Academic literature on the topic 'Carbamoyl phosphate synthetase'

1. Carbamoyl-phosphate synthetase (EC 6.3.5.5.) catalyses the synthesis of carbamoyl phosphate, the immediate precursor of arginine and pyrimidine biosynthesis, and is highly conserved throughout evolution. The large subunit of all carbamoyl-phosphate synthetases sequenced to date comprises two highly homologous halves, the product of a proposed ancestral gene duplication. The sequences of the enzymes of Escherichia coli, Drosophila melanogaster, Saccharomyces cerevisiae, rat and Syrian hamster all have duplications, suggesting that this event occurred in the progenote predating the separation of the major phylae. Until now, only limited data on carbamoyl-phosphate synthetase were available for the primitive eukaryote Dictyostelium discoideum and for the Archaea Methanosarcina barkeri MS. The DNA sequence of the D. discoideum carbamoylphosphate gene and additional sequence for the carbamoyl-phosphate synthetase gene of M. barkeri MS have been determined, and a duplicated structure for both is clearly demonstrated. 2. Genes with ancient duplications provide unique information on their evolution. A study of the intron/exon organization of the rat carbamoylphosphate synthetase I gene and the carbamoylphosphate synthetase hamster II gene in the CAD multi-gene complex shows that at least some of their introns are very old. Evidence is provided that some introns must have been present in the ancestral precursor before its duplication. 3. The human carbamoyl-phosphate synthetase I gene has been isolated and characterized. A human liver cDNA library was constructed and probed for carbamoyl-phosphate synthetase I. A human genomic DNA cosmid library was also probed for the carbamoyl-phosphate synthetase I gene. The cDNA sequence of the human carbamoyl-phosphate synthetase I gene has been determined, and work has been initiated to confirm that at least part of this gene is contained within two cosmids spanning 46 kb. This will enable future studies to be made on mutations in this gene in the rare autosomal recessive deficiency of carbamoyl-phosphate synthetase I.

The first two steps of urea synthesis in liver of marine elasmobranchs involve formation of glutamine from ammonia and of carbamoyl phosphate from glutamine, catalysed by glutamine synthetase and carbamoyl-phosphate synthetase, respectively [Anderson & Casey (1984) J. Biol. Chem. 259, 456-462]; both of these enzymes are localized exclusively in the mitochondrial matrix. The objective of this study was to establish the enzymology of carbamoyl phosphate formation and utilization for pyrimidine nucleotide biosynthesis in Squalus acanthias (spiny dogfish), a representative elasmobranch. Aspartate carbamoyltransferase could not be detected in liver of dogfish. Spleen extracts, however, had glutamine-dependent carbamoyl-phosphate synthetase, aspartate carbamoyltransferase, dihydro-orotase, and glutamine synthetase activities, all localized in the cytosol; dihydro-orotate dehydrogenase, orotate phosphoribosyltransferase, and orotidine-5′-decarboxylase activities were also present. Except for glutamine synthetase, the levels of all activities were very low. The carbamoyl-phosphate synthetase activity is inhibited by UTP and is activated by 5-phosphoribosyl 1-pyrophosphate. The first three enzyme activities of the pyrimidine pathway were eluted in distinctly different positions during gel filtration chromatography under a number of different conditions; although complete proteolysis of inter-domain regions of a multifunctional complex during extraction cannot be excluded, the evidence suggests that in dogfish, in contrast to mammalian species, these three enzymes of the pyrimidine pathway exist as individual polypeptide chains. These results: (1) establish that dogfish express two different glutamine-dependent carbamoyl-phosphate synthetase activities, (2) confirm the report [Smith, Ritter & Campbell (1987) J. Biol. Chem. 262, 198-202] that dogfish express two different glutamine synthetases, and (3) provide indirect evidence that glutamine may not be available in liver for biosynthetic reactions other than urea formation.

The activity changes of the urea-cycle enzymes were monitored in cultured foetal hepatocytes after dexamethasone and insulin treatments. Addition of dexamethasone induced the development of carbamoyl-phosphate synthetase, argininosuccinate synthetase, argininosuccinase and arginase activities as soon as day 16.5 of gestation. When insulin was added together with dexamethasone, it markedly inhibited the steroid-induced increase in carbamoyl-phosphate synthetase, argininosuccinate synthetase and argininosuccinase activities.

