1
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Characterization and assembly of the Pseudomonas aeruginosa aspartate transcarbamoylase-pseudo dihydroorotase complex. PLoS One 2020; 15:e0229494. [PMID: 32126100 PMCID: PMC7053772 DOI: 10.1371/journal.pone.0229494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 02/09/2020] [Indexed: 02/02/2023] Open
Abstract
Pseudomonas aeruginosa is a virulent pathogen that has become more threatening with the emergence of multidrug resistance. The aspartate transcarbamoylase (ATCase) of this organism is a dodecamer comprised of six 37 kDa catalytic chains and six 45 kDa chains homologous to dihydroorotase (pDHO). The pDHO chain is inactive but is necessary for ATCase activity. A stoichiometric mixture of the subunits associates into a dodecamer with full ATCase activity. Unlike other known ATCases, the P. aeruginosa catalytic chain does not spontaneously assemble into a trimer. Chemical-crosslinking and size-exclusion chromatography showed that P. aeruginosa ATCase is monomeric which accounts for its lack of catalytic activity since the active site is a composite comprised of residues from adjacent monomers in the trimer. Circular dichroism spectroscopy indicated that the ATCase chain adopts a structure that contains secondary structure elements although neither the ATCase nor the pDHO subunits are very stable as determined by a thermal shift assay. Formation of the complex increases the melting temperature by about 30°C. The ATCase is strongly inhibited by all nucleotide di- and triphosphates and exhibits extreme cooperativity. Previous studies suggested that the regulatory site is located in an 11-residue extension of the amino end of the catalytic chain. However, deletion of the extensions did not affect catalytic activity, nucleotide inhibition or the assembly of the dodecamer. Nucleotides destabilized the dodecamer which probably accounts for the inhibition and apparent cooperativity of the substrate saturation curves. Contrary to previous interpretations, these results suggest that P. aeruginosa ATCase is not allosterically regulated by nucleotides.
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2
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Shi D, Caldovic L, Tuchman M. Sources and Fates of Carbamyl Phosphate: A Labile Energy-Rich Molecule with Multiple Facets. BIOLOGY 2018; 7:biology7020034. [PMID: 29895729 PMCID: PMC6022934 DOI: 10.3390/biology7020034] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/25/2018] [Accepted: 06/07/2018] [Indexed: 11/16/2022]
Abstract
Carbamyl phosphate (CP) is well-known as an essential intermediate of pyrimidine and arginine/urea biosynthesis. Chemically, CP can be easily synthesized from dihydrogen phosphate and cyanate. Enzymatically, CP can be synthesized using three different classes of enzymes: (1) ATP-grasp fold protein based carbamyl phosphate synthetase (CPS); (2) Amino-acid kinase fold carbamate kinase (CK)-like CPS (anabolic CK or aCK); and (3) Catabolic transcarbamylase. The first class of CPS can be further divided into three different types of CPS as CPS I, CPS II, and CPS III depending on the usage of ammonium or glutamine as its nitrogen source, and whether N-acetyl-glutamate is its essential co-factor. CP can donate its carbamyl group to the amino nitrogen of many important molecules including the most well-known ornithine and aspartate in the arginine/urea and pyrimidine biosynthetic pathways. CP can also donate its carbamyl group to the hydroxyl oxygen of a variety of molecules, particularly in many antibiotic biosynthetic pathways. Transfer of the carbamyl group to the nitrogen group is catalyzed by the anabolic transcarbamylase using a direct attack mechanism, while transfer of the carbamyl group to the oxygen group is catalyzed by a different class of enzymes, CmcH/NodU CTase, using a different mechanism involving a three-step reaction, decomposition of CP to carbamate and phosphate, transfer of the carbamyl group from carbamate to ATP to form carbamyladenylate and pyrophosphate, and transfer of the carbamyl group from carbamyladenylate to the oxygen group of the substrate. CP is also involved in transferring its phosphate group to ADP to generate ATP in the fermentation of many microorganisms. The reaction is catalyzed by carbamate kinase, which may be termed as catabolic CK (cCK) in order to distinguish it from CP generating CK. CP is a thermally labile molecule, easily decomposed into phosphate and cyanate, or phosphate and carbamate depending on the pH of the solution, or the presence of enzyme. Biological systems have developed several mechanisms including channeling between enzymes, increased affinity of CP to enzymes, and keeping CP in a specific conformation to protect CP from decomposition. CP is highly important for our health as both a lack of, or decreased, CP production and CP accumulation results in many disease conditions.
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Affiliation(s)
- Dashuang Shi
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA.
- Department of Genomics and Precision Medicine, The George Washington University, Washington, DC 20010, USA.
| | - Ljubica Caldovic
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA.
- Department of Genomics and Precision Medicine, The George Washington University, Washington, DC 20010, USA.
| | - Mendel Tuchman
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA.
- Department of Genomics and Precision Medicine, The George Washington University, Washington, DC 20010, USA.
