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Zhang X, Liu L, Ma C, Zhang H, Liu H, Fang H. Improving the level of the cytidine biosynthesis in E. coli through atmospheric room temperature plasma mutagenesis and metabolic engineering. J Appl Microbiol 2024; 135:lxae133. [PMID: 38830792 DOI: 10.1093/jambio/lxae133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/09/2024] [Accepted: 06/01/2024] [Indexed: 06/05/2024]
Abstract
AIMS Cytidine, as an important commercial precursor in the chemical synthesis of antiviral and antitumor drugs, is in great demand in the market. Therefore, the purpose of this study is to build a microbial cell factory with high cytidine production. METHODS AND RESULTS A mutant E. coli NXBG-11-F34 with high tolerance to uridine monophosphate structural analogs and good genetic stability was obtained by atmospheric room temperature plasma (ARTP) mutagenesis combined with high-throughput screening. Then, the udk and rihA genes involved in cytidine catabolism were knocked out by CRISPR/Cas9 gene editing technology, and the recombinant strain E. coli NXBG-13 was constructed. The titer, yield, and productivity of cytidine fermented in a 5 l bioreactor were 15.7 g l-1, 0.164 g g-1, and 0.327 g l-1 h-1, respectively. Transcriptome analysis of the original strain and the recombinant strain E. coli NXBG-13 showed that the gene expression profiles of the two strains changed significantly, and the cytidine de novo pathway gene of the recombinant strain was up-regulated significantly. CONCLUSIONS ARTP mutagenesis combined with metabolic engineering is an effective method to construct cytidine-producing strains.
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Affiliation(s)
- Xiangjun Zhang
- School of Life Science, Ningxia University, Yinchuan 750021, China
| | - Lu Liu
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
| | - Cong Ma
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
| | - Haojie Zhang
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
| | - Huiyan Liu
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
| | - Haitian Fang
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
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2
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Makris G, Lauber M, Rüfenacht V, Gemperle C, Diez-Fernandez C, Caldovic L, Froese DS, Häberle J. Clinical and structural insights into potential dominant negative triggers of proximal urea cycle disorders. Biochimie 2020; 183:89-99. [PMID: 33309754 DOI: 10.1016/j.biochi.2020.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 12/31/2022]
Abstract
Despite biochemical and genetic testing being the golden standards for identification of proximal urea cycle disorders (UCDs), genotype-phenotype correlations are often unclear. Co-occurring partial defects affecting more than one gene have not been demonstrated so far in proximal UCDs. Here, we analyzed the mutational spectrum of 557 suspected proximal UCD individuals. We probed oligomerizing forms of NAGS, CPS1 and OTC, and evaluated the surface exposure of residues mutated in heterozygously affected individuals. BN-PAGE and gel-filtration chromatography were employed to discover protein-protein interactions within recombinant enzymes. From a total of 281 confirmed patients, only 15 were identified as "heterozygous-only" candidates (i.e. single defective allele). Within these cases, the only missense variants to potentially qualify as dominant negative triggers were CPS1 p.Gly401Arg and NAGS p.Thr181Ala and p.Tyr512Cys, as assessed by residue oligomerization capacity and surface exposure. However, all three candidates seem to participate in critical intramolecular functions, thus, unlikely to facilitate protein-protein interactions. This interpretation is further supported by BN-PAGE and gel-filtration analyses revealing no multiprotein proximal urea cycle complex formation. Collectively, genetic analysis, structural considerations and in vitro experiments point against a prominent role of dominant negative effects in human proximal UCDs.
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Affiliation(s)
- Georgios Makris
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Matthias Lauber
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Véronique Rüfenacht
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Corinne Gemperle
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Carmen Diez-Fernandez
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland; Nextech Invest, Bahnhofstrasse 18, 8001, Zurich, Switzerland
| | - Ljubica Caldovic
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA
| | - D Sean Froese
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Johannes Häberle
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland.
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3
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Del Caño-Ochoa F, Moreno-Morcillo M, Ramón-Maiques S. CAD, A Multienzymatic Protein at the Head of de Novo Pyrimidine Biosynthesis. Subcell Biochem 2020; 93:505-538. [PMID: 31939163 DOI: 10.1007/978-3-030-28151-9_17] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
CAD is a 1.5 MDa particle formed by hexameric association of a 250 kDa protein that carries the enzymatic activities for the first three steps in the de novo biosynthesis of pyrimidine nucleotides: glutamine-dependent Carbamoyl phosphate synthetase, Aspartate transcarbamoylase and Dihydroorotase. This metabolic pathway is essential for cell growth and proliferation and is conserved in all living organisms. However, the fusion of the first three enzymatic activities of the pathway into a single multienzymatic protein only occurs in animals. In prokaryotes, by contrast, these activities are encoded as distinct monofunctional enzymes that function independently or by forming more or less transient complexes. Whereas the structural information about these enzymes in bacteria is abundant, the large size and instability of CAD has only allowed a fragmented characterization of its structure. Here we retrace some of the most significant efforts to decipher the architecture of CAD and to understand its catalytic and regulatory mechanisms.
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Affiliation(s)
- Francisco Del Caño-Ochoa
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolas Cabrera 1, 28049, Madrid, Spain
| | - María Moreno-Morcillo
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolas Cabrera 1, 28049, Madrid, Spain
| | - Santiago Ramón-Maiques
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolas Cabrera 1, 28049, Madrid, Spain.
