Asparate transcarbamoylase catalyzes the first committed step in the de novo synthesis of pyrmidine nucleotides UMP, UDP, UTP, and CTP. The archetype enzyme found in Escherichia coli (310 kDa) exhibits sigmodial substrate binding kinetics with positive control by ATP and negative control with CTP and UTP. The ATCase characterized in this study is from the extreme thermophilic Archaebacterium, Methanococcus jannaschii. The enzyme was very stable at elevated temperatures and possessed activity from 20 degrees Celsius to 90 degrees Celsius. M. Jannaschii ATCase retained 75% of its activity after incubation at 100 degrees Celsius for a period of 90 minutes. No sigmodial allosteric response to substrate for the enzyme was observed. Velocity substrate plots gave Michaelis-Menten (hyperbolic) kinetics. The Km for aspartate was 7 mM at 30 degrees Celsius and the KM for carbamoylphosphate was .125 mM. The enzyme from M. jannaschii had a broad pH response with an optimum above pH 9. Kinetic measurements were significantly affected by changes in pH and temperature. The enzyme catalyzed reaction had an energy of activation of 10,300 calories per mole. ATCase from M. jannaschii was partially purified. The enzyme was shown to have a molecular weight of 110,000 Da., with a subunit molecular weight of 37,000 Da. The enzyme was thus a trimer composed of three identical subunits. The enzyme did not possess any regulatory response and no evidence for a regulatory polypeptide was found, DNA from M. jannaschii did hybridize to probes corresponding to genes for both the catalytic and regulatory subunits from E. coli. Analysis of DNA sequences for the M. jannaschii ATCase genes showed that the gene for the catalytic subunits shares significant homology with the pyrB genes from E. coli, and maximum homology amongst known ATCase genes to pyrB from Bacillus. An unlinked gene homologous to E. coli pyrl encoding the regulatory subunit was identified, though its expression and true function remain uncharacterized.

The faithful replication of DNA depends on the appropriate balance of DNA precursors. From studies conducted in bacteriophage T4, models for deoxyribonucleotide biosynthesis producing pools appropriate for DNA replication have made it possible to understand more complex systems. A portion of that body of evidence supports the concept that deoxyribonucleotide biosynthesis for bacteriophage T4 is carried out by an association of enzymes and other cellular components in a complex called the dNTP synthetase complex. This dissertation explores potential direct protein-protein interactions within this complex for the preparation of pyrimidine deoxyribonucleotides. Direct associations for enzymes involved in pyrimidine deoxyribonucleotide biosynthesis were examined by affinity chromatography. It was determined that there was a significant direct relationship between T4 thymidylate synthase and T4 dCMP deaminase, between T4 dCTPase/dUTPase and T4 dCMP deaminase as well. The interaction between thymidylate synthase and dCMP deaminase was significantly influenced by the presence of dCTP, a positive effector of dCMP deaminase. Furthermore, protein associations changed the kinetic character of pyrimidine deoxyribonucleotide production. T4 dCTPase/dUTPase, a member of the dNTP synthetase complex, significantly alters the kinetic nature of thymidylate synthase by working with thymidylate synthase in a reciprocal relationship. T4 single-stranded DNA binding protein, a member of the replication complex, alters the activity of thymidylate synthase as well. Attempts to isolate a kinetically coupled complex from two or more constituent proteins of the dNTP synthetase complex were frustrated by protein degradation to fragments under 10 kDa in size. Pyrimidine deoxyribonucleotide synthesis is located between the significant energy investment of ribonucleotide reductase and phosphate attachments by kinases to prepare the deoxyribonucleotide molecules for DNA replication. In bacteriophage T4, intermediate reactions are driven by mass action but are modulated by subtleties including direct protein associations and the presence of small molecules that influence enzyme function. Through these and potentially similar controls, pools of deoxyribonucleotides are prepared and delivered in a timely, balanced manner to the DNA replication apparatus. / Graduation date: 2002

Thesis (Ph. D.)--University of Hong Kong, 1993. / Includes bibliographical references (leaves 164-199).

Pyrimidine nucleotide biosynthesis was studies in Acinetobacter calcoaceticus ADP-1. Pyrimidine auxotrophic mutants were isolated and characterized for this purpose. One such Pyr mutant, strain ADP-1-218 was chosen for further study.

published_or_final_version / Biochemistry / Doctoral / Doctor of Philosophy

Thesis (Ph. D.)--Illinois State University, 1978. / Title from title page screen, viewed Jan. 24, 2005. Dissertation Committee: Fritz Schwalm (chair), Herman Brockman, Harry Huizinga, Mathew Nadakavukaren, Arlan Richardson. Includes bibliographical references (leaves 96-105) and abstract. Also available in print.

Thesis (M.S.)--The University of North Carolina at Greensboro, 2009. / Directed by Lakshmi P. Kotra; submitted to the Dept. of Chemistry and Biochemistry. Title from PDF t.p. (viewed May 17, 2010). Includes bibliographical references (p. 41-43).

Rhizobium aspartate transcarbamoylase (ATCase; EC 2.1.3.2) was previously believed to be similar to the Pseudomonas ATCase which has been studied extensively. To facilitate the study of the Rhizobium ATCase a pyrimidine-requiring mutant of R. meliloti was isolated and used in the purification of the enzyme.

Aspartate transcarbamoylase (ATCase) is encoded by the pyrBI genes in E. coli. Expression of these genes is reduced four-fold by attenuation when grown on uracil. Using plasmid, pRO1727. the pyrB and the pyrBI genes from E. coli were cloned into a P. putida pyrB auxotroph. A recombinant pyrB gene was recovered that encoded a functional hybrid ATCase with a molecular weight of 470 kDa.

Serine transhydroxymethylase (STHM), a pyridoxal 5'- phosphate requiring enzyme is indirectly involved in pyrimidine deoxynucleotide metabolism. A decrease in the activity of this enzyme could lead to altered deoxycytidine (dC) metabolism. This study was undertaken to determine if a vitamin B-6 deficiency affects dC metabolism. The effect of a vitamin B-6 deficiency on the activity of STHM in liver, thymus, spleen and bone marrow was examined. In addition, the effect of a vitamin B-6 deficiency on urinary excretion of dC was examined. The effect of a vitamin B-6 deficiency on the urinary excretion and tissue retention of ³H label from ip injected ³H-dC was monitored. Rats were assigned in groups of six to one of four treatment groups: ad libitum control (ALC), pair fed control (PFC), ad libitum deficient (ALD) or meal fed deficient (MFD). At the end of weeks 2 and 6, rats from each treatment group received an ip injection of ³H-dC. Urines were collected for 24 hours following the ip inhibited due to lack of cofactor, then dTMP levels would fall. In an attempt to increase the concentration of dTMP, enzymes active in the conversion of dC and dCMP to dUMP would be expected to increase. Thus, dC salvage pathways would increase and dC synthesis would decrease as metabolism shifts toward production of deoxythymidine triphosphate (dTTP). The result would be lower urinary dC excretion. The present study was undertaken to explore the relationship between vitamin B-6 and pyrimidine deoxynucleotide metabolism. There were four hypothesis tested: Vitamin B-6 deficient rats will excrete less urinary dC than either ad libitum or pair fed controls; vitamin B-6 deficient rats will excrete a lower percentage of labeled dC in urine than control rats; vitamin B-6 deficient rats will incorporate less labeled dC into DNA than control rats but may retain more label in tissues as dC metabolites; activity of STHM from tissues of vitamin B-6 deficient rats will be lower than that from the control rats. / Graduation date: 1990