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3
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Ruiz-Ramos A, Velázquez-Campoy A, Grande-García A, Moreno-Morcillo M, Ramón-Maiques S. Structure and Functional Characterization of Human Aspartate Transcarbamoylase, the Target of the Anti-tumoral Drug PALA. Structure 2016; 24:1081-94. [PMID: 27265852 DOI: 10.1016/j.str.2016.05.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/03/2016] [Accepted: 05/03/2016] [Indexed: 01/30/2023]
Abstract
CAD, the multienzymatic protein that initiates and controls de novo synthesis of pyrimidines in animals, associates through its aspartate transcarbamoylase (ATCase) domain into particles of 1.5 MDa. Despite numerous structures of prokaryotic ATCases, we lack structural information on the ATCase domain of CAD. Here, we report the structure and functional characterization of human ATCase, confirming the overall similarity with bacterial homologs. Unexpectedly, human ATCase exhibits cooperativity effects that reduce the affinity for the anti-tumoral drug PALA. Combining structural, mutagenic, and biochemical analysis, we identified key elements for the necessary regulation and transmission of conformational changes leading to cooperativity between subunits. Mutation of one of these elements, R2024, was recently found to cause the first non-lethal CAD deficit. We reproduced this mutation in human ATCase and measured its effect, demonstrating that this arginine is part of a molecular switch that regulates the equilibrium between low- and high-affinity states for the ligands.
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Affiliation(s)
- Alba Ruiz-Ramos
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fdez. Almagro, 3, Madrid 28029, Spain
| | - Adrián Velázquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; Department of Biochemistry and Molecular and Cell Biology, Universidad de Zaragoza, 50009 Zaragoza, Spain; Aragon Institute for Health Research (IIS Aragon), 50009 Zaragoza, Spain; Fundacion ARAID, Government of Aragon, 50018 Zaragoza, Spain
| | - Araceli Grande-García
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fdez. Almagro, 3, Madrid 28029, Spain
| | - María Moreno-Morcillo
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fdez. Almagro, 3, Madrid 28029, Spain
| | - Santiago Ramón-Maiques
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fdez. Almagro, 3, Madrid 28029, Spain.
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4
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Singh R, Trivedi VD, Phale PS. Purification and characterization of NAD+ -dependent salicylaldehyde dehydrogenase from carbaryl-degrading Pseudomonas sp. strain C6. Appl Biochem Biotechnol 2014; 172:806-19. [PMID: 24122667 DOI: 10.1007/s12010-013-0581-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 10/01/2013] [Indexed: 10/26/2022]
Abstract
NAD+-dependent salicylaldehyde dehydrogenase (SALDH) which catalyzes the oxidation of salicylaldehyde to salicylate was purified form carbaryl-degrading Pseudomonas sp. strain C6. The enzyme was found to be a functional homotrimer (150 kDa) with subunit molecular mass of 50 kDa and contained calcium (1.8 mol/mol of enzyme). These properties were found to be unique. External addition of metal ions showed no effect on the activity and addition of chelators showed moderate inhibition of the activity. Potassium ions were found to enhance the activity significantly. SALDH showed higher affinity for salicylaldehyde (Km = 4.5 μM) and accepts mono- as well as di-aromatic aldehydes; however it showed poor activity on aliphatic aldehydes. Chloro-/nitro-substituted benzaldehydes were potent substrate inhibitors as compared to benzaldehyde and 3-hydroxybenzaldehyde, while 2-naphthaldehyde and salicylaldehyde were moderate. The kinetic data revealed that SALDH, though having broad specificity, is more efficient for the oxidation of salicylaldehyde as compared to other aromatic aldehyde dehydrogenases which gives an advantage for Pseudomonas sp. strain C6 to bioremediate carbaryl and other aromatic aldehydes efficiently.
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Harris KM, Cockrell GM, Puleo DE, Kantrowitz ER. Crystallographic snapshots of the complete catalytic cycle of the unregulated aspartate transcarbamoylase from Bacillus subtilis. J Mol Biol 2011; 411:190-200. [PMID: 21663747 PMCID: PMC3211067 DOI: 10.1016/j.jmb.2011.05.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 05/19/2011] [Accepted: 05/24/2011] [Indexed: 01/07/2023]
Abstract
Here, we report high-resolution X-ray structures of Bacillus subtilis aspartate transcarbamoylase (ATCase), an enzyme that catalyzes one of the first reactions in pyrimidine nucleotide biosynthesis. Structures of the enzyme have been determined in the absence of ligands, in the presence of the substrate carbamoyl phosphate, and in the presence of the bisubstrate/transition state analog N-phosphonacetyl-L-aspartate. Combining the structural data with in silico docking and electrostatic calculations, we have been able to visualize each step in the catalytic cycle of ATCase, from the ordered binding of the substrates, to the formation and decomposition of the tetrahedral intermediate, to the ordered release of the products from the active site. Analysis of the conformational changes associated with these steps provides a rationale for the lack of cooperativity in trimeric ATCases that do not possess regulatory subunits.