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4
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Yap S, Gougeard N, Hart AR, Barcelona B, Rubio V. N-carbamoylglutamate-responsive carbamoyl phosphate synthetase 1 (CPS1) deficiency: A patient with a novel CPS1 mutation and an experimental study on the mutation's effects. JIMD Rep 2019; 48:36-44. [PMID: 31392111 PMCID: PMC6606979 DOI: 10.1002/jmd2.12034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/01/2019] [Indexed: 12/16/2022] Open
Abstract
N-carbamoyl-l-glutamate (NCG), the N-acetyl-l-glutamate analogue used to treat N-acetylglutamate synthase deficiency, has been proposed as potential therapy of carbamoyl phosphate synthetase 1 deficiency (CPS1D). Previous findings in five CPS1D patients suggest that NCG-responsiveness could be mutation-specific. We report on a patient with CPS1D, homozygous for the novel p.(Pro1211Arg) CPS1 mutation, who presented at 9 days of life with hyperammonemic coma which was successfully treated with emergency measures. He remained metabolically stable on merely oral NCG, arginine, and modest protein restriction. Ammonia scavengers were only added after poor dietary compliance following solid food intake at age 1 year. The patient received a liver transplantation at 3.9 years of age, having normal cognitive, motor, and quality of life scores despite repeated but successfully treated episodes of hyperammonemia. Studies using recombinantly produced mutant CPS1 confirmed the partial nature of the CPS1D triggered by the p.(Pro1211Arg) mutation. This mutation decreased the solubility and yield of CPS1 as expected for increased tendency to misfold, and reduced the thermal stability, maximum specific activity (V max; ~2-fold reduction), and apparent affinity (~5-fold reduction) for ATP of the purified enzyme. By increasing the saturation of the NAG site in vivo, NCG could stabilize CPS1 and minimize the decrease in the effective affinity of the enzyme for ATP. These observations, together with prior experience, support the ascertainment of clinical responsiveness to NCG in CPS1 deficient patients, particularly when decreased stability or lowered affinity for NAG of the mutant enzyme are suspected or proven.
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Affiliation(s)
- Sufin Yap
- Department of Inherited Metabolic DisordersSheffield Children's HospitalSheffieldUK
| | - Nadine Gougeard
- Structural Enzymopathology UnitInstituto de Biomedicina de Valencia of the CSIC (IBV‐CSIC)ValenciaSpain
- Group 739, Centro de Investigación Biomédica en Red para Enfermedades Raras (CIBERER‐ISCIII)MadridSpain
| | - Anthony R. Hart
- Department of NeurologySheffield Children's HospitalSheffieldUK
| | - Belén Barcelona
- Structural Enzymopathology UnitInstituto de Biomedicina de Valencia of the CSIC (IBV‐CSIC)ValenciaSpain
- Group 739, Centro de Investigación Biomédica en Red para Enfermedades Raras (CIBERER‐ISCIII)MadridSpain
| | - Vicente Rubio
- Structural Enzymopathology UnitInstituto de Biomedicina de Valencia of the CSIC (IBV‐CSIC)ValenciaSpain
- Group 739, Centro de Investigación Biomédica en Red para Enfermedades Raras (CIBERER‐ISCIII)MadridSpain
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5
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Fan X, Wu H, Li G, Yuan H, Zhang H, Li Y, Xie X, Chen N. Improvement of uridine production of Bacillus subtilis by atmospheric and room temperature plasma mutagenesis and high-throughput screening. PLoS One 2017; 12:e0176545. [PMID: 28472077 PMCID: PMC5417507 DOI: 10.1371/journal.pone.0176545] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/12/2017] [Indexed: 12/30/2022] Open
Abstract
In the present study, a novel breeding strategy of atmospheric and room temperature plasma (ARTP) mutagenesis was used to improve the uridine production of engineered Bacillus subtilis TD12np. A high-throughput screening method was established using both resistant plates and 96-well microplates to select the ideal mutants with diverse phenotypes. Mutant F126 accumulated 5.7 and 30.3 g/L uridine after 30 h in shake-flask and 48 h in fed-batch fermentation, respectively, which represented a 4.4- and 8.7-fold increase over the parent strain. Sequence analysis of the pyrimidine nucleotide biosynthetic operon in the representative mutants showed that proline 1016 and glutamate 949 in the large subunit of B. subtilis carbamoyl phosphate synthetase were of importance for the allosteric regulation caused by uridine 5′-monophosphate. The proposed mutation method with efficient high-throughput screening assay was proved to be an appropriate strategy to obtain uridine-overproducing strain.
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Affiliation(s)
- Xiaoguang Fan
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin, P. R. China
- Key Laboratory of Microbial Engineering of China Light Industry, Tianjin University of Science and Technology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P. R. China
| | - Heyun Wu
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin, P. R. China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P. R. China
| | - Guoliang Li
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin, P. R. China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P. R. China
| | - Hui Yuan
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin, P. R. China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P. R. China
| | - Hongchao Zhang
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin, P. R. China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P. R. China
| | - Yanjun Li
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin, P. R. China
- Key Laboratory of Microbial Engineering of China Light Industry, Tianjin University of Science and Technology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P. R. China
| | - Xixian Xie
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin, P. R. China
- Key Laboratory of Microbial Engineering of China Light Industry, Tianjin University of Science and Technology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P. R. China
- * E-mail: (XX); (NC)
| | - Ning Chen
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin, P. R. China
- Key Laboratory of Microbial Engineering of China Light Industry, Tianjin University of Science and Technology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P. R. China
- * E-mail: (XX); (NC)
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Abstract
Early investigations on arginine biosynthesis brought to light basic features of metabolic regulation. The most significant advances of the last 10 to 15 years concern the arginine repressor, its structure and mode of action in both E. coli and Salmonella typhimurium, the sequence analysis of all arg structural genes in E. coli and Salmonella typhimurium, the resulting evolutionary inferences, and the dual regulation of the carAB operon. This review provides an overall picture of the pathways, their interconnections, the regulatory circuits involved, and the resulting interferences between arginine and polyamine biosynthesis. Carbamoylphosphate is a precursor common to arginine and the pyrimidines. In both Escherichia coli and Salmonella enterica serovar Typhimurium, it is produced by a single synthetase, carbamoylphosphate synthetase (CPSase), with glutamine as the physiological amino group donor. This situation contrasts with the existence of separate enzymes specific for arginine and pyrimidine biosynthesis in Bacillus subtilis and fungi. Polyamine biosynthesis has been particularly well studied in E. coli, and the cognate genes have been identified in the Salmonella genome as well, including those involved in transport functions. The review summarizes what is known about the enzymes involved in the arginine pathway of E. coli and S. enterica serovar Typhimurium; homologous genes were identified in both organisms, except argF (encoding a supplementary OTCase), which is lacking in Salmonella. Several examples of putative enzyme recruitment (homologous enzymes performing analogous functions) are also presented.