Carbamoyl phosphate synthetase I, the most abundant protein of rat liver mitochondria, plays a key role in synthesis of urea. Because aging affects some liver functions, and because there is no information on the levels of carbamoyl phosphate synthetase I during aging, we assayed the activity of this enzyme and determined immunologically the level of carbamoyl phosphate synthetase I in liver homogenates from young (4 months) and old (18 or 26 months) rats. In addition, we used electron microscopic immunogold procedures to locate and measure the amount of the enzyme in the mitochondrial matrix. There is no significant change in enzyme activity or enzyme protein content with age, although there is a higher concentration of the enzyme in the mitochondria (c. 1.5 times greater) from old rats, which is compensated by a decrease in the fractional volume of the mitochondrial compartment during aging.

Carbamoyl phosphate synthetase (CPS) catalyzes the formation of carbamoyl phosphate (CP) from MgATP, bicarbonate, and glutamine. It has three active sites, one present on the small subunit and the two phosphorylation sites present on the large subunit. These two nucleotide binding sites are homologous. Six compounds were designed to mimic the reactive intermediate species carboxy phosphate, and product cabamoyl phosphate. The apparent Ki values calculated estimated the inhibitory strengths of these compounds. These plots were also utilized in identifying the linear inhibitors, nonlinear inhibitors and partial inhibitors. Inhibition patterns were obtained with these compounds using various assay formats. Partial inhibition displayed by phosphono formate for the full biosynthetic reaction can be utilized in support of the sequential mechanism for CPS.

The oligomerization of CPS from E. coli was investigated in order to examine the influence of this property on the catalytic activity. Mutations at the two interfacial sites of oligomerization were constructed in an attempt to elucidate the mechanism for assembly of the (αβ)4 tetramer through disruption of the molecular binding interactions between monomeric units. The results are consistent with a model for the structure of the (αβ)2 dimer that is formed through molecular contact between two pairs of allosteric domains. No significant dependence of the specific catalytic activity on the protein concentration could be detected. The molecular tunnel within CPS was inspected in order to characterize the role on kinetic properties. Gln-22, Ala-23, and Gly-575 from the large subunit of CPS were substituted by mutagenesis with bulkier amino acids in an attempt to obstruct and/or hinder the passage of the unstable intermediate through the carbamate tunnel. The kinetic data are consistent with a model for the catalytic mechanism of CPS that requires the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain to yield a final product carbamoyl phosphate. In addition, a unique feature of the carbamate tunnel has been noted where five highly conserved glutamates are located on a particular interior face of the tunnel. It has been postulated that the negative charge stabilizes the acid-labile intermediate, and facilitates catalysis. Also, the proposed gate keeping residues, Arg-306 and Arg-848, have been mutated to alanines to test their roles. However, since the arginines directly interact with MgATP, the mutation appeared to interrupt the binding of the substrate. The ammonia tunnel has been engineered to contain a hole to further support the proposed role of the tunnel that it is utilized in guiding diffusion of ammonia from the site of glutamine hydrolysis to the subsequent active site in the large subunit. Triple mutant αP360A/αH361A/βR265A exhibited kinetic behaviors consistent with a model of an impaired channeling.

Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2007.
Title from electronic title page (viewed Mar. 26, 2008). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Pharmacology." Discipline: Pharmacology; Department/School: Medicine.