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Affiliation(s)
- Katharine M. Harris
- Department of Chemistry, Boston College, Merkert Chemistry Center, Chestnut Hill, MA 02467 USA
| | - Gregory M. Cockrell
- Department of Chemistry, Boston College, Merkert Chemistry Center, Chestnut Hill, MA 02467 USA
| | - David E. Puleo
- Department of Chemistry, Boston College, Merkert Chemistry Center, Chestnut Hill, MA 02467 USA
| | - Evan R. Kantrowitz
- Department of Chemistry, Boston College, Merkert Chemistry Center, Chestnut Hill, MA 02467 USA
- Corresponding author. E. R. Kantrowitz, Department of Chemistry, Boston College, Merkert Chemistry Center 239, Chestnut Hill, MA 02467 USA.,
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Van de Casteele M, Desmarez L, Legrain C, Chen PG, Lierde KV, Piérard A, Glansdorff N. Genes Encoding Thermophilic Aspartate Carbamoyltransferases ofThermus AquaticusZ05 andThermotoga MaritimaMSB8: Modes of Expression inE. Coliand Properties of Their Products. ACTA ACUST UNITED AC 2009. [DOI: 10.3109/10242429409034386] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- M. Van de Casteele
- Laboratorium voor Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussel
| | | | | | - P. G. Chen
- Laboratorium voor Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussel
| | - K. Van Lierde
- Laboratorium voor Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussel
| | - A. Piérard
- Research Institute, CERIA-COOVI
- Laboratoire de Microbiologie, Université Libre de Bruxelles, avenue Emile Gryson 1, B-1070, Brussels, Belgium
| | - N. Glansdorff
- Laboratorium voor Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussel
- Research Institute, CERIA-COOVI
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Affiliation(s)
- Robert L Switzer
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA.
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8
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Regulation of pyrimidine biosynthetic gene expression in bacteria: repression without repressors. Microbiol Mol Biol Rev 2008; 72:266-300, table of contents. [PMID: 18535147 DOI: 10.1128/mmbr.00001-08] [Citation(s) in RCA: 135] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
SUMMARY DNA-binding repressor proteins that govern transcription initiation in response to end products generally regulate bacterial biosynthetic genes, but this is rarely true for the pyrimidine biosynthetic (pyr) genes. Instead, bacterial pyr gene regulation generally involves mechanisms that rely only on regulatory sequences embedded in the leader region of the operon, which cause premature transcription termination or translation inhibition in response to nucleotide signals. Studies with Escherichia coli and Bacillus subtilis pyr genes reveal a variety of regulatory mechanisms. Transcription attenuation via UTP-sensitive coupled transcription and translation regulates expression of the pyrBI and pyrE operons in enteric bacteria, whereas nucleotide effects on binding of the PyrR protein to pyr mRNA attenuation sites control pyr operon expression in most gram-positive bacteria. Nucleotide-sensitive reiterative transcription underlies regulation of other pyr genes. With the E. coli pyrBI, carAB, codBA, and upp-uraA operons, UTP-sensitive reiterative transcription within the initially transcribed region (ITR) leads to nonproductive transcription initiation. CTP-sensitive reiterative transcription in the pyrG ITRs of gram-positive bacteria, which involves the addition of G residues, results in the formation of an antiterminator RNA hairpin and suppression of transcription attenuation. Some mechanisms involve regulation of translation rather than transcription. Expression of the pyrC and pyrD operons of enteric bacteria is controlled by nucleotide-sensitive transcription start switching that produces transcripts with different potentials for translation. In Mycobacterium smegmatis and other bacteria, PyrR modulates translation of pyr genes by binding to their ribosome binding site. Evidence supporting these conclusions, generalizations for other bacteria, and prospects for future research are presented.
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9
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Vitali J, Colaneri MJ, Kantrowitz E. Crystal structure of the catalytic trimer ofMethanococcus jannaschiiaspartate transcarbamoylase. Proteins 2007; 71:1324-34. [PMID: 18058907 DOI: 10.1002/prot.21667] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jacqueline Vitali
- Department of Physics, Cleveland State University, Euclid Avenue at East 24th Street, Cleveland, Ohio 44115, USA.