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7
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The Study of Carbamoyl Phosphate Synthetase 1 Deficiency Sheds Light on the Mechanism for Switching On/Off the Urea Cycle. J Genet Genomics 2015; 42:249-60. [DOI: 10.1016/j.jgg.2015.03.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 03/22/2015] [Accepted: 03/25/2015] [Indexed: 12/31/2022]
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8
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Diez-Fernandez C, Martínez AI, Pekkala S, Barcelona B, Pérez-Arellano I, Guadalajara AM, Summar M, Cervera J, Rubio V. Molecular Characterization of Carbamoyl-Phosphate Synthetase (CPS1) Deficiency Using Human Recombinant CPS1 as a Key Tool. Hum Mutat 2013; 34:1149-59. [DOI: 10.1002/humu.22349] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 04/18/2013] [Indexed: 12/30/2022]
Affiliation(s)
- Carmen Diez-Fernandez
- Instituto de Biomedicina de Valencia (IBV-CSIC); Valencia Spain
- Centro de Investigación Príncipe Felipe; Valencia Spain
| | | | - Satu Pekkala
- Centro de Investigación Príncipe Felipe; Valencia Spain
| | - Belén Barcelona
- Instituto de Biomedicina de Valencia (IBV-CSIC); Valencia Spain
- Centro de Investigación Príncipe Felipe; Valencia Spain
- Group 739, CIBERER, ISCIII; Spain
| | - Isabel Pérez-Arellano
- Centro de Investigación Príncipe Felipe; Valencia Spain
- Group 739, CIBERER, ISCIII; Spain
| | | | - Marshall Summar
- Childrens National Medical Center; Washington District of Columbia
| | - Javier Cervera
- Instituto de Biomedicina de Valencia (IBV-CSIC); Valencia Spain
- Centro de Investigación Príncipe Felipe; Valencia Spain
- Group 739, CIBERER, ISCIII; Spain
| | - Vicente Rubio
- Instituto de Biomedicina de Valencia (IBV-CSIC); Valencia Spain
- Group 739, CIBERER, ISCIII; Spain
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9
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Häberle J, Shchelochkov OA, Wang J, Katsonis P, Hall L, Reiss S, Eeds A, Willis A, Yadav M, Summar S, Lichtarge O, Rubio V, Wong LJ, Summar M. Molecular defects in human carbamoy phosphate synthetase I: mutational spectrum, diagnostic and protein structure considerations. Hum Mutat 2011; 32:579-89. [PMID: 21120950 DOI: 10.1002/humu.21406] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 10/27/2010] [Indexed: 11/09/2022]
Abstract
Deficiency of carbamoyl phosphate synthetase I (CPSI) results in hyperammonemia ranging from neonatally lethal to environmentally induced adult-onset disease. Over 24 years, analysis of tissue and DNA samples from 205 unrelated individuals diagnosed with CPSI deficiency (CPSID) detected 192 unique CPS1 gene changes, of which 130 are reported here for the first time. Pooled with the already reported mutations, they constitute a total of 222 changes, including 136 missense, 15 nonsense, 50 changes of other types resulting in enzyme truncation, and 21 other changes causing in-frame alterations. Only ∼10% of the mutations recur in unrelated families, predominantly affecting CpG dinucleotides, further complicating the diagnosis because of the "private" nature of such mutations. Missense changes are unevenly distributed along the gene, highlighting the existence of CPSI regions having greater functional importance than other regions. We exploit the crystal structure of the CPSI allosteric domain to rationalize the effects of mutations affecting it. Comparative modeling is used to create a structural model for the remainder of the enzyme. Missense changes are found to directly correlate, respectively, with the one-residue evolutionary importance and inversely correlate with solvent accessibility of the mutated residue. This is the first large-scale report of CPS1 mutations spanning a wide variety of molecular defects highlighting important regions in this protein.
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Affiliation(s)
- Johannes Häberle
- University Children's Hospital Zurich, Division of Metabolism, Zurich, Switzerland.
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10
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Martínez AI, Pérez-Arellano I, Pekkala S, Barcelona B, Cervera J. Genetic, structural and biochemical basis of carbamoyl phosphate synthetase 1 deficiency. Mol Genet Metab 2010; 101:311-23. [PMID: 20800523 DOI: 10.1016/j.ymgme.2010.08.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 08/02/2010] [Accepted: 08/02/2010] [Indexed: 01/28/2023]
Abstract
Carbamoyl phosphate synthetase 1 (CPS1) plays a paramount role in liver ureagenesis since it catalyzes the first and rate-limiting step of the urea cycle, the major pathway for nitrogen disposal in humans. CPS1 deficiency (CPS1D) is an autosomal recessive inborn error which leads to hyperammonemia due to mutations in the CPS1 gene, or is caused secondarily by lack of its allosteric activator NAG. Proteolytic, immunological and structural data indicate that human CPS1 resembles Escherichia coli CPS in structure, and a 3D model of CPS1 has been presented for elucidating the pathogenic role of missense mutations. Recent availability of CPS1 expression systems also can provide valuable tools for structure-function analysis and pathogenicity-testing of mutations in CPS1. In this paper, we provide a comprehensive compilation of clinical CPS1 mutations, and discuss how structural knowledge of CPS enzymes in combination with in vitro analyses can be a useful tool for diagnosis of CPS1D.