[EN] Carbamoyl phosphate synthetase 1 (CPS1), a 1462-residue mitochondrial enzyme, catalyzes the entry of ammonia into the urea cycle, which converts ammonia, the neurotoxic waste product of protein catabolism, into barely toxic urea. The urea cycle inborn error and rare disease CPS1 deficiency (CPS1D) is inherited with mendelian autosomal recessive inheritance, being due to CPS1 gene mutations (>200 mutations reported), and causing life-threatening hyperammonemia. We have produced recombinantly human CPS1 (hCPS1) in a baculovirus/insect cell expression system, isolating the enzyme in active and highly purified form, in massive amounts. This has allowed enzyme crystallization for structural studies by X-ray diffraction (an off-shoot of the present studies). This hCPS1 production system allows site-directed mutagenesis and enzyme characterization as catalyst (activity, kinetics) and as protein (stability, aggregation state, domain composition). We have revealed previously unexplored traits of hCPS1 such as its domain composition, the ability of glycerol to replace the natural and essential CPS1 activator N-acetyl-L-glutamate (NAG), and the hCPS1 protection (chemical chaperoning) by NAG and by its pharmacological analog N-carbamyl-L-glutamate (NCG). We have exploited this system to explore the effects on the activity, kinetic parameters and stability/folding of the enzyme, and to test the disease-causing nature, of mutations identified in patients with CPS1 deficiency (CPS1D). These results, supplemented with those obtained with other non-clinical mutations, have provided novel information on the functions of three non-catalytic domains of CPS1. We have introduced three CPS1D-associated mutations and one trivial polymorphism in the glutaminase-like domain of CPS1, supporting a stabilizing and an activity-enhancing function of this non-catalytic domain. Two mutations introduced into the bicarbonate phosphorylation domain have shed light on bicarbonate binding and have directly confirmed the importance of this domain for NAG binding to the distant (in the sequence) C-terminal CPS1 domain. The introduction of 18 CPS1D-associated missense mutations mapping in a clinically highly eloquent central non-catalytic domain have proven the disease-causing nature of most of these mutations while showing that in most of the cases they trigger enzyme misfolding and/or destabilization. These results, by proving an important role of this domain in the structural integration of the multidomain CPS1 protein, have led us to call this domain the Integrating Domain. Finally, we have examined the effects of eight CPS1D-associated mutations, of one trivial polymorphism and of five non-clinical mutations, all of them mapping in the C-terminal domain of the enzyme where NAG binds, whereas we have re-analyzed prior results with another four clinical and five non-clinical mutations affecting this domain. We have largely confirmed the pathogenic nature of the clinical mutations, predominantly because of decreased activity, in many cases due to hampered NAG binding. A few mutations had substantial negative effects on CPS1 stability/folding. Our analysis reveals that NAG activation begins with a movement of the final part of the ß4-¿4 loop of the NAG site. Transmission of the activating signal to the phosphorylation domains involves helix ¿4 from this domain and is possibly transmitted by the mutually homologous loops 1313-1332 and 778-787 (figures are residue numbers) belonging, respectively, to the carbamate and bicarbonate phosphorylation domains. These two homologous loops are called from here on Signal Transmission Loops.
[ES] La carbamil fosfato sintetasa 1 (CPS1), una enzima mitocondrial, cataliza la entrada del amonio en el ciclo de la urea, que convierte esta neurotoxina derivada del catabolismo de las proteínas en urea, mucho menos tóxica. El déficit de CPS1 (CPS1D) es un error innato del ciclo de la urea, una enfermedad rara autosómica recesiva, que se debe a mutaciones en el gen CPS1 (>200 mutaciones descritas) y que cursa con hiperamonemia. Hemos producido CPS1 humana recombinante (hCPS1) en un sistema de expresión de células de insecto y baculovirus, y la hemos aislado en forma activa, muy pura y en cantidad elevada. Este sistema de producción de hCPS1 permite la realización de mutagénesis dirigida y la caracterización de la enzima como catalizador (actividad, cinética) y como proteína (estabilidad, estado de agregación y composición de dominios). Hemos revelado características de la hCPS1 antes no exploradas como es la composición de dominios, la capacidad que tiene el glicerol para reemplazar al activador natural y esencial de la CPS1, N-acetil-L-glutamato (NAG), y la protección de la hCPS1 por NAG y por su análogo farmacológico N-carbamil-L-glutamato (NCG) (chaperonas químicas). Hemos utilizado este sistema para explorar los efectos en actividad, parámetros cinéticos y estabilidad/plegamiento de la enzima, y para comprobar la naturaleza patogénica de mutaciones identificadas en pacientes con CPS1D. Estos resultados, junto con los obtenidos con otras mutaciones no clínicas, han aportado información novedosa sobre tres de los dominios no catalíticos de CPS1. Las observaciones realizadas tras introducir en el dominio de tipo glutaminasa de la enzima tres mutaciones asociadas a CPS1D y un polimorfismo trivial, apoyan la contribución de este dominio no catalítico a la estabilidad y a aumentar la actividad de la enzima. Dos mutaciones introducidas en el dominio de fosforilación de bicarbonato han arrojado luz sobre el modo de unión del bicarbonato (un sustrato). Los resultados de estas mutaciones también han confirmado la contribución de este dominio para la unión de NAG, cuyo sitio de unión se encuentra en el dominio C-terminal de CPS1, bastante alejado (en la secuencia) del dominio