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10
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Evrin C, Straut M, Slavova-Azmanova N, Bucurenci N, Onu A, Assairi L, Ionescu M, Palibroda N, Bârzu O, Gilles AM. Regulatory mechanisms differ in UMP kinases from gram-negative and gram-positive bacteria. J Biol Chem 2007; 282:7242-53. [PMID: 17210578 DOI: 10.1074/jbc.m606963200] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this work, we examined the regulation by GTP and UTP of the UMP kinases from eight bacterial species. The enzyme from Gram-positive organisms exhibited cooperative kinetics with ATP as substrate. GTP decreased this cooperativity and increased the affinity for ATP. UTP had the opposite effect, as it decreased the enzyme affinity for ATP. The nucleotide analogs 5-bromo-UTP and 5-iodo-UTP were 5-10 times stronger inhibitors than the parent compound. On the other hand, UMP kinases from the Gram-negative organisms did not show cooperativity in substrate binding and catalysis. Activation by GTP resulted mainly from the reversal of inhibition caused by excess UMP, and inhibition by UTP was accompanied by a strong increase in the apparent K(m) for UMP. Altogether, these results indicate that, depending on the bacteria considered, GTP and UTP interact with different enzyme recognition sites. In Gram-positive bacteria, GTP and UTP bind to a single site or largely overlapping sites, shifting the T R equilibrium to either the R or T form, a scenario corresponding to almost all regulatory proteins, commonly called K systems. In Gram-negative organisms, the GTP-binding site corresponds to the unique allosteric site of the Gram-positive bacteria. In contrast, UTP interacts cooperatively with a site that overlaps the catalytic center, i.e. the UMP-binding site and part of the ATP-binding site. These characteristics make UTP an original regulator of UMP kinases from Gram-negative organisms, beyond the common scheme of allosteric control.
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Affiliation(s)
- Cécile Evrin
- UnitédeGénétique des Génomes Bactériens, Institut Pasteur, 75724 Paris Cedex, France
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11
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Lipscomb WN. Aspartate transcarbamylase from Escherichia coli: activity and regulation. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 68:67-151. [PMID: 8154326 DOI: 10.1002/9780470123140.ch3] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- W N Lipscomb
- Department of Chemistry, Harvard University, Cambridge, MA
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12
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Vickrey JF, Herve G, Evans DR. Pseudomonas aeruginosa aspartate transcarbamoylase. Characterization of its catalytic and regulatory properties. J Biol Chem 2002; 277:24490-8. [PMID: 11959858 DOI: 10.1074/jbc.m200009200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aspartate transcarbamoylase from Pseudomonadaceae is a class A enzyme consisting of six copies of a 36-kDa catalytic chain and six copies of a 45-kDa polypeptide of unknown function. The 45-kDa polypeptide is homologous to dihydroorotase but lacks catalytic activity. Pseudomonas aeruginosa aspartate transcarbamoylase was overexpressed in Escherichia coli. The homogeneous His-tagged protein isolated in high yield, 30 mg/liter of culture, by affinity chromatography and crystallized. Attempts to dissociate the catalytic and pseudo-dihydroorotase (pDHO) subunits or to express catalytic subunits only were unsuccessful suggesting that the pDHO subunits are required for the proper folding and assembly of the complex. As reported previously, the enzyme was inhibited by micromolar concentrations of all nucleotide triphosphates. In the absence of effectors, the aspartate saturation curves were hyperbolic but became strongly sigmoidal in the presence of low concentrations of nucleotide triphosphates. The inhibition was unusual in that only free ATP, not MgATP, inhibits the enzyme. Moreover, kinetic and binding studies with a fluorescent ATP analog suggested that ATP induces a conformational change that interferes with the binding of carbamoyl phosphate but has little effect once carbamoyl phosphate is bound. The peculiar allosteric properties suggest that the enzyme may be a potential target for novel chemotherapeutic agents designed to combat Pseudomonas infection.
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Affiliation(s)
- John F Vickrey
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michiagan 48201, USA
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13
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Hack ES, Vorobyova T, Sakash JB, West JM, Macol CP, Hervé G, Williams MK, Kantrowitz ER. Characterization of the aspartate transcarbamoylase from Methanococcus jannaschii. J Biol Chem 2000; 275:15820-7. [PMID: 10748118 DOI: 10.1074/jbc.m909220199] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The genes from the thermophilic archaeabacterium Methanococcus jannaschii that code for the putative catalytic and regulatory chains of aspartate transcarbamoylase were expressed at high levels in Escherichia coli. Only the M. jannaschii PyrB (Mj-PyrB) gene product exhibited catalytic activity. A purification protocol was devised for the Mj-PyrB and M. jannaschii PyrI (Mj-PyrI) gene products. Molecular weight measurements of the Mj-PyrB and Mj-PyrI gene products revealed that the Mj-PyrB gene product is a trimer and the Mj-PyrI gene product is a dimer. Preliminary characterization of the aspartate transcarbamoylase from M. jannaschii cell-free extract revealed that the enzyme has a similar molecular weight to that of the E. coli holoenzyme. Kinetic analysis of the M. jannaschii aspartate transcarbamoylase from the cell-free extract indicates that the enzyme exhibited limited homotropic cooperativity and little if any regulatory properties. The purified Mj-catalytic trimer exhibited hyperbolic kinetics, with an activation energy similar to that observed for the E. coli catalytic trimer. Homology models of the Mj-PyrB and Mj-PyrI gene products were constructed based on the three-dimensional structures of the homologous E. coli proteins. The residues known to be critical for catalysis, regulation, and formation of the quaternary structure from the well characterized E. coli aspartate transcarbamoylase were compared.
