Publications

• A functional analysis of the pyrimidine catabolic pathway in Arabidopsis.

  Zrenner R., Riegler H., Marquard C.R., Lange P.R., Geserick C., Bartosz C.E., Chen C.T., Slocum R.D.

  * Reductive catabolism of pyrimidine nucleotides occurs via a three-step pathway in which uracil is degraded to beta-alanine, CO(2) and NH(3) through sequential activities of dihydropyrimidine dehydrogenase (EC 1.3.1.2, PYD1), dihydropyrimidinase (EC 3.5.2.2, PYD2) and beta-ureidopropionase (EC 3. ... >> More

  * Reductive catabolism of pyrimidine nucleotides occurs via a three-step pathway in which uracil is degraded to beta-alanine, CO(2) and NH(3) through sequential activities of dihydropyrimidine dehydrogenase (EC 1.3.1.2, PYD1), dihydropyrimidinase (EC 3.5.2.2, PYD2) and beta-ureidopropionase (EC 3.5.1.6, PYD3). * A proposed function of this pathway, in addition to the maintenance of pyrimidine homeostasis, is the recycling of pyrimidine nitrogen to general nitrogen metabolism. PYD expression and catabolism of [2-(14)C]-uracil are markedly elevated in response to nitrogen limitation in plants, which can utilize uracil as a nitrogen source. * PYD1, PYD2 and PYD3 knockout mutants were used for functional analysis of this pathway in Arabidopsis. pyd mutants exhibited no obvious phenotype under optimal growing conditions. pyd2 and pyd3 mutants were unable to catabolize [2-(14)C]-uracil or to grow on uracil as the sole nitrogen source. By contrast, catabolism of uracil was reduced by only 40% in pyd1 mutants, and pyd1 seedlings grew nearly as well as wild-type seedlings with a uracil nitrogen source. These results confirm PYD1 function and suggest the possible existence of another, as yet unknown, activity for uracil degradation to dihydrouracil in this plant. * The localization of PYD-green fluorescent protein fusions in the plastid (PYD1), secretory system (PYD2) and cytosol (PYD3) suggests potentially complex metabolic regulation. << Less

  New Phytol. 183:117-132(2009) [PubMed] [EuropePMC]

  This publication is cited by 2 other entries.

• Pyrimidine catabolism: individual characterization of the three sequential enzymes with a new assay.

  Traut T.W., Loechel S.

  We have developed a one-dimensional thin-layer chromatography procedure that resolves the initial substrate uracil and its catabolic derivatives dihydrouracil, N-carbamoyl-beta-alanine (NCBA) and beta-alanine. This separation scheme also simplifies the preparation of the radioisotopes of N-carbamo ... >> More

  We have developed a one-dimensional thin-layer chromatography procedure that resolves the initial substrate uracil and its catabolic derivatives dihydrouracil, N-carbamoyl-beta-alanine (NCBA) and beta-alanine. This separation scheme also simplifies the preparation of the radioisotopes of N-carbamoyl-beta-alanine and dihydrouracil. Combined, these methods make it possible to assay easily and unambiguously, jointly or individually, all three enzyme activities of uracil catabolism: dihydropyrimidine dehydrogenase, dihydropyrimidinase, and N-carbamoyl-beta-alanine amidohydrolase. Earlier reports had presented data suggesting that these three enzyme activities were combined in a complex because they appeared to be controlled at a single genetic locus [Dagg, C. P., Coleman, D.L., & Fraser, G.M. (1964) Genetics 49, 979-989] and because they appeared able to channel metabolites [Barrett, H.W., Munavalli, S.N., & Newmark, P. (1964) Biochim. Biophys. Acta 91, 199-204]. Although the three enzymes from rat liver have similar sizes, with apparent molecular weights of 218 000 for dihydropyrimidine dehydrogenase, 226 000 for dihydropyrimidinase, and 234 000 for NC beta A amidohydrolase, they are easily separated from each other. Kinetic studies show no evidence of substrate channeling and therefore do not support a model for an enzyme complex. The earlier reports may be explained by our studies on the amidohydrolase, which suggest that under certain conditions this enzyme may become the rate-limiting step in uracil catabolism. << Less

  Biochemistry 23:2533-2539(1984) [PubMed] [EuropePMC]

• Eukaryotic beta-alanine synthases are functionally related but have a high degree of structural diversity.

