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del Caño-Ochoa F, Ng BG, Rubio-del-Campo A, Mahajan S, Wilson MP, Vilar M, Rymen D, Sánchez-Pintos P, Kenny J, Martos ML, Campos T, Wortmann SB, Freeze HH, Ramón-Maiques S. Beyond genetics: Deciphering the impact of missense variants in CAD deficiency. J Inherit Metab Dis 2023; 46:1170-1185. [PMID: 37540500 PMCID: PMC10838372 DOI: 10.1002/jimd.12667] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/29/2023] [Accepted: 08/01/2023] [Indexed: 08/05/2023]
Abstract
CAD is a large, 2225 amino acid multienzymatic protein required for de novo pyrimidine biosynthesis. Pathological CAD variants cause a developmental and epileptic encephalopathy which is highly responsive to uridine supplements. CAD deficiency is difficult to diagnose because symptoms are nonspecific, there is no biomarker, and the protein has over 1000 known variants. To improve diagnosis, we assessed the pathogenicity of 20 unreported missense CAD variants using a growth complementation assay that identified 11 pathogenic variants in seven affected individuals; they would benefit from uridine treatment. We also tested nine variants previously reported as pathogenic and confirmed the damaging effect of seven. However, we reclassified two variants as likely benign based on our assay, which is consistent with their long-term follow-up with uridine. We found that several computational methods are unreliable predictors of pathogenic CAD variants, so we extended the functional assay results by studying the impact of pathogenic variants at the protein level. We focused on CAD's dihydroorotase (DHO) domain because it accumulates the largest density of damaging missense changes. The atomic-resolution structures of eight DHO pathogenic variants, combined with functional and molecular dynamics analyses, provided a comprehensive structural and functional understanding of the activity, stability, and oligomerization of CAD's DHO domain. Combining our functional and protein structural analysis can help refine clinical diagnostic workflow for CAD variants in the genomics era.
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Affiliation(s)
- Francisco del Caño-Ochoa
- Structure of Macromolecular Targets Unit. Instituto de Biomedicina de Valencia (IBV), CSIC. Valencia, Spain
| | - Bobby G. Ng
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Antonio Rubio-del-Campo
- Structure of Macromolecular Targets Unit. Instituto de Biomedicina de Valencia (IBV), CSIC. Valencia, Spain
| | - Sonal Mahajan
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Matthew P. Wilson
- Laboratory for Molecular Diagnosis, Center for Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Marçal Vilar
- Molecular Basis of Neurodegeneration Unit. Instituto de Biomedicina de Valencia (IBV), CSIC. Valencia, Spain
| | - Daisy Rymen
- Department of Pediatrics - Center for Metabolic Diseases, University Hospitals of Leuven, Belgium
| | - Paula Sánchez-Pintos
- Unidad de Diagnóstico y Tratamiento de Enfermedades Metabólicas Congénitas. C.S.U.R. de Enfermedades Metabólicas. MetabERN. Hospital Clínico Universitario de Santiago de Compostela, La Coruña, Spain
- Instituto de Investigación Sanitaria Santiago de Compostela (IDIS), La Coruña, Spain
| | - Janna Kenny
- Children's Health Ireland at Crumlin, Ireland
| | - Myriam Ley Martos
- Pediatric Neurology Unit. Hospital Universitario Puerta del Mar, Cádiz, Spain
| | - Teresa Campos
- Reference Center of Inherited Metabolic Diseases of Hospital de São João, Porto, Portugal
| | - Saskia B. Wortmann
- University Children’s Hospital, Paracelsus Medical University (PMU), Salzburg, Austria
- Amalia Children’s Hospital, Radboudumc, Nijmegen, The Netherlands
| | - Hudson H. Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Santiago Ramón-Maiques
- Structure of Macromolecular Targets Unit. Instituto de Biomedicina de Valencia (IBV), CSIC. Valencia, Spain
- Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)–Instituto de Salud Carlos III, Valencia, Spain
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2
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Vitali J, Nix JC, Newman HE, Colaneri MJ. Crystal structure of Methanococcus jannaschii dihydroorotase. Proteins 2023; 91:91-98. [PMID: 35978488 PMCID: PMC9771888 DOI: 10.1002/prot.26412] [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: 04/29/2022] [Revised: 08/02/2022] [Accepted: 08/11/2022] [Indexed: 12/24/2022]
Abstract
In this paper, we report the structural analysis of dihydroorotase (DHOase) from the hyperthermophilic and barophilic archaeon Methanococcus jannaschii. DHOase catalyzes the reversible cyclization of N-carbamoyl-l-aspartate to l-dihydroorotate in the third step of de novo pyrimidine biosynthesis. DHOases form a very diverse family of enzymes and have been classified into types and subtypes with structural similarities and differences among them. This is the first archaeal DHOase studied by x-ray diffraction. Its structure and comparison with known representatives of the other subtypes help define the structural features of the archaeal subtype. The M. jannaschii DHOase is found here to have traits from all subtypes. Contrary to expectations, it has a carboxylated lysine bridging the two Zn ions in the active site, and a long catalytic loop. It is a monomeric protein with a large β sandwich domain adjacent to the TIM barrel. Loop 5 is similar to bacterial type III and the C-terminal extension is long.