de fosforilación de bicarbonato. Además, hemos introducido 18 mutaciones de cambio de sentido asociadas a CPS1D, las cuales están localizadas en un dominio no catalítico, central y de elevada elocuencia clínica. Estos resultados han demostrado la naturaleza patogénica de estas mutaciones, ya que en la mayoría de los casos estas mutaciones producen un mal plegamiento o/y desestabilización de la enzima. Debido a que estos resultados han puesto de manifiesto el importante papel de este dominio en la integración estructural de la proteína multidominio CPS1, lo hemos llamado Dominio Integrador. Finalmente, hemos examinado los efectos de 8 mutaciones asociadas a CPS1D, de un polimorfismo trivial y de 5 mutaciones no clínicas, todas localizadas en el dominio C-terminal de la enzima, donde se une NAG. Además, hemos reanalizado resultados anteriores con otras 4 mutaciones clínicas y 5 no clínicas afectando a este dominio. Hemos confirmado el carácter patogénico de las mutaciones clínicas, las cuales predominantemente causan una disminución en la actividad enzimática, en muchos casos debida a que la unión de NAG se encuentra obstaculizada. Unas pocas mutaciones mostraron efectos negativos en la estabilidad/plegamiento de CPS1. Nuestros análisis revelan que la activación por el NAG empieza con un movimiento de la parte final del bucle ß4-¿4 del sitio de NAG. La transmisión de la señal activadora a los dominios de fosforilación implica a la hélice ¿4 de este dominio y posiblemente se transmite a través de los bucles homólogos 1313-1332 y 778-787 (numeración de residuos) pertenecientes, respectivamente, a los dominios de fosforilación de carbamato y bicarbonato. Por ello, hemos llamado a ambos bucles Bucles de
[CAT] La carbamil fosfat sintetasa 1 (CPS1), un enzim mitocondrial, catalitza l'entrada d'amoni en el cicle de la urea, que convertix l'amoni, producte neurotòxic del catabolisme de les proteïnes, en urea, una molècula molt poc tòxica. El dèficit de CPS1 (CPS1D) és un error innat del cicle de la urea, una malaltia rara autosòmica recessiva, que es deu a mutacions en el gen CPS1 (>200 mutacions descrites) i que cursa amb hiperamonièmia. Hem produït CPS1 humana recombinant (hCPS1) en un sistema d'expressió de cèl·lules d'insecte i baculovirus, i l'hem aïllada en forma activa, molt pura i en gran quantitat. Això ha permés la cristal·lització de l'enzim per a estudis estructurals amb difracció de raios-X (treball no inclòs en esta tesi Aquest sistema de producció de hCPS1 permet la realització de mutagènesi dirigida i la caracterització de l'enzim com a catalitzador (activitat, cinètica) i com a proteïna (estabilitat, estat d'agregació i composició de dominis). Hem revelat característiques de la hCPS1 no explorades abans com és la composició de dominis, la capacitat que té el glicerol per a reemplaçar l'activador natural i essencial de CPS1, N-acetil-L-glutamat (NAG), i la protecció de la hCPS1 per NAG i pel seu anàleg farmacològic N-carbamil-L-glutamat (NCG) (xaperones químiques) . Hem utilitzat aquest sistema per a explorar els efectes en l'activitat, els paràmetres cinètics i l'estabilitat/plegament de l'enzim, i per a comprovar la naturalesa patogènica de mutacions identificades en pacients amb CPS1D. Aquestos resultats, junt amb els obtinguts amb altres mutacions no clíniques, han aportat informació nova sobre tres dels dominis no catalítics de la CPS1. Les observacions, després d'introduir tres mutacions associades a CPS1D i un polimorfisme trivial en el domini tipus glutaminasa de CPS1, recolzen la contribució d'aquest domini no catalític a l'estabilitat i a l'optimització de l'activitat enzimàtica. Dues mutacions introduïdes en el domini de fosforilació de bicarbonat han esclarit el mode d'unió de bicarbonat. Els resultats d'aquestes mutacions també han confirmat la contribució d'aquest domini per a la unió de NAG, el lloc d'unió de la qual es troba en el domini C-terminal de CPS1, prou allunyat (en la seqüència) del domini de fosforilació de bicarbonat. A més, hem introduït 18 mutacions de canvi de sentit associades a CPS1D, les quals estan localitzades en un domini no catalític, central i d'elevada eloqüència clínica. Aquestos resultats han demostrat la naturalesa patogènica d'aquestes mutacions, ja que, en la majoria dels casos produïxen un mal plegament o/i desestabilització de l'enzim. Pel fet que aquestos resultats han posat de manifest l'important paper d'aquest domini en la integració estructural de la proteïna multidomini CPS1, l'hem anomenat Domini Integrador. Finalment, hem examinat els efectes de huit mutacions associades a CPS1D, un polimorfisme trivial i cinc mutacions no clíniques, totes elles localitzades en el domini C-terminal de l'enzim, on s'unix NAG. A més, hem reanalitzat resultats anteriors amb altres quatre mutacions clíniques i cinc no clíniques que afecten aquest domini. Hem confirmat el caràcter patogènic de les mutacions clíniques, les quals predominantment causen una disminució en l'activitat enzimàtica, en molts casos pel fet que la unió de NAG es troba obstaculitzada. Unes poques mutacions van mostrar efectes negatius substancials en l'estabilitat/plegament de CPS1. Les nostres anàlisis revelen que l'activació de NAG comença amb un moviment de la part final del bucle ß4-¿4 del lloc de NAG. La transmissió del senyal activadora als dominis de fosforilació involucra l'hèlix ¿4 d'aquest domini i es transmet, possiblement, a través dels bucles homòlegs 1313-1332 i 778-787 (numeració dels residus), pertanyents, respectivament, als dominis de fosforilació de carbamato i bicarbonat. Per això, hem anomenat a ambd
Díez Fernández, C. (2015). USING RECOMBINANT HUMAN CARBAMOYL PHOSPHATE SYNTHETASE 1 (CPS1) FOR STUDYING THIS ENZYME'S FUNCTION, REGULATION, PATHOLOGY AND STRUCTURE [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/52855
TESIS