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Affiliation(s)
- Ana Isabel Martínez
- Molecular Recognition Laboratory, Centro de Investigación Príncipe Felipe (CIPF) Valencia, Spain
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11
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Structural insight on the control of urea synthesis: identification of the binding site for N-acetyl-L-glutamate, the essential allosteric activator of mitochondrial carbamoyl phosphate synthetase. Biochem J 2009; 424:211-20. [PMID: 19754428 DOI: 10.1042/bj20090888] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
NAG (N-acetyl-L-glutamate), the essential allosteric activator of the first urea cycle enzyme, CPSI (carbamoyl phosphate synthetase I), is a key regulator of this crucial cycle for ammonia detoxification in animals (including humans). Automated cavity searching and flexible docking have allowed identification of the NAG site in the crystal structure of human CPSI C-terminal domain. The site, a pocket lined by invariant residues and located between the central beta-sheet and two alpha-helices, opens at the beta-sheet C-edge and is roofed by a three-residue lid. It can tightly accommodate one extended NAG molecule having the delta-COO- at the pocket entry, the alpha-COO- and acetamido groups tightly hydrogen bonded to the pocket, and the terminal methyl of the acetamido substituent surrounded by hydrophobic residues. This binding mode is supported by the observation of reduced NAG affinity upon mutation of NAG-interacting residues of CPSI (recombinantly expressed using baculovirus/insect cells); by the fine-mapping of the N-chloroacetyl-L-glutamate photoaffinity labelling site of CPSI; and by previously established structure-activity relationships for NAG analogues. The location of the NAG site is identical to that of the weak bacterial CPS activator IMP (inosine monophosphate) in Escherichia coli CPS, indicating a common origin for these sites and excluding any relatedness to the binding site of the other bacterial CPS activator, ornithine. Our findings open the way to the identification of CPSI deficiency patients carrying NAG site mutations, and to the possibility of tailoring the activator to fit a given NAG site mutation, as exemplified here with N-acetyl-L(+/-)-beta-phenylglutamate for the W1410K CPSI mutation.
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12
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Purcarea C, Fernando R, Evans HG, Evans DR. The sole serine/threonine protein kinase and its cognate phosphatase from Aquifex aeolicus targets pyrimidine biosynthesis. Mol Cell Biochem 2008; 311:199-213. [PMID: 18270660 DOI: 10.1007/s11010-008-9710-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2007] [Accepted: 01/10/2008] [Indexed: 10/22/2022]
Abstract
Serine/Threonine kinases participate in complex, interacting signaling pathways in eukaryotes, prokaryotes, and archae. While most organisms contain many different kinases, the extreme hyperthermophile, Aquifex aeolicus encodes a single hypothetical Ser/Thr kinase. A gene homologous to eukaryotic protein phosphatases overlaps the kinase gene by a single base pair. The putative kinase, AaSTPK and phosphatase, AaPPM, were cloned and expressed in E. coli, purified to homogeneity and found to be functional. AaSTPK is a 34-kDa monomer that can use MgATP, MnATP, or MnGTP as co-substrates, although MgATP appears to be the preferred substrate. AaSTPK was autophosphorylated on a threonine residue and was dephosphorylated by AaPPM. AaPPM phosphatase is homologous to the PPM sub-family of Ser/Thr phosphatases and was stimulated by MnCl2 and CoCl2 but not MgCl2. AaSTPK also phosphorylated one threonine residue on the carbamoyl phosphate synthetase, CPS.A subunit. Carbamoyl phosphate synthetase reconstituted with phosphorylated CPS.A had unaltered catalytic activity but allosteric inhibition by UMP and activation by the arginine intermediate, ornithine, were both appreciably attenuated. These changes in allosteric regulation would be expected to activate pyrimidine biosynthesis by releasing the constraints imposed on carbamoyl phosphate synthetase activity by UMP and uncoupling the regulation of pyrimidine and arginine biosynthesis. CPS.A was also dephosphorylated by AaPPM. Aquifex aeolicus occupies the lowest branch on the prokaryotic phylogenetic tree. The Thr/Ser kinase, its cognate phosphatase and a protein substrate may be elements of a simple signaling pathway, perhaps the most primitive example of this mode of regulation described thus far.
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Affiliation(s)
- Cristina Purcarea
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, 540 E. Canfield Street, Detroit, MI 48201, USA
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13
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Schröder M, Giermann N, Zrenner R. Functional analysis of the pyrimidine de novo synthesis pathway in solanaceous species. PLANT PHYSIOLOGY 2005; 138:1926-38. [PMID: 16024685 PMCID: PMC1183384 DOI: 10.1104/pp.105.063693] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Revised: 05/14/2005] [Accepted: 05/16/2005] [Indexed: 05/03/2023]
Abstract
Pyrimidines are particularly important in dividing tissues as building blocks for nucleic acids, but they are equally important for many biochemical processes, including sucrose and cell wall polysaccharide metabolism. In recent years, the molecular organization of nucleotide biosynthesis in plants has been analyzed. Here, we present a functional analysis of the pyrimidine de novo synthesis pathway. Each step in the pathway was investigated using transgenic plants with reduced expression of the corresponding gene to identify controlling steps and gain insights into the phenotypic and metabolic consequences. Inhibition of expression of 80% based on steady-state mRNA level did not lead to visible phenotypes. Stepwise reduction of protein abundance of Asp transcarbamoylase or dihydro orotase resulted in a corresponding inhibition of growth. This was not accompanied by pleiotropic effects or by changes in the developmental program. A more detailed metabolite analysis revealed slightly different responses in roots and shoots of plants with decreased abundance of proteins involved in pyrimidine de novo synthesis. Whereas in leaves the nucleotide and amino acid levels were changed only in the very strong inhibited plants, the roots show a transient increase of these metabolites in intermediate plants followed by a decrease in the strong inhibited plants. Growth analysis revealed that elongation rates and number of organs per plant were reduced, without large changes in the average cell size. It is concluded that reduced pyrimidine de novo synthesis is compensated for by reduction in growth rates, and the remaining nucleotide pools are sufficient for running basic metabolic processes.