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Affiliation(s)
- Jacqueline Vitali
- Department of PhysicsCleveland State UniversityClevelandOhioUSA
- Department of Biological, Geological and Environmental SciencesCleveland State UniversityClevelandOhioUSA
| | - Jay C. Nix
- Molecular Biology Consortium, Advanced Light SourceLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Haley E. Newman
- Department of Biological, Geological and Environmental SciencesCleveland State UniversityClevelandOhioUSA
| | - Michael J. Colaneri
- Department of Chemistry and PhysicsThe State University of New York CollegeOld WestburyNew YorkUSA
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3
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Alqahtani SS, Koltai T, Ibrahim ME, Bashir AHH, Alhoufie STS, Ahmed SBM, Molfetta DD, Carvalho TMA, Cardone RA, Reshkin SJ, Hifny A, Ahmed ME, Alfarouk KO. Role of pH in Regulating Cancer Pyrimidine Synthesis. J Xenobiot 2022; 12:158-180. [PMID: 35893264 PMCID: PMC9326563 DOI: 10.3390/jox12030014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/17/2022] [Accepted: 06/28/2022] [Indexed: 11/18/2022] Open
Abstract
Replication is a fundamental aspect of cancer, and replication is about reproducing all the elements and structures that form a cell. Among them are DNA, RNA, enzymes, and coenzymes. All the DNA is doubled during each S (synthesis) cell cycle phase. This means that six billion nucleic acids must be synthesized in each cycle. Tumor growth, proliferation, and mutations all depend on this synthesis. Cancer cells require a constant supply of nucleotides and other macromolecules. For this reason, they must stimulate de novo nucleotide synthesis to support nucleic acid provision. When deregulated, de novo nucleic acid synthesis is controlled by oncogenes and tumor suppressor genes that enable increased synthesis and cell proliferation. Furthermore, cell duplication must be achieved swiftly (in a few hours) and in the midst of a nutrient-depleted and hypoxic environment. This also means that the enzymes participating in nucleic acid synthesis must work efficiently. pH is a critical factor in enzymatic efficiency and speed. This review will show that the enzymatic machinery working in nucleic acid synthesis requires a pH on the alkaline side in most cases. This coincides with many other pro-tumoral factors, such as the glycolytic phenotype, benefiting from an increased intracellular pH. An increased intracellular pH is a perfect milieu for high de novo nucleic acid production through optimal enzymatic performance.