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Affiliation(s)
- E S Hack
- Department of Chemistry, Boston College, Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, USA
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14
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Durbecq V, Thia-Toong TL, Charlier D, Villeret V, Roovers M, Wattiez R, Legrain C, Glansdorff N. Aspartate carbamoyltransferase from the thermoacidophilic archaeon Sulfolobus acidocaldarius. Cloning, sequence analysis, enzyme purification and characterization. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 264:233-41. [PMID: 10447693 DOI: 10.1046/j.1432-1327.1999.00619.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The genes coding for aspartate carbamoyltransferase (ATCase) in the extremely thermophilic archaeon Sulfolobus acidocaldarius have been cloned by complementation of a pyrBI deletion mutant of Escherichia coli. Sequencing revealed the existence of an enterobacterial-like pyrBI operon encoding a catalytic chain of 299 amino acids (34 kDa) and a regulatory chain of 170 amino acids (17.9 kDa). The deduced amino acid sequences of the pyrB and pyrI genes showed 27.6-50% identity with archaeal and enterobacterial ATCases. The recombinant S. acidocaldarius ATCase was purified to homogeneity, allowing the first detailed studies of an ATCase isolated from a thermophilic organism. The recombinant enzyme displayed the same properties as the ATCase synthesized in the native host. It is highly thermostable and exhibits Michaelian saturation kinetics for carbamoylphosphate (CP) and positive homotropic cooperative interactions for the binding of L-aspartate. Moreover, it is activated by nucleoside triphosphates whereas the catalytic subunits alone are inhibited. The holoenzyme purified from recombinant E. coli cells or present in crude extract of the native host have an Mr of 340 000 as estimated by gel filtration, suggesting that it has a quaternary structure similar to that of E. coli ATCase. Only monomers could be found in extracts of recombinant E. coli or Saccharomyces cerevisiae cells expressing the pyrB gene alone. In the presence of CP these monomers assembled into trimers. The stability of S. acidocaldarius ATCase and the allosteric properties of the enzyme are discussed in function of a modeling study.
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Affiliation(s)
- V Durbecq
- Laboratoire de Microbiologie, Université de Libre de Bruxelles, Belgium
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15
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Becker J, Brendel M. Molecular cloning and characterization of the pyrB gene of Lactobacillus leichmannii encoding aspartate transcarbamylase. Biochimie 1996; 78:3-13. [PMID: 8725005 DOI: 10.1016/0300-9084(96)81323-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The Lactobacillus leichmannii pyrB gene, encoding pyrimidine biosynthetic enzyme aspartate transcarbamylase (ATCase), was cloned from a partial genomic library lying on a 1468 bp Sa/I/BstXI fragment. The predicted polypeptide sequence extending over 351 amino acid residues (M(r) 39 855 Da) was compared to those of various other organisms revealing clear identities towards them and important conservative stretches, implying that these proteins are closely related. Transcriptional initiation was mapped by primer extension and occurred 54 bp upstream of the pyrB open reading frame (ORF). Northern blot analysis indicates that the pyrB gene is transcribed as a single mRNA and not together with the following overlapping pyrC gene as a bicistronic mRNA. At high copy number the pyrB gene of L leichmannii seems to be lethal for its E coli host; inserted in a low copy vector it complements the uracil auxotrophy of an E coli pyrB mutant which shows distinct ATCase activity in the cell extract. With an excess of uracil in the growth medium the gene is apparently repressed and no ATCase activity can be measured.
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Affiliation(s)
- J Becker
- Institut für Mikrobiologie, JW Goethe-Universität, Frankfurt/Main, Germany
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16
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Masood R, Venkitasubramanian TA. Purification and properties of aspartate transcarbamylase from Mycobacterium smegmatis. BIOCHIMICA ET BIOPHYSICA ACTA 1988; 953:106-13. [PMID: 3342242 DOI: 10.1016/0167-4838(88)90014-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Aspartate transcarbamylase (carbamoyl-phosphate: L-aspartate carbamoyltransferase, EC 2.1.3.2) has been purified from Mycobacterium smegmatis TMC 1546 using streptomycin sulphate precipitation, ammonium sulphate precipitation, DE-52 chromatography, second ammonium sulphate precipitation, Sephadex G-200 gel filtration, and aspartate-linked CNBr-activated Sepharose 4B affinity chromatography in successive order. The enzyme was purified 231.6-fold, and the preparation was found to be homogeneous on column chromatography and polyacrylamide gel electrophoresis. The purified enzyme had a molecular weight of 246,000 and was composed of two asymmetrical subunits. The kinetic and regulatory properties of aspartate transcarbamylase from M. smegmatis were also studied. The enzyme was found to be an allosteric in nature with carbamyl phosphate showing positive cooperativity and UMP exhibiting a negative cooperativity. CTP was found to be the most potent inhibitor among nucleotides. Phosphate acted as a non-competitive product inhibitor with respect to aspartate. Succinate and maleate exerted a competitive inhibition when aspartate was the variable substrate.
