of the exocyclic double bond decreased the potency 200 times and the shrinkage of the side chain to a decrease of 25 times, showing the importance of the exocyclic bond for the inhibitors affinity for the enzyme. The electrophilicity of this bond lead to an identification of a new scaffold for novel inhibitors, the Neq411.

Bacterial aspartate transcarbamoylases (ATCase's) are divided into three classes that correspond to taxonomic relationships within the bacteria. The opportunistic pathogen Moraxeila catarrhalis has undergone several reclassifications based on traditional microbiological criteria. The previously uncharacterized ATCase from M. catarrhalis was purified to homogeneity and its chemical properties characterized. The ATCase from M. catarrhalis is a class C ATCase with an apparent molecular mass of 480-520 kDa. The M. catarrhalis ATCase is a dodecomer composed of six 35 kDa polypeptides and six 45 kDa polypeptides. The enzyme has an unusually high pH optimum of greater than pH 10. The enzyme exhibited hyperbolic kinetic with a Km for aspartate of 2 mM. A single, separate 78 kDa dihydroorotase from M. catarrhalis was identified and it was not associated with ATCase. These data support the reclassification of M. catarrhalis out of the Neisseriaceae family.

Dihydroorotase (4,5-L-dihydro-orotate amidohydrolase, EC 3.5.2.3) which catalyzes the reversible cyclization of N-carbamyl-1-aspartate toL-dihydro-orotate has been purified from orotate-grown Clostridium oroticum by a combination of streptomycin sulfate fractionation, DEAE-Sephadex chromatography, and hydroxylapatite chromatograpy. The enzyme has been shown to be omogeneous when subjected to polyacrylamide gel electrophoresis. Thin-layer gel chromatography with Sephadex G-200 indicated the enzyme to have a molecular weight of 110,000 ± 10,000. Sodium dodecyl sulfate gel electrophoresis using two different buffer systems indicate the enzyme to be composed of two identical subunits with a molecular weight of 56,000 ± 5300. Dihydroorotase has been shown to be a zinc-containing metalloenzyme by atomic absorption spectroscopy with two g atoms of zinc per 56,000 g of protein. The pH optima for the conversion of N-carbamyl-L-aspartate to L-dihydroorotate and L-dihydroorotate to N-carbamyl-L-aspartate have been determined to be at pH 6.0 and pH 8.2 respectively. The binding constant of the enzyme for each substrate has been investigated with values of 0 .13 mM for N--carbamyl-L--aspartate and .07 mM for L-dihydroorotate.

The pyrimidine salvage enzyme, nucleoside hydrolase, is catalyzes the irreversible hydrolysis of nucleosides into the free nucleic acid base and D-ribose. Nucleoside hydrolases have varying degrees of specificity towards purine and pyrimidine nucleosides. In E. coli, three genes were found that encode homologues of several known nucleoside hydrolases in protozoa. All three genes (designated yaaF, yeiK, and ybeK) were amplified by PCR and cloned. Two of the gene products (yeiK and ybeK) encode pyrimidine-specific nucleoside hydrolases, while the third (yaaF) encodes a nonspecific nucleoside hydrolase. All three were expressed at low levels and had different modes of regulation. As a comparative analysis, the homologous genes of Pseudomonas aeruginosa and P. fluorescens (designated nuh) were cloned. Both were determined to encode nonspecific nucleoside hydrolases. The nucleoside hydrolases of the pseudomonads exhibited markedly different modes of regulation. Both have unique promoter structures and genetic organization. Furthermore, both pseudomonad nucleoside hydrolase were found to contain an N-terminal extension of 30-35 amino acids that is shown to act as a periplasmic-signaling sequence. These are the first two nucleoside hydrolases, to date,that have been conclusively demonstrated to be exported to the periplasmic space. The physiological relevance of this is explained.

The aspartate transcarbamoylase (ATCase) was purified from Burkholderia cepacia 25416. In the course of purification, three different ATCase activities appeared namely dodecameric 550 kDa holoenzyme, and two trimeric ATCases of 140 kDa (consists of 47 kDa PyrB subunits) and 120 kDa (consists of 40 kDa PyrB subunits) each. The 120 kDa PyrB polypeptide arose by specific cleavage of the PyrB polypeptide between Ser74 and Val75 creating an active polypeptide short by 74 amino acids. Both the 40 and 47 kDa polypeptides produced active trimers. To compare the enzyme activity of these trimers, an effector assay using nucleotides was performed. The 140 kDa trimer showed inhibition while the 120 kDa polypeptide showed less inhibition. To verify the composition of the pyrBC holoenzyme complex, B. cepacia dihydroorotase (DHOase, subunit size of 45 kDa) was purified by the pMAL protein fusion and purification system and holoenzyme reconstruction was performed using purified ATCase and DHOase. Both the 140 kDa and the 120 kDa trimers could produce holoenzymes of 550 kDa and 510 kDa, respectively. The reconstructed ATCase holoenzyme from cleaved ATCase showed better reconstruction compared to that from uncleaved ATCase in the conventional ATCase activity gel assay. To characterize the relationship between pyrimidine pathway and virulence factor production, motility tests and biofilm assays were conducted using pyrC- mutant. Even though no significant difference in growth rates was observed, there were significant differences between the wild type and mutant in the production of biofilm and virulence factors. This study will help us to understand the structure and regulation of ATCase holoenzyme with DHOase, and facilitate the use of B. cepacia as an applicable bio-tool. Additionally, we can potentially pursue more efficient drug targets for B. cepacia.