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Cederfelt D, Badgujar D, Au Musse A, Lohkamp B, Danielson UH, Dobritzsch D. The Allosteric Regulation of Β-Ureidopropionase Depends on Fine-Tuned Stability of Active-Site Loops and Subunit Interfaces. Biomolecules 2023; 13:1763. [PMID: 38136634 PMCID: PMC10741476 DOI: 10.3390/biom13121763] [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: 10/11/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
The activity of β-ureidopropionase, which catalyses the last step in the degradation of uracil, thymine, and analogous antimetabolites, is cooperatively regulated by the substrate and product of the reaction. This involves shifts in the equilibrium of the oligomeric states of the enzyme, but how these are achieved and result in changes in enzyme catalytic competence has yet to be determined. Here, the regulation of human β-ureidopropionase was further explored via site-directed mutagenesis, inhibition studies, and cryo-electron microscopy. The active-site residue E207, as well as H173 and H307 located at the dimer-dimer interface, are shown to play crucial roles in enzyme activation. Dimer association to larger assemblies requires closure of active-site loops, which positions the catalytically crucial E207 stably in the active site. H173 and H307 likely respond to ligand-induced changes in their environment with changes in their protonation states, which fine-tunes the active-site loop stability and the strength of dimer-dimer interfaces and explains the previously observed pH influence on the oligomer equilibrium. The correlation between substrate analogue structure and effect on enzyme assembly suggests that the ability to favourably interact with F205 may distinguish activators from inhibitors. The cryo-EM structure of human β-ureidopropionase assembly obtained at low pH provides first insights into the architecture of its activated state. and validates our current model of the allosteric regulation mechanism. Closed entrance loop conformations and dimer-dimer interfaces are highly conserved between human and fruit fly enzymes.
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Affiliation(s)
- Daniela Cederfelt
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
| | - Dilip Badgujar
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
- Department of Cell and Molecular Biology, Uppsala University, 751 23 Uppsala, Sweden
| | - Ayan Au Musse
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
- School of Science and Technology, Örebro University, 701 82 Örebro, Sweden
| | - Bernhard Lohkamp
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Stockholm, Sweden;
| | - U. Helena Danielson
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
| | - Doreen Dobritzsch
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
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Cooper AJL, Dorai T, Pinto JT, Denton TT. Metabolic Heterogeneity, Plasticity, and Adaptation to "Glutamine Addiction" in Cancer Cells: The Role of Glutaminase and the GTωA [Glutamine Transaminase-ω-Amidase (Glutaminase II)] Pathway. BIOLOGY 2023; 12:1131. [PMID: 37627015 PMCID: PMC10452834 DOI: 10.3390/biology12081131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/06/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023]
Abstract
Many cancers utilize l-glutamine as a major energy source. Often cited in the literature as "l-glutamine addiction", this well-characterized pathway involves hydrolysis of l-glutamine by a glutaminase to l-glutamate, followed by oxidative deamination, or transamination, to α-ketoglutarate, which enters the tricarboxylic acid cycle. However, mammalian tissues/cancers possess a rarely mentioned, alternative pathway (the glutaminase II pathway): l-glutamine is transaminated to α-ketoglutaramate (KGM), followed by ω-amidase (ωA)-catalyzed hydrolysis of KGM to α-ketoglutarate. The name glutaminase II may be confused with the glutaminase 2 (GLS2) isozyme. Thus, we recently renamed the glutaminase II pathway the "glutamine transaminase-ω-amidase (GTωA)" pathway. Herein, we summarize the metabolic importance of the GTωA pathway, including its role in closing the methionine salvage pathway, and as a source of anaplerotic α-ketoglutarate. An advantage of the GTωA pathway is that there is no net change in redox status, permitting α-ketoglutarate production during hypoxia, diminishing cellular energy demands. We suggest that the ability to coordinate control of both pathways bestows a metabolic advantage to cancer cells. Finally, we discuss possible benefits of GTωA pathway inhibitors, not only as aids to studying the normal biological roles of the pathway but also as possible useful anticancer agents.
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Affiliation(s)
- Arthur J. L. Cooper
- Department of Biochemistry and Molecular Biology, New York Medical College, 15 Dana Road, Valhalla, NY 10595, USA; (T.D.); (J.T.P.)
| | - Thambi Dorai
- Department of Biochemistry and Molecular Biology, New York Medical College, 15 Dana Road, Valhalla, NY 10595, USA; (T.D.); (J.T.P.)
- Department of Urology, New York Medical College, Valhalla, NY 10595, USA
| | - John T. Pinto
- Department of Biochemistry and Molecular Biology, New York Medical College, 15 Dana Road, Valhalla, NY 10595, USA; (T.D.); (J.T.P.)
| | - Travis T. Denton
- Department Pharmaceutical Sciences, College of Pharmacy & Pharmaceutical Sciences, Washington State University Health Sciences Spokane, Spokane, WA 99202, USA
- Department of Translational Medicine and Physiology, Elson S. Floyd College of Medicine, Washington State University Health Sciences Spokane, Spokane, WA 99164, USA
- Steve Gleason Institute for Neuroscience, Washington State University Health Sciences Spokane, Spokane, WA 99164, USA
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3
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Schwartz SL, Rangel LT, Payette JG, Fournier GP. A Proterozoic microbial origin of extant cyanide-hydrolyzing enzyme diversity. Front Microbiol 2023; 14:1130310. [PMID: 37065136 PMCID: PMC10098168 DOI: 10.3389/fmicb.2023.1130310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/07/2023] [Indexed: 04/03/2023] Open
Abstract
In addition to its role as a toxic environmental contaminant, cyanide has been hypothesized to play a key role in prebiotic chemistry and early biogeochemical evolution. While cyanide-hydrolyzing enzymes have been studied and engineered for bioremediation, the extant diversity of these enzymes remains underexplored. Additionally, the age and evolution of microbial cyanide metabolisms is poorly constrained. Here we provide comprehensive phylogenetic and molecular clock analyses of the distribution and evolution of the Class I nitrilases, thiocyanate hydrolases, and nitrile hydratases. Molecular clock analyses indicate that bacterial cyanide-reducing nitrilases were present by the Paleo- to Mesoproterozoic, and were subsequently horizontally transferred into eukaryotes. These results present a broad diversity of microbial enzymes that could be optimized for cyanide bioremediation.
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Affiliation(s)
- Sarah L. Schwartz
- Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA, United States
- Graduate Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
- *Correspondence: Sarah L. Schwartz,
| | - L. Thiberio Rangel
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Jack G. Payette
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Gregory P. Fournier
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
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4
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Magalhães RP, Fernandes HS, Sousa SF. The critical role of Asp206 stabilizing residues on the catalytic mechanism of the Ideonella sakaiensis PETase. Catal Sci Technol 2022. [DOI: 10.1039/d1cy02271g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We described the catalytic mechanism of IsPETase, a polyethylene-terephthalate degrading enzyme. The reaction was found to progress in four steps, divided in two events: formation of the first transition intermediate and hydrolysis of the adduct.
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Affiliation(s)
- Rita P. Magalhães
- UCIBIO – Applied Molecular Biosciences Unit, BioSIM – Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Henrique S. Fernandes
- UCIBIO – Applied Molecular Biosciences Unit, BioSIM – Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Sérgio F. Sousa
- UCIBIO – Applied