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Affiliation(s)
- Saad Saeed Alqahtani
- Department of Pharmacy Practice, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia;
- Pharmacy Practice Research Unit, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia
| | | | - Muntaser E. Ibrahim
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum 11111, Sudan; (M.E.I.); (A.H.H.B.)
| | - Adil H. H. Bashir
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum 11111, Sudan; (M.E.I.); (A.H.H.B.)
| | - Sari T. S. Alhoufie
- Medical Laboratories Technology Department, College of Applied Medical Sciences, Taibah University, Medina 42353, Saudi Arabia;
| | - Samrein B. M. Ahmed
- Department of Biosciences and Chemistry, College of Health, Wellbeing and Life Sciences, Sheffield Hallam University, Sheffield S1 1WB, UK;
| | - Daria Di Molfetta
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari, 70126 Bari, Italy; (D.D.M.); (T.M.A.C.); (R.A.C.); (S.J.R.)
| | - Tiago M. A. Carvalho
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari, 70126 Bari, Italy; (D.D.M.); (T.M.A.C.); (R.A.C.); (S.J.R.)
| | - Rosa Angela Cardone
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari, 70126 Bari, Italy; (D.D.M.); (T.M.A.C.); (R.A.C.); (S.J.R.)
| | - Stephan Joel Reshkin
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari, 70126 Bari, Italy; (D.D.M.); (T.M.A.C.); (R.A.C.); (S.J.R.)
| | | | - Mohamed E. Ahmed
- Research Center, Zamzam University College, Khartoum 11123, Sudan;
| | - Khalid Omer Alfarouk
- Research Center, Zamzam University College, Khartoum 11123, Sudan;
- Alfarouk Biomedical Research LLC, Temple Terrace, FL 33617, USA
- Hala Alfarouk Cancer Center, Khartoum 11123, Sudan
- Correspondence:
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4
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Del Caño-Ochoa F, Ramón-Maiques S. Deciphering CAD: Structure and function of a mega-enzymatic pyrimidine factory in health and disease. Protein Sci 2021; 30:1995-2008. [PMID: 34288185 PMCID: PMC8442968 DOI: 10.1002/pro.4158] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 11/17/2022]
Abstract
CAD is a 1.5 MDa particle formed by hexameric association of a 250 kDa protein divided into different enzymatic domains, each catalyzing one of the initial reactions for de novo biosynthesis of pyrimidine nucleotides: glutaminase‐dependent Carbamoyl phosphate synthetase, Aspartate transcarbamoylase, and Dihydroorotase. The pathway for de novo pyrimidine synthesis is essential for cell proliferation and is conserved in all living organisms, but the covalent linkage of the first enzymatic activities into a multienzymatic CAD particle is unique to animals. In other organisms, these enzymatic activities are encoded as monofunctional proteins for which there is abundant structural and biochemical information. However, the knowledge about CAD is scarce and fragmented. Understanding CAD requires not only to determine the three‐dimensional structures and define the catalytic and regulatory mechanisms of the different enzymatic domains, but also to comprehend how these domains entangle and work in a coordinated and regulated manner. This review summarizes significant progress over the past 10 years toward the characterization of CAD's architecture, function, regulatory mechanisms, and cellular compartmentalization, as well as the recent finding of a new and rare neurometabolic disorder caused by defects in CAD activities.
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Affiliation(s)
- Francisco Del Caño-Ochoa
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain.,Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) - Instituto de Salud Carlos III, Valencia, Spain
| | - Santiago Ramón-Maiques
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain.,Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) - Instituto de Salud Carlos III, Valencia, Spain
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5
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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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Del Caño-Ochoa F, Ramón-Maiques S. The multienzymatic protein CAD leading the de novo biosynthesis of pyrimidines localizes exclusively in the cytoplasm and does not translocate to the nucleus. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 39:1320-1334. [PMID: 31997698 DOI: 10.1080/15257770.2019.1706743] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
CAD, the multienzymatic protein that initiates and controls the de novo biosynthesis of pyrimidines, plays a major role in nucleotide homeostasis, cell growth and proliferation. Despite its interest as a potential antitumoral target, there is a lack of understanding on CAD's structure and functioning mechanisms. Although mainly identified as a cytosolic complex, different studies support the translocation of CAD into the nucleus, where it could have a yet undefined function. Here, we track the subcellular localization of CAD by using fluorescent chimeras, cell fractionation and immunoblotting with specific antibodies. Contradicting previous studies, we demonstrate that CAD is exclusively localized at the cytosol and discard a possible translocation to the nucleus.