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Affiliation(s)
- R Masood
- Department of Biochemistry, Vallabhbhai Patel Chest Institute, University of Delhi, India
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17
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Traut TW. Enzymes of nucleotide metabolism: the significance of subunit size and polymer size for biological function and regulatory properties. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1988; 23:121-69. [PMID: 3048887 DOI: 10.3109/10409238809088318] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The 72 enzymes in nucleotide metabolism, from all sources, have a distribution of subunit sizes similar to those from other surveys: an average subunit Mr of 47,900, and a median size of 33,300. The same enzyme, from whatever source, usually has the same subunit size (there are exceptions); enzymes having a similar activity (e.g., kinases, deaminases) usually have a similar subunit size. Most simple enzymes in all EC classes (except class 6, ligases/synthetases) have subunit sizes of less than 30,000. Since structural domains defined in proteins tend to be in the Mr range of 5,000 to 30,000, it may be that most simple enzymes are formed as single domains. Multifunctional proteins and ligases have subunits generally much larger than Mr 40,000. Analyses of several well-characterized ligases suggest that they also have two or more distinct catalytic sites, and that ligases therefore are also multifunctional proteins, containing two or more domains. Cooperative kinetics and evidence for allosteric regulation are much more frequently associated with larger enzymes: such complex functions are associated with only 19% of enzymes having a subunit Mr less than or equal to 29,000, and with 86% of all enzymes having a subunit Mr greater than 50,000. In general, larger enzymes have more functions. Only 20% of these enzymes appear to be monomers; the rest are homopolymers and rarely are they heteropolymers. Evidence for the reversible dissociation of homopolymers has been found for 15% of the enzymes. Such changes in quaternary structure are usually mediated by appropriate physiological effectors, and this may serve as a mechanism for their regulation between active and less active forms. There is considerable structural organization of the various pathways: 19 enzymes are found in various multifunctional proteins, and 13 enzymes are found in different types of multienzyme complexes.
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Affiliation(s)
- T W Traut
- Department of Biochemistry, University of North Carolina School of Medicine, Chapel Hill
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Doremus HD. Organization of the pathway of de novo pyrimidine nucleotide biosynthesis in pea (Pisum sativum L. cv Progress No. 9) leaves. Arch Biochem Biophys 1986; 250:112-9. [PMID: 2876681 DOI: 10.1016/0003-9861(86)90707-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The organization of the enzymes of de novo pyrimidine nucleotide biosynthesis in pea (Pisum sativum L. cv Progress No. 9) has been studied. The first three enzymes of the pathway, carbamoyl-phosphate synthetase, aspartate carbamoyltransferase, and dihydroorotase, are readily separable from one another; they are not part of a multifunctional complex. The final two activities of the pathway, orotate phosphoribosyltransferase and orotidylate decarboxylase, copurify and appear to be complexed in vivo. This organizational pattern is distinct from those reported for bacteria, yeast, and mammals. The differences in organization, in a pathway which is present in all organisms, make the pyrimidine biosynthetic pathway a very interesting candidate for evolutionary studies.
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Lerner CG, Switzer RL. Cloning and structure of the Bacillus subtilis aspartate transcarbamylase gene (pyrB). J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)67362-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Prasad PV, Rao NA. Purification and regulation of aspartate transcarbamylase from germinated mung bean (Vigna radiata) seedlings. J Biosci 1984. [DOI: 10.1007/bf02702645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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22
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Paulus H. The evolutionary history of the ornithine cycle as a determinant of its structure and regulation. CURRENT TOPICS IN CELLULAR REGULATION 1983; 22:177-200. [PMID: 6223788 DOI: 10.1016/b978-0-12-152822-5.50010-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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23
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Bond RW, Field AS, Switzer RL. Nutritional regulation of degradation of aspartate transcarbamylase and of bulk protein in exponentially growing Bacillus subtilis cells. J Bacteriol 1983; 153:253-8. [PMID: 6401278 PMCID: PMC217363 DOI: 10.1128/jb.153.1.253-258.1983] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The rate of degradation of aspartate transcarbamylase in exponentially growing Bacillus subtilis cells was determined by measurement of enzyme activity after the addition of uridine to repress further enzyme synthesis and by specific immunoprecipitation of the enzyme from cells grown in the presence of [3H]leucine. Aspartate transcarbamylase was degraded with a half-life of about 1.5 h in cells growing on a glucose-salts medium with NH4+ ions as the sole source of nitrogen. Replacement of NH4+ in this medium with a combination of the amino acids aspartate, glutamate, isoleucine, proline, and threonine reduced the degradation rate to an undetectable level. Various other amino acids and amino acid mixtures had smaller effects on the rate of degradation. The carbon source also influenced the degradation rate, but to a smaller extent than the nitrogen source. The effects of these nutritional variables on the rate of bulk protein turnover in growing cells were generally similar to their effects on degradation of aspartate transcarbamylase. Since the degradation of aspartate transcarbamylase has been shown to be 10 to 20 times faster than bulk protein turnover, the results suggest that a substantial portion of protein turnover in growing cells represents regulable, rapid degradation of a number of normal proteins, of which aspartate transcarbamylase is an example.