Molecular aspects of nitrogen metabolism in vertebrates is an interesting area of physiology and evolution to explore due to the different ways in which animals excrete nitrogenous waste as they transition from an aquatic to a terrestrial lifestyle. Two main products of nitrogen metabolism in fishes are ammonia and urea. Ammonia is produced during protein catabolism and build up of ammonia is toxic. Some aquatic vertebrates convert ammonia into a less toxic compound urea via de novo synthesis through the ornithine-urea cycle (O-UC). Five enzymes are involved in the O-UC: carbamoyl phosphate synthetase (CPS), ornithine carbamoyl transferase (OCT), argininosuccinate synthetase (ASS), argininosuccinate lyase (ASL), and arginase (ARG). An accessory enzyme, glutamine synthetase (GS) also participates in the "fish-type" O-UC. Teleosts excrete ammonia passively over their gills into the aquatic environment. The teleost, Opsanus beta, has been shown to increase urea production after 48 hours of crowding. This thesis explored how crowding stress affected nitrogen metabolite levels of ammonia and urea and O-UC gene expression and enzyme activity in O. beta. Lungfishes while in an aquatic environment avoid ammonia toxicity by releasing excess ammonia across their gills, but when stranded on land they produce urea through the O-UC. Urea production via the O-UC has a metabolic cost of at least four ATP molecules. This thesis explored the response of a lungfish, Protopterus annectens, to six days of aerial exposure and re-immersion conditions by measuring concentrations of O-UC mRNA expression and enzyme activity and nitrogen metabolites ammonia and urea. CPS acts as the entry point to the O-UC and based on enzymatic studies, most aquatic vertebrates utilize one isoform of this enzyme (CPSIII) while terrestrial vertebrates utilize a different isoform of this enzyme (CPSI). Lungfishes are a particularly interesting group of air-breathing fishes, not only because of their link to the origins of tetrapods, but also because CPS I may have originated within this group. Both CPS III and CPS I have been enzymatically described within this group. This thesis uses phylogenetics to investigate how CPS nucleotide sequences in lungfishes evolved compared to other vertebrates.