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Affiliation(s)
- Francisco Del Caño-Ochoa
- Genome Dynamics and Function Program, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain
| | - Santiago Ramón-Maiques
- Genome Dynamics and Function Program, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain
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7
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Del Caño-Ochoa F, Grande-García A, Reverte-López M, D'Abramo M, Ramón-Maiques S. Characterization of the catalytic flexible loop in the dihydroorotase domain of the human multi-enzymatic protein CAD. J Biol Chem 2018; 293:18903-18913. [PMID: 30315107 DOI: 10.1074/jbc.ra118.005494] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/08/2018] [Indexed: 11/06/2022] Open
Abstract
The dihydroorotase (DHOase) domain of the multifunctional protein carbamoyl-phosphate synthetase 2, aspartate transcarbamoylase, and dihydroorotase (CAD) catalyzes the third step in the de novo biosynthesis of pyrimidine nucleotides in animals. The crystal structure of the DHOase domain of human CAD (huDHOase) revealed that, despite evolutionary divergence, its active site components are highly conserved with those in bacterial DHOases, encoded as monofunctional enzymes. An important element for catalysis, conserved from Escherichia coli to humans, is a flexible loop that closes as a lid over the active site. Here, we combined mutagenic, structural, biochemical, and molecular dynamics analyses to characterize the function of the flexible loop in the activity of CAD's DHOase domain. A huDHOase chimera bearing the E. coli DHOase flexible loop was inactive, suggesting the presence of distinctive elements in the flexible loop of huDHOase that cannot be replaced by the bacterial sequence. We pinpointed Phe-1563, a residue absolutely conserved at the tip of the flexible loop in CAD's DHOase domain, as a critical element for the conformational equilibrium between the two catalytic states of the protein. Substitutions of Phe-1563 with Ala, Leu, or Thr prevented the closure of the flexible loop and inactivated the protein, whereas substitution with Tyr enhanced the interactions of the loop in the closed position and reduced fluctuations and the reaction rate. Our results confirm the importance of the flexible loop in CAD's DHOase domain and explain the key role of Phe-1563 in configuring the active site and in promoting substrate strain and catalysis.
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Affiliation(s)
- Francisco Del Caño-Ochoa
- From the Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid 28049, Spain
| | - Araceli Grande-García
- the Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain, and
| | - María Reverte-López
- From the Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid 28049, Spain
| | - Marco D'Abramo
- the Department of Chemistry, Sapienza University of Rome, Rome 00185, Italy
| | - Santiago Ramón-Maiques
- From the Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid 28049, Spain,
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8
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Moreno-Morcillo M, Grande-García A, Ruiz-Ramos A, Del Caño-Ochoa F, Boskovic J, Ramón-Maiques S. Structural Insight into the Core of CAD, the Multifunctional Protein Leading De Novo Pyrimidine Biosynthesis. Structure 2017; 25:912-923.e5. [PMID: 28552578 DOI: 10.1016/j.str.2017.04.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/05/2017] [Accepted: 04/28/2017] [Indexed: 11/17/2022]
Abstract
CAD, the multifunctional protein initiating and controlling de novo biosynthesis of pyrimidines in animals, self-assembles into ∼1.5 MDa hexamers. The structures of the dihydroorotase (DHO) and aspartate transcarbamoylase (ATC) domains of human CAD have been previously determined, but we lack information on how these domains associate and interact with the rest of CAD forming a multienzymatic unit. Here, we prove that a construct covering human DHO and ATC oligomerizes as a dimer of trimers and that this arrangement is conserved in CAD-like from fungi, which holds an inactive DHO-like domain. The crystal structures of the ATC trimer and DHO-like dimer from the fungus Chaetomium thermophilum confirm the similarity with the human CAD homologs. These results demonstrate that, despite being inactive, the fungal DHO-like domain has a conserved structural function. We propose a model that sets the DHO and ATC complex as the central element in the architecture of CAD.