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Wild JR, Foltermann KF, O'Donovan GA. Regulatory divergence of aspartate transcarbamoylases within the enterobacteriaceae. Arch Biochem Biophys 1980; 201:506-17. [PMID: 7396519 DOI: 10.1016/0003-9861(80)90539-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Jeffrey PD, Andrwes PR. Application of calculated sedimentation ratios in the specification of models for protein dimers, trimers, tetramers and pentamers. Biophys Chem 1980; 11:61-70. [PMID: 16997238 DOI: 10.1016/0301-4622(80)85008-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/1979] [Revised: 05/04/1979] [Indexed: 11/20/2022]
Abstract
In the preceding paper a systematic method for delineating quaternary structures compatible with the sedimentation behaviour of oligomeric assemblies was developed. In this companion paper the approach is illustrated by its application to a number of oligomeric proteins, namely beta-lactoglobulin, aminoacyl transferase, succinic semialdehyde dehydrogenase, arginine decarboxylase, and the arthropod hemocyanins. Structures of these proteins based on comparisons of calculated and experimental sedimentation coefficients are presented and, wherever possible, compared with those obtained by other techniques. The usefulness and limitations of the method are assessed. It is concluded that the sedimentation analysis will usually yield a reasonably good representation of the mode of assembly of protein molecules in oligomeric structures if accurate experimental data are available. A high degree of resolution of structural detail is not expected and since, in addition, the sedimentation ratio method is seldom definitive to one structure, it is most valuable when used in a conformatory or eliminative way with results from techniques more specifically designed for structure determination.
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Affiliation(s)
- P D Jeffrey
- Department of Physical Biochemistry, John Curtin School of Medical Research, Australian National University, Canberra, A.C.T. 2601, Australia
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Wargnies B, Lauwers N, Stalon V. Structure and properties of the putrescine carbamoyltransferase of Streptococcus faecalis. EUROPEAN JOURNAL OF BIOCHEMISTRY 1979; 101:143-52. [PMID: 116850 DOI: 10.1111/j.1432-1033.1979.tb04226.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ornithine and putrescine carbamoyltransferases from Streptococcus faecalis ATCC11700 have been purified and their structural properties compared. The molecular weight of native ornithine carbamoyltransferase, measured by molecular sieving, is 250 000. It is composed of six apparently identical subunits with a molecular weight of 39 000, as determined by cross-linking with the bifunctional reagent glutaraldehyde followed by polyacrylamide gel electrophoresis in the presence of sodium dodecylsulfate. Using the same method, putrescine carbamoyltransferase is a trimer of 140 000 consisting of three identical subunits with a molecular weight of 40 000. Ornithine carbamoyltransferase displays a narrow specificity towards its substrate, ornithine. In contrast, putrescine carbamoyltransferase carbamoylates ornithine and several diamines (diaminopropane, diaminohexane, spermine, spermidine, cadaverine) in addition to its preferred substrate, putrescine, but with a considerable lower efficiency than for putrescine. The kinetic mechanism of putrescine carbamoyltransferase has been investigated. Initial velocity studies yield intersecting plots using either putrescine or ornithine as substrate, indicating a sequential mechanism. The patterns of protection of the enzyme by the reactants during heat inactivation as well as the results of product and dead-end inhibition studies provide evidence for a random addition of the substrates. The putrescine inhibition that is induced by phosphate does, however, suggest that a preferred pathway exists in which carbamoylphosphate is the leading substrate. The different kinetic constants have been established. The properties of putrescine carbamoyltransferase are compared to the known properties of other carbamoyltransferases. The evolutionary implications of this comparison are discussed.