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Affiliation(s)
- Michael Schröder
- Botanisches Institut, Im Neuenheimer Feld 360, Ruprecht-Karls-Universität Heidelberg, 69120 Heidelberg, Germany
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14
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Yefimenko I, Fresquet V, Marco-Marín C, Rubio V, Cervera J. Understanding carbamoyl phosphate synthetase deficiency: impact of clinical mutations on enzyme functionality. J Mol Biol 2005; 349:127-41. [PMID: 15876373 DOI: 10.1016/j.jmb.2005.03.078] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2004] [Revised: 02/23/2005] [Accepted: 03/08/2005] [Indexed: 10/25/2022]
Abstract
Carbamoyl phosphate synthetase I (CPSI) deficiency, a recessively inherited error of the urea cycle, causes life-threatening hyperammonaemia. CPSI is a multidomain 1500-residue liver mitochondrial matrix protein that is allosterically activated by N-acetyl-l-glutamate, and which synthesises carbamoyl phosphate (CP) in three steps: bicarbonate phosphorylation by ATP, carbamate synthesis from carboxyphosphate and ammonia, and carbamate phosphorylation by ATP. Several missense mutations of CPSI have been reported in patients with CPSI deficiency, but the actual pathogenic potential and effects on the enzyme of these mutations remain non-characterised. Since the structure of Escherichia coli CPS is known and systems for its overexpression and purification are available, we have constructed and purified eight site-directed mutants of E.coli CPS affecting the enzyme large subunit (A126M, R169H, Q262P, N301K, P360L, V640R, R675L, S789P) that are homologous to corresponding missense mutations found in patients with CPSI deficiency, studying their stability and their ability to catalyse the CPS reaction as well as the partial reactions that reflect the different reactional steps, and analysing the substrate kinetics for the overall and partial reactions. The results show that all the mutations significantly decrease CP synthesis without completely inactivating the enzyme (as reflected in the catalysis of at least one partial reaction), that one of these mutations (Q262P) causes marked enzyme instability, and validate the use of E.coli CPS as a pathogenicity testing model for CPSI deficiency. The causality of the reported clinical mutations is supported and the derangements caused by the mutations are identified, revealing the specific roles of the residues that are mutated. In particular, the findings highlight the importance for carbamate phosphorylation and for allosteric activation of a loop that coordinates K(+), stress the key role of intersubunit interactions for CPS stability, and suggest that lid opening at both phosphorylation sites is concerted.
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Affiliation(s)
- Igor Yefimenko
- Centro de Investigación Príncipe Felipe, FVIB, Avda. Autopisca del Saler, 16, Valencia 46013, Spain
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15
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Pierrat OA, Raushel FM. A functional analysis of the allosteric nucleotide monophosphate binding site of carbamoyl phosphate synthetase. Arch Biochem Biophys 2002; 400:34-42. [PMID: 11913968 DOI: 10.1006/abbi.2002.2767] [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: 11/22/2022]
Abstract
The catalytic activity of carbamoyl phosphate synthetase (CPS) from Escherichia coli is allosterically regulated by UMP, IMP, and ornithine. Thirteen amino acids within the domain that harbors the overlapping binding sites for IMP and UMP were mutated to alanine and characterized. The four residues that interact directly with the phosphate moiety of IMP in the X-ray crystal structure (K954, T974, T977, and K993) were shown to have the greatest impact on the dissociation constants for the binding of IMP and UMP and the associated allosteric effects on the kinetic constants of CPS. Of the four residues that interact with the ribose moiety of IMP (S948, N1015, T1017, and S1026), S1026 was shown to be more important for the binding of IMP than UMP. Five residues (V994, I1001, D1025, V1028, and I1029) were mutated in the region of the allosteric domain that surrounds the hypoxanthine ring of IMP. With the exception of V994A, these mutations had a modest influence on the binding and subsequent allosteric effects by UMP and IMP.
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Affiliation(s)
- Olivier A Pierrat
- Department of Chemistry, Texas A&M University, College Station, Texas, 77842-3012
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16
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Fresquet V, Mora P, Rochera L, Ramón-Maiques S, Rubio V, Cervera J. Site-directed mutagenesis of the regulatory domain of Escherichia coli carbamoyl phosphate synthetase identifies crucial residues for allosteric regulation and for transduction of the regulatory signals. J Mol Biol 2000; 299:979-91. [PMID: 10843852 DOI: 10.1006/jmbi.2000.3794] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Carbamoyl phosphate (CP), the essential precursor of pyrimidines and arginine, is made in Escherichia coli by a single carbamoyl phosphate synthetase (CPS) consisting of 41.4 and 117.7 kDa subunits, which is feed-back inhibited by UMP and activated by IMP and ornithine. The large subunit catalyzes CP synthesis from ammonia in three steps, and binds the effectors in its 15 kDa C-terminal domain. Fifteen site-directed mutations were introduced in 13 residues of this domain to investigate the mechanism of allosteric modulation by UMP and IMP. Two mutations, K993A and V994A, decreased significantly or abolished enzyme activity, apparently by interfering with the step of carbamate synthesis, and one mutation, T974A, negatively affected ornithine activation. S948A, K954A, T974A, K993A and K993W/H995A abolished or greatly hampered IMP activation and UMP inhibition as well as the binding of both effectors, monitored using photoaffinity labeling and ultracentrifugation binding assays. V994A also decreased significantly IMP and UMP binding. L990A, V991A, H995A, G997A and G1008A had more modest effects or affected more the modulation by and the binding of one than of the other nucleotide. K993W, R1020A, R1021A and K1061A were without substantial effects. The results confirm the independence of the regulatory and catalytic centers, and also confirm functional predictions based on the X-ray structure of an IMP-CPS complex. They prove that the inhibitor UMP and the activator IMP bind in the same site, and exclude that the previously observed binding of ornithine and glutamine in this site were relevant for enzyme activation. K993 and V994 appear to be involved in the transmission of the regulatory signals triggered by UMP and IMP binding. These effectors possibly change the position of K993 and V994, and alter the intermolecular contacts mediated by the regulatory domain.