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Affiliation(s)
- María Moreno-Morcillo
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, Madrid 28029, Spain
| | - Araceli Grande-García
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, Madrid 28029, Spain
| | - Alba Ruiz-Ramos
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, Madrid 28029, Spain
| | - Francisco Del Caño-Ochoa
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, Madrid 28029, Spain
| | - Jasminka Boskovic
- Electron Microscopy Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández 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 Fernández Almagro, 3, Madrid 28029, Spain; Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera, 1, Madrid 28049, Spain.
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9
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Biochemical characterization of dihydroorotase of Leishmania donovani: Understanding pyrimidine metabolism through its inhibition. Biochimie 2016; 131:45-53. [DOI: 10.1016/j.biochi.2016.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 09/15/2016] [Indexed: 11/22/2022]
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10
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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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11
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Grande-García A, Lallous N, Díaz-Tejada C, Ramón-Maiques S. Structure, functional characterization, and evolution of the dihydroorotase domain of human CAD. Structure 2013; 22:185-98. [PMID: 24332717 DOI: 10.1016/j.str.2013.10.016] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 10/28/2013] [Accepted: 10/30/2013] [Indexed: 12/30/2022]
Abstract
Upregulation of CAD, the multifunctional protein that initiates and controls the de novo biosynthesis of pyrimidines in animals, is essential for cell proliferation. Deciphering the architecture and functioning of CAD is of interest for its potential usage as an antitumoral target. However, there is no detailed structural information about CAD other than that it self-assembles into hexamers of ∼1.5 MDa. Here we report the crystal structure and functional characterization of the dihydroorotase domain of human CAD. Contradicting all assumptions, the structure reveals an active site enclosed by a flexible loop with two Zn²⁺ ions bridged by a carboxylated lysine and a third Zn coordinating a rare histidinate ion. Site-directed mutagenesis and functional assays prove the involvement of the Zn and flexible loop in catalysis. Comparison with homologous bacterial enzymes supports a reclassification of the DHOase family and provides strong evidence against current models of the architecture of CAD.
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Affiliation(s)
- Araceli Grande-García
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Nada Lallous
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Celsa Díaz-Tejada
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Santiago Ramón-Maiques
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain.
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12
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The mononuclear metal center of type-I dihydroorotase from Aquifex aeolicus. BMC BIOCHEMISTRY 2013; 14:36. [PMID: 24314009 PMCID: PMC3880350 DOI: 10.1186/1471-2091-14-36] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Accepted: 10/28/2013] [Indexed: 01/22/2023]
Abstract
BACKGROUND Dihydroorotase (DHO) is a zinc metalloenzyme, although the number of active site zinc ions has been controversial. E. coli DHO was initially thought to have a mononuclear metal center, but the subsequent X-ray structure clearly showed two zinc ions, α and β, at the catalytic site. Aquifex aeolicus DHO, is a dodecamer comprised of six DHO and six aspartate transcarbamoylase (ATC) subunits. The isolated DHO monomer, which lacks catalytic activity, has an intact α-site and conserved β-site ligands, but the geometry of the second metal binding site is completely disrupted. However, the putative β-site is restored when the complex with ATC is formed and DHO activity is regained. Nevertheless, the X-ray structure of the complex revealed a single zinc ion at the active site. The structure of DHO from the pathogenic organism, S. aureus showed that it also has a single active site metal ion. RESULTS Zinc analysis showed that the enzyme has one zinc/DHO subunit and the addition of excess metal ion did not stimulate catalytic activity, nor alter the kinetic parameters. The metal free apoenzyme was inactive, but the full activity was restored upon the addition of one equivalent of Zn2+ or Co2+. Moreover, deletion of the β-site by replacing the His180 and His232 with alanine had no effect on catalysis in the presence or absence of excess zinc. The 2.2 Å structure of the double mutant confirmed that the β-site was eliminated but that the active site remained otherwise intact. CONCLUSIONS Thus, kinetically competent A. aeolicus DHO has a mononuclear metal center. In contrast, elimination of the putative second metal binding site in amidohydrolyases with a binuclear metal center, resulted in the abolition of catalytic activity. The number of active site metal ions may be a consideration in the design of inhibitors that selectively target either the mononuclear or binuclear enzymes.
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