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Davidson JN, Carnright DV, Patterson D. Biochemical genetic analysis of pyrimidine biosynthesis in mammalian cells: III. Association of carbamyl phosphate synthetase, aspartate transcarbamylase, and dihydroorotase in mutants of cultured Chinese hamster cells. SOMATIC CELL GENETICS 1979; 5:175-91. [PMID: 39353 DOI: 10.1007/bf01539159] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Carbamyl phosphate synthetase (EC 2.7.2.9), aspartate transcarbamylase (EC 2.1.3.2), and dihydroorotase (EC 3.5.2.3), the first three enzymes in de novo pyrimidine synthesis in Chinese hamster ovary cell strain Kl (CHO-Kl), cose diment through a glycerol gradient. When an extract from Urd- A, a pyrimidine-requiring auxotroph reduced in all three activities, is run on a glycerol gradient, the enzyme activities appear in two peaks higher in the gradient, a peak of aspartate transcarbamylase separated from a peak of carbamyl phosphate synthetase and dihydroorotase. Revertants of Urd- A have increased activity of all three enzymes and give glycerol gradient patterns similar to either CHO-Kl or Urd- A. The gradient pattern for Urd- A and some of its revertants can be mimicked by treating the CHO-Kl cell extract with trypsin. Hybrids made between a CHO-Kl purine-requiring auxotroph (Ade- C) and a Urd- A revertant gave a glycerol gradient pattern which is a composite of the CHO-Kl and revertant patterns. A model is presented for the structure of this multifunctional protein.
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Paulus TJ, Switzer RL. Characterization of pyrimidine-repressible and arginine-repressible carbamyl phosphate synthetases from Bacillus subtilis. J Bacteriol 1979; 137:82-91. [PMID: 216664 PMCID: PMC218421 DOI: 10.1128/jb.137.1.82-91.1979] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The number and properties of carbamyl phosphate synthetases in Bacillus subtilis have been uncertain because of conflicting genetic results and instability of the enzyme in extracts. The discovery of a previously unrecognized requirement of B. subtilis carbamyl phosphate synthetases for a high concentration of potassium ions for activity and stability permitted unequivocal demonstration that this bacterium elaborates two carbamyl phosphate synthetases. Carbamyl phosphate synthetase A was shown to be repressed by arginine, to have a molecular weight of about 200,000, and to be coded for by a gene that maps near argC4. This isozyme was insensitive to metabolites of the arginine and pyrimidine biosynthetic pathways. Carbamyl phosphate synthetase P was found to be repressed by uracil, to have a molecular weight of 90,000 to 100,000, and to be coded for by a gene that maps near the other pyr genes. This isozyme was activated by phosphoridine nucleotides. Other kinetic properties of the two isozymes were compared. Bacillus thus resembles eucaryotic microbes in producing two carbamyl phosphate synthetases, rather than the enteric bacteria, which produce a single carbamyl phosphate synthetase.
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Maurizi M, Brabson J, Switzer R. Immunochemical studies of the inactivation of aspartate transcarbamylase by stationary phase Bacillus subtilis cells. Evidence for selective, energy-dependent degradation. J Biol Chem 1978. [DOI: 10.1016/s0021-9258(17)30307-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Makoff AJ, Buxton FP, Radford A. A possible model for the structure of the Neurospora carbamoyl phosphate synthase-aspartate carbamoyl transferase complex enzyme. MOLECULAR & GENERAL GENETICS : MGG 1978; 161:297-304. [PMID: 209307 DOI: 10.1007/bf00331004] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The pyrimidine-3 locus of Neurospora crassa specifies a multienzyme complex comprising pyrimidine-specific carbamoyl phosphate synthase (CPSpyr) and aspartate carbamoyl transferase (ACT). It appears to be divided into a translationally proximal CPS-specific region and a distal ACT-specific region. Levels of complementation for ACT activity between pairs of four pyr-3 CPS+ ACT- mutants showed a range from 12% to 68% of the wild-type level of the enzyme. This is interpreted as interallelic complementation, contradicting certain earlier suggestion of two dissimilar ACT subunits. Proteolysis of an extract from a heterokaryon formed from two of the above CPS+ ACT- alleles (alpha and beta) did not lead to loss of ACT activity, but led to the formation of a fragment with ACT activity with a similar molecular weight (92,000 daltons) to that produced in extracts of wild type strain. The pyr-3 polar mutant 43-174 which is enzymatically CPS+ ACT- and which fails to complement with any other CPS+ ACT- alleles, thus suggesting its location towards the proximal end of the ACT region, has CPS activity associated with a form of 180,000 daltons molecular weight. These findings are used to contruct a model for structure of the native enzyme complex.
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Traut TW, Jones ME. Mammalian synthesis of UMP from orotate: the regulation of and conformers of complex U. ADVANCES IN ENZYME REGULATION 1977; 16:21-41. [PMID: 358793 DOI: 10.1016/0065-2571(78)90065-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Gigot D, Glansdorff N, Legrain C, Piérard A, Stalon V, Konigsberg W, Caplier I, Strosberg AD, Hervé G. Comparison of the N-terminal sequences of aspartate and ornithine carbamoyltransferases of Escherichia coli. FEBS Lett 1977; 81:28-32. [PMID: 332525 DOI: 10.1016/0014-5793(77)80920-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Kirschenbaum DM. Molar absorptivity and A 1% 1cm values for proteins at selected wavelengths of the ultraviolet and visible regions. XIII. Anal Biochem 1977; 81:220-46. [PMID: 332005 DOI: 10.1016/0003-2697(77)90615-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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