  Gojkovic Z., Sandrini M.P., Piskur J.

  beta-Alanine synthase (EC 3.5.1.6), which catalyzes the final step of pyrimidine catabolism, has only been characterized in mammals. A Saccharomyces kluyveri pyd3 mutant that is unable to grow on N-carbamyl-beta-alanine as the sole nitrogen source and exhibits diminished beta-alanine synthase acti ... >> More

  beta-Alanine synthase (EC 3.5.1.6), which catalyzes the final step of pyrimidine catabolism, has only been characterized in mammals. A Saccharomyces kluyveri pyd3 mutant that is unable to grow on N-carbamyl-beta-alanine as the sole nitrogen source and exhibits diminished beta-alanine synthase activity was used to clone analogous genes from different eukaryotes. Putative PYD3 sequences from the yeast S. kluyveri, the slime mold Dictyostelium discoideum, and the fruit fly Drosophila melanogaster complemented the pyd3 defect. When the S. kluyveri PYD3 gene was expressed in S. cerevisiae, which has no pyrimidine catabolic pathway, it enabled growth on N-carbamyl-beta-alanine as the sole nitrogen source. The D. discoideum and D. melanogaster PYD3 gene products are similar to mammalian beta-alanine synthases. In contrast, the S. kluyveri protein is quite different from these and more similar to bacterial N-carbamyl amidohydrolases. All three beta-alanine synthases are to some degree related to various aspartate transcarbamylases, which catalyze the second step of the de novo pyrimidine biosynthetic pathway. PYD3 expression in yeast seems to be inducible by dihydrouracil and N-carbamyl-beta-alanine, but not by uracil. This work establishes S. kluyveri as a model organism for studying pyrimidine degradation and beta-alanine production in eukaryotes. << Less

  Genetics 158:999-1011(2001) [PubMed] [EuropePMC]

• Cloning, sequencing, and expression of a cDNA encoding beta-alanine synthase from rat liver.

  Kvalnes-Krick K.L., Traut T.W.

  A cDNA for beta-alanine synthase from rat liver has been isolated, sequenced, and characterized. beta-Alanine synthase clones were isolated from rat liver cDNA libraries in lambda gt11, using affinity-purified polyclonal antibodies against beta-alanine synthase protein. beta-Alanine synthase prote ... >> More

  A cDNA for beta-alanine synthase from rat liver has been isolated, sequenced, and characterized. beta-Alanine synthase clones were isolated from rat liver cDNA libraries in lambda gt11, using affinity-purified polyclonal antibodies against beta-alanine synthase protein. beta-Alanine synthase protein was not expressed with equal efficiency by all clones. One of the expressed fusion proteins has normal specific enzyme activity, and a second has reduced specific activity. Both clones were completely sequenced and yielded identical DNA sequence, except that one clone contained an additional 36 bases of 5' sequence. The various clones of this cDNA code for an EcoRI insert of 1.5 +/-0.1 kb, and the open reading frame corresponds to a protein of 393 amino acids (M(r) = 44,042), in good agreement with the M(r) of approximately 42,000 for the native enzyme on SDS-gel electrophoresis. An 11-amino acid sequence was obtained from a tryptic peptide of native beta-alanine synthase; 11 codons for these same amino acids were found at the expected site in the sequenced cDNA, and confirm the open reading frame of the beta-alanine synthase cDNA. Chemical analysis of the native enzyme shows 2 zinc atoms per subunit, and the sequence of beta-alanine synthase contains 2 putative zinc-binding site motifs. Comparison of amino acid sequence, deduced from the cDNA sequence, to sequences in the protein data base showed that it is a unique sequence and that it has about 20% identity to aspartate carbamoyltransferase, ornithine carbamoyltransferase, urease, and leucine aminopeptidase; enzymes that bind comparable ligands or have a similar mechanism. << Less

  J. Biol. Chem. 268:5686-5693(1993) [PubMed] [EuropePMC]

• Yeast beta-alanine synthase shares a structural scaffold and origin with dizinc-dependent exopeptidases.

  Lundgren S., Gojkovic Z., Piskur J., Dobritzsch D.

  beta-Alanine synthase (beta AS) is the final enzyme of the reductive pyrimidine catabolic pathway, which is responsible for the breakdown of pyrimidine bases, including several anticancer drugs. In eukaryotes, beta ASs belong to two subfamilies, which exhibit a low degree of sequence similarity. W ... >> More

  beta-Alanine synthase (beta AS) is the final enzyme of the reductive pyrimidine catabolic pathway, which is responsible for the breakdown of pyrimidine bases, including several anticancer drugs. In eukaryotes, beta ASs belong to two subfamilies, which exhibit a low degree of sequence similarity. We determined the structure of beta AS from Saccharomyces kluyveri to a resolution of 2.7 A. The subunit of the homodimeric enzyme consists of two domains: a larger catalytic domain with a dizinc metal center, which represents the active site of beta AS, and a smaller domain mediating the majority of the intersubunit contacts. Both domains exhibit a mixed alpha/beta-topology. Surprisingly, the observed high structural homology to a family of dizinc-dependent exopeptidases suggests that these two enzyme groups have a common origin. Alterations in the ligand composition of the metal-binding site can be explained as adjustments to the catalysis of a different reaction, the hydrolysis of an N-carbamyl bond by beta AS compared with the hydrolysis of a peptide bond by exopeptidases. In contrast, there is no resemblance to the three-dimensional structure of the functionally closely related N-carbamyl-d-amino acid amidohydrolases. Based on comparative structural analysis and observed deviations in the backbone conformations of the eight copies of the subunit in the asymmetric unit, we suggest that conformational changes occur during each catalytic cycle. << Less

  J Biol Chem 278:51851-51862(2003) [PubMed] [EuropePMC]

• Characterization of plant beta-ureidopropionase and functional overexpression in Escherichia coli.