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Affiliation(s)
- V Fresquet
- Instituto de Investigaciones Citológicas (FVIB), Amadeo de Saboya 4, Valencia, 46010, Spain
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17
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Ramón-Maiques S, Marina A, Uriarte M, Fita I, Rubio V. The 1.5 A resolution crystal structure of the carbamate kinase-like carbamoyl phosphate synthetase from the hyperthermophilic Archaeon pyrococcus furiosus, bound to ADP, confirms that this thermostable enzyme is a carbamate kinase, and provides insight into substrate binding and stability in carbamate kinases. J Mol Biol 2000; 299:463-76. [PMID: 10860751 DOI: 10.1006/jmbi.2000.3779] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Carbamoyl phosphate (CP), an essential precursor of arginine and the pyrimidine bases, is synthesized by CP synthetase (CPS) in three steps. The last step, the phosphorylation of carbamate, is also catalyzed by carbamate kinase (CK), an enzyme used by microorganisms to produce ATP from ADP and CP. Although the recently determined structures of CPS and CK show no obvious mutual similarities, a CK-like CPS reported in hyperthermophilic archaea was postulated to be a missing link in the evolution of CP biosynthesis. The 1.5 A resolution structure of this enzyme from Pyrococcus furiosus shows both a subunit topology and a homodimeric molecular organization, with a 16-stranded open beta-sheet core surrounded by alpha-helices, similar to those in CK. However, the pyrococcal enzyme exhibits many solvent-accessible ion-pairs, an extensive, strongly hydrophobic, intersubunit surface, and presents a bound ADP molecule, which does not dissociate at 22 degrees C from the enzyme. The ADP nucleotide is sequestered in a ridge formed over the C-edge of the core sheet, at the bottom of a large cavity, with the purine ring enclosed in a pocket specific for adenine. Overall, the enzyme structure is ill-suited for catalyzing the characteristic three-step reaction of CPS and supports the view that the CK-like CPS is in fact a highly thermostable and very slow (at 37 degrees C) CK that, in the extreme environment of P. furiosus, may have the new function of making, rather than using, CP. The thermostability of the enzyme may result from the extension of the hydrophobic intersubunit contacts and from the large number of exposed ion-pairs, some of which form ion-pair networks across several secondary structure elements in each enzyme subunit. The structure provides the first information on substrate binding and catalysis in CKs, and suggests that the slow rate at 37 degrees C is possibly a consequence of slow product dissociation.
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Affiliation(s)
- S Ramón-Maiques
- Consejo Superior de Investigaciones Científicas (IBV-CSIC), Instituto de Biomedicina de Valencia, C/Jaime Roig 11, Valencia, 46010, Spain
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18
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Mora P, Rubio V, Fresquet V, Cervera J. Localization of the site for the nucleotide effectors of Escherichia coli carbamoyl phosphate synthetase using site-directed mutagenesis. FEBS Lett 1999; 446:133-6. [PMID: 10100629 DOI: 10.1016/s0014-5793(99)00197-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Replacement by alanine of Ser-948, Thr-974 and Lys-954 of Escherichia coli carbamoyl phosphate synthetase (CPS) shows that these residues are involved in binding the allosteric inhibitor UMP and the activator IMP. The mutant CPSs are active in vivo and in vitro and exhibit normal activation by ornithine, but the modulation by both UMP and IMP is either lost or diminished. The results demonstrate that the sites for UMP and IMP overlap and that the activator ornithine binds elsewhere. Since the mutated residues were found in the crystal structure of CPS near a bound phosphate, Ser-948, Thr-974 and Lys-954 bind the phosphate moiety of UMP and IMP.
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Affiliation(s)
- P Mora
- Instituto de Investigaciones Citológicas (FVIB), Valencia, Spain
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19
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Sahay N, Guy HI, Liu X, Evans DR. Regulation of an Escherichia coli/mammalian chimeric carbamoyl-phosphate synthetase. J Biol Chem 1998; 273:31195-202. [PMID: 9813025 DOI: 10.1074/jbc.273.47.31195] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Carbamoyl-phosphate synthetase (CPSase) consists of a 120-kDa synthetase domain (CPS) that makes carbamoyl phosphate from ATP, bicarbonate, and ammonia usually produced by a separate glutaminase domain. CPS is composed of two subdomains, CPS.A and CPS.B. Although CPS.A and CPS.B have specialized functions in intact CPSase, the separately cloned subdomains can catalyze carbamoyl phosphate synthesis. This report describes the construction of a 58-kDa chimeric CPSase composed of Escherichia coli CPS.A catalytic subdomains and the mammalian regulatory subdomain. The catalytic parameters are similar to those of the E. coli enzyme, but the activity is regulated by the mammalian effectors and protein kinase A phosphorylation. The chimera has a single site that binds phosphoribosyl 5'-pyrophosphate (PRPP) with a dissociation constant of 25 microM. The dissociation constant for UTP of 0.23 mM was inferred from its effect on PRPP binding. Thus, the regulatory subdomain is an exchangeable ligand binding module that can control both CPS.A and CPS.B domains, and the pathway for allosteric signal transmission is identical in E. coli and mammalian CPSase. A deletion mutant that truncates the polypeptide within a postulated regulatory sequence is as active as the parent chimera but is insensitive to effectors. PRPP and UTP bind to the mutant, suggesting that the carboxyl half of the subdomain is essential for transmitting the allosteric signal but not for ligand binding.