  Walsh T.A., Green S.B., Larrinua I.M., Schmitzer P.R.

  Pyrimidine bases are rapidly catabolized in growing plant tissues. The final enzyme of the catabolic pathway, beta-ureidopropionase (beta-UP; EC 3.5.1.6), was partially purified from the shoots of etiolated maize (Zea mays) seedlings. The enzyme had a K(m) for beta-ureidopropionate (the substrate ... >> More

  Pyrimidine bases are rapidly catabolized in growing plant tissues. The final enzyme of the catabolic pathway, beta-ureidopropionase (beta-UP; EC 3.5.1.6), was partially purified from the shoots of etiolated maize (Zea mays) seedlings. The enzyme had a K(m) for beta-ureidopropionate (the substrate derived from uracil) of 11 microM. Only one enantiomer of racemic beta-ureidoisobutyrate (derived from thymine) was processed with a K(m) of 6 microM. The enzyme was inactivated by dialysis against 1,10-phenanthroline and activity could be partially restored by addition of Zn(2+). Maize beta-UP was very sensitive to inactivation by iodoacetamide. This could be prevented by addition of substrate, indicating the presence of an active site Cys. The enzyme was strongly inhibited by short chain aliphatic acids and aryl propionates, the most potent inhibitor of which was 2-(2, 6-dinitrophenoxy)-propionate (I(50) = 0.5 microM). A gene for Arabidopsis beta-UP encodes a polypeptide of 405 amino acids and has about 55% homology with the enzymes from other eukaryotic organisms. Several highly conserved residues link the plant beta-UP with a larger class of prokaryotic and eukaryotic amidohydrolases. An Arabidopsis cDNA truncated at the N terminus by 14 residues was cloned and overexpressed in Escherichia coli. The recombinant enzyme (43.7 kD) was soluble, functional, and purified to homogeneity with yields of 15 to 20 mg per 30 g fresh weight of E. coli cells. The recombinant enzyme from Arabidopsis and the native enzyme from maize had molecular masses of approximately 440 kD, indicating the enzyme is a decamer at pH 7. << Less

  Plant Physiol. 125:1001-1011(2001) [PubMed] [EuropePMC]

• Beta-ureidopropionase deficiency: an inborn error of pyrimidine degradation associated with neurological abnormalities.

  van Kuilenburg A.B.P., Meinsma R., Beke E., Assmann B., Ribes A., Lorente I., Busch R., Mayatepek E., Abeling N.G.G.M., van Cruchten A., Stroomer A.E.M., van Lenthe H., Zoetekouw L., Kulik W., Hoffmann G.F., Voit T., Wevers R.A., Rutsch F., van Gennip A.H.

  beta-Ureidopropionase deficiency is an inborn error of the pyrimidine degradation pathway, affecting the cleavage of N-carbamyl-beta-alanine and N-carbamyl-beta-aminoisobutyric acid. In this study, we report the elucidation of the genetic basis underlying a beta-ureidopropionase deficiency in four ... >> More

  beta-Ureidopropionase deficiency is an inborn error of the pyrimidine degradation pathway, affecting the cleavage of N-carbamyl-beta-alanine and N-carbamyl-beta-aminoisobutyric acid. In this study, we report the elucidation of the genetic basis underlying a beta-ureidopropionase deficiency in four patients presenting with neurological abnormalities and strongly elevated levels of N-carbamyl-beta-alanine and N-carbamyl-beta-aminoisobutyric acid in plasma, cerebrospinal fluid and urine. No beta-ureidopropionase activity could be detected in a liver biopsy obtained from one of the patients, which reflected the complete absence of the beta-ureidopropionase protein. Analysis of the beta-ureidopropionase gene (UPB1) of these patients revealed the presence of two splice-site mutations (IVS1-2A>G and IVS8-1G>A) and one missense mutation (A85E). Heterologous expression of the mutant enzyme in Escherichia coli showed that the A85E mutation resulted in a mutant beta-ureidopropionase enzyme without residual activity. Our results demonstrate that the N-carbamyl-beta-amino aciduria in these patients is due to a deficiency of beta-ureidopropionase, which is caused by mutations in the UPB1 gene. Furthermore, an altered homeostasis of beta-aminoisobutyric acid and/or increased oxidative stress might contribute to some of the clinical abnormalities encountered in patients with a beta-ureidopropionase deficiency. An analysis of the presence of the two splice site mutations and the missense mutation in 95 controls identified one individual who proved to be heterozygous for the IVS8-1G>A mutation. Thus, a beta-ureidopropionase deficiency might not be as rare as is generally considered. << Less

  Hum. Mol. Genet. 13:2793-2801(2004) [PubMed] [EuropePMC]