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Affiliation(s)
- N Sahay
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan 48201, USA
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20
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Zheng W, Lim AL, Powers-Lee SG. Identification of critical amino acid residues of Saccharomyces cerevisiae carbamoyl-phosphate synthetase: definition of the ATP site involved in carboxy-phosphate formation. BIOCHIMICA ET BIOPHYSICA ACTA 1997; 1341:35-48. [PMID: 9300807 DOI: 10.1016/s0167-4838(97)00058-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Carbamoyl-phosphate synthetases (CPSases) utilize two molecules of ATP at two homologous domains, B and C, with ATP(B) used to form the enzyme-bound intermediate carboxy-phosphate and ATP(C) used to phosphorylate the carbamate intermediate. To further define the role of one CPSase peptide suggested by affinity labeling studies to be near the ATP(B) site, we have carried out site-directed mutagenic analysis of peptide 234-242 of the Saccharomyces cerevisiae arginine-specific CPSase. Mutants E234A, E234D, E236A, E236D and E238A were unable to complement the CPSase-deficient yeast strain LPL26 whereas mutants Y237A, E238D, R241K, R241E and R241P supported LPL26 growth as well as wild-type CPSase. Kinetic analysis of E234A and Y237A indicated impaired utilization of ATP(B) but not of ATP(C). D242A, a temperature-sensitive mutant, retained no detectable activity when assayed in vitro. These findings, together with the affinity labeling data and primary sequence analysis, strongly suggest that the yeast CPSase peptide 234-242 is located at the ATP(B) site and that some of its residues are important for functioning of the enzyme. D242 appears to occupy a critical structural position and E234, E236 and E238 appear to be critical for function, with the spatial arrangement of the carboxyl side chain also critical for E234 and E236.
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Affiliation(s)
- W Zheng
- Department of Biology, Northeastern University, Boston, MA 02115, USA
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21
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Lim AL, Powers-Lee SG. Critical roles for arginine 1061/1060 and tyrosine 1057 in Saccharomyces cerevisiae arginine-specific carbamoyl-phosphate synthetase. Arch Biochem Biophys 1997; 339:344-52. [PMID: 9056267 DOI: 10.1006/abbi.1997.9887] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Carbamoyl-phosphate synthetases (CPSases) bind two molecules of ATP at two internally duplicated domains. Previous affinity labeling studies with the ATP analog 5'-p-fluorosulfonylbenzoyladenosine (FSBA; Kim, H., Kelly, R. E., and Evans, D. R. (1991) Biochemistry 30, 10322-10329; Potter, M. D., and Powers-Lee, S. G. (1992) J. Biol. Chem. 267, 2023-2031) have identified several peptides as being near the ATP sites, with most of the FSBA-labeled peptides localized to the internally duplicated domains. However, two of the FSBA-labeled peptides were localized to the third domain of CPSase, an autonomously folded but flexible domain at the extreme C-terminus of the protein. These findings suggested that the C-terminal domain is also involved in interaction with both molecules of ATP and that it might serve to complement the ATP binding sites on the duplicated domains by participating in catalytic processing of the ATP molecules. To further define the role of the C-terminal domain in ATP utilization, we have now carried out site-directed mutagenic analysis of peptide 1052-1061 of the Saccharomyces cerevisiae arginine-specific CPSase. Aspartate residues at positions 1053, 1054, and 1056 did not appear to play a significant role in CPSase structure or function. However, tyrosine 1057 was critical for CPSase structure and the presence of one of the tandem arginyl residues at positions 1061 and 1060 was critical for CPSase catalytic function.
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Affiliation(s)
- A L Lim
- Department of Biology, Northeastern University, Boston, Massachusetts, 02115, USA
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22
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McCudden CR, Powers-Lee SG. Required allosteric effector site for N-acetylglutamate on carbamoyl-phosphate synthetase I. J Biol Chem 1996; 271:18285-94. [PMID: 8663466 DOI: 10.1074/jbc.271.30.18285] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Carbamoyl-phosphate synthetase I (CPSase I) catalyzes the entry and rate-limiting step in the urea cycle, the pathway by which mammals detoxify ammonia. One facet of CPSase I regulation is a requirement for N-acetylglutamate (AGA), which induces an active enzyme conformation and does not participate directly in the chemical reaction. We have utilized labeling with carbodiimide-activated [14C]AGA to identify peptides 120-127, 234-237, 625-630, and 1351-1356 as potentially being near the binding site for AGA. Identification of peptide 1351-1356 confirms the previous demonstration (Rodriquez-Aparicio, L. B., Guadalajara, A. M., and Rubio, V.(1989) Biochemistry 28, 3070-3074) that the C-terminal region is involved in binding AGA. Identification of peptides 120-127 and 234-237 constitutes the first evidence that the N-terminal region of the synthetase is involved in ligand binding. Since peptides 631-638 and 1327-1348 have been identified near the ATP site of CPSase I (Potter, M. D., and Powers-Lee, S. G.(1992) J. Biol. Chem. 267, 2023-2031), the present finding of involvement of peptides 625-630 and 1351-1356 at an "allosteric" activator site was unexpected. The idea that portions of the AGA effector site might be derived from an ancestral glutamine substrate site via a gene duplication and diversification event was considered.
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Affiliation(s)
- C R McCudden
- Department of Biology, Northeastern University, Boston, Massachusetts 02115, USA
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23
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Guy HI, Evans DR. Function of the major synthetase subdomains of carbamyl-phosphate synthetase. J Biol Chem 1996; 271:13762-9. [PMID: 8662713 DOI: 10.1074/jbc.271.23.13762] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The amidotransferase domain (GLNase) of mammalian carbamyl-phosphate synthetase II hydrolyzes glutamine and transfers ammonia to the synthetase domain where carbamyl phosphate is formed in a three-step reaction sequence. The synthetase domain consists of two homologous subdomains, CPS.A and CPS.B. Recent studies suggest that CPS.A catalyzes the initial ATP dependent-activation of bicarbonate, whereas CPS.B uses a second ATP to form carbamyl phosphate. To establish the function of these substructural elements, we have cloned and expressed the mammalian protein and its subdomains in Escherichia coli. Recombinant CPSase (GLNase-CPS.A-CPS.B) was found to be fully functional. Two other proteins were made; the first consisted of only GLNase and CPS.A, whereas the second lacked CPS.A and had the GLNase domain fused directly to CPS.B. Remarkably, both proteins catalyzed the entire series of reactions involved in glutamine-dependent carbamyl phosphate synthesis. The stoichiometry, like that of the native enzyme, was 2 mol of ATP utilized per mol of carbamyl phosphate formed. GLN-CPS.B is allosterically regulated, whereas GLN-CPS.A was insensitive to effectors, a result consistent with evidence showing that allosteric effectors bind to CPS.B. These properties are not peculiar to the mammalian protein, because the separately cloned CPS.A subdomain of the E. coli enzyme was also found to catalyze carbamyl phosphate synthesis. Gel filtration chromatography and chemical cross-linking studies showed that these molecules are dimers, a structural organization that may be a prerequisite for the overall reaction. Thus, the homologous CPS.A and CPS.B subdomains are functionally equivalent, although in the native enzyme they may have different functions resulting from their juxtaposition relative to the other components in the complex.
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Affiliation(s)
- H I Guy
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan 48201, USA
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Cervera J, Bendala E, Britton HG, Bueso J, Nassif Z, Lusty CJ, Rubio V. Photoaffinity labeling with UMP of lysine 992 of carbamyl phosphate synthetase from Escherichia coli allows identification of the binding site for the pyrimidine inhibitor. Biochemistry 1996; 35:7247-55. [PMID: 8679554 DOI: 10.1021/bi952549u] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
UMP is a highly specific reagent for photoaffinity labeling of the allosteric inhibitor site of carbamyl phosphate synthetase (CPS) from Escherichia coli and has been found to be photoincorporated in the COOH-terminal domain of the large subunit [Rubio et al. (1991) Biochemistry 30, 1068-1075]. In the present work we identify lysine 992 as the residue that is covalently attached to UMP. This identification is based on two lines of evidence. First, [14C]UMP is found to be incorporated between residues 939 and 1006, as shown by peptide mapping and by mass estimates of [14C]UMP-peptides generated by chemical and enzymatic cleavage of CPS. Secondly, we have purified two radioactive peptides derived exclusively from those enzyme molecules (approximately 5% of the total enzyme) that had incorporated [14C]-UMP. Edman analyses show the sequences of the labeled peptides (989)LVNXVHEGRPHIQD and (989)LVNXVHE to be overlapping. Since neither a phenylthiohydantoin (Pth) derivative (in cycle 4) nor any radioactivity is released from the membrane during sequencing, we can conclude that Lys992 and [14C]-UMP form a covalent adduct that remains bound to the membrane. Formation of this adduct agrees with all of the evidence and with the finding that UMP labeling prevents trypsin cleavage at Lys992. Lysine 992 is invariant in those CPSs that are inhibited by UMP, and is located 30 residues upstream of the site whose phosphorylation in hamster CAD reduces inhibition of CAD by UTP. Multiple sequence alignment of the residues surrounding Lys992 of the E. coli enzyme and the corresponding residues of the yeast and animal enzymes supports the existence of a uridine nucleotide binding fold in this region of the protein. We conclude that sequence changes in the binding fold provide a structural basis for the different regulatory properties found among CPSs I, II, and III.
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Affiliation(s)
- J Cervera
- Instituto de Investigaciones Citológicas (FIB and CSIC), Valencia, Spain
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25
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Lim AL, Powers-Lee SG. Requirement for the carboxyl-terminal domain of Saccharomyces cerevisiae carbamoyl-phosphate synthetase. J Biol Chem 1996; 271:11400-9. [PMID: 8626695 DOI: 10.1074/jbc.271.19.11400] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The arginine-specific carbamoyl phosphate synthetase of Saccharomyces cerevisiae is a heterodimeric enzyme, with a 45-kDa CPA1 subunit binding and cleaving glutamine, and a 124-kDa CPA2 subunit accepting the ammonia moiety cleaved from glutamine, binding all of the remaining substrates and carrying out all of the other catalytic events. CPA2 is composed of two apparently duplicated amino acid sequences involved in binding the two ATP molecules needed for carbamoyl phosphate synthesis and a carboxyl-terminal domain which appears to be less tightly folded than the remainder of the protein. Using deletion mutagenesis, we have established that essentially all of the carboxyl-terminal domain of CPA2 is required for catalytic function and that even small truncations lead to significant changes in the CPA2 conformation. In addition, we have demonstrated that the C-terminal region of CPA2 can be expressed as an autonomously folded unit which is stabilized by specific interactions with the remainder of CPA2. We also made the unexpected finding that, even when ammonia is used as the substrate and there is no catalytic role for CPA1, interaction with CPA1 led to an increase in the Vmax of CPA2 in crude extracts.
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Affiliation(s)
- A L Lim
- Department of Biology, Northeastern University, Boston, Massachusetts 02115, USA
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Marina A, Bravo J, Fita I, Rubio V. Crystallization, characterization, and preliminary crystallographic studies of mitochondrial carbamoyl phosphate synthetase I of Rana catesbeiana. Proteins 1995; 22:193-6. [PMID: 7567968 DOI: 10.1002/prot.340220213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Carbamoyl phosphate synthetase I (ammonia; E C 6.3.4.16) was purified from the liver of Rana catesbeiana (bullfrog). Crystals of the protein have been obtained at 22 degrees C by the hanging drop vapor diffusion technique, with polyethylene glycol as precipitant. Tetragonal crystals of about 0.3 x 0.3 x 0.7 mm diffract at room temperature to at least 3.5 A using a conventional source and are stable to X-radiation for about 12 h. Therefore, these crystals are suitable for high resolution studies. The space group is P4(1)2(1)2 (or its enantiomorph P4(3)2(1)2), with unit cell dimensions a = b = 291.6 A and c = 189.4 A. Density packing considerations are consistent with the presence of 4-6 monomers (M(r) of the monomer, 160,000) in the asymmetric unit. Amino-terminal sequence of the enzyme and of a chymotryptic fragment of 73.7 kDa containing the COOH-terminus has been obtained. The extensive sequence identity with rat and human carbamoyl phosphate synthetase I indicates the relevance for mammals of structural data obtained with the frog enzyme.
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Affiliation(s)
- A Marina
- Instituto de Investigaciones Citológicas de la Fundación Valenciana de Investigaciones Biomédicas (Centro Asociado del CSIC), Spain
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27
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Liu X, Guy HI, Evans DR. Identification of the regulatory domain of the mammalian multifunctional protein CAD by the construction of an Escherichia coli hamster hybrid carbamyl-phosphate synthetase. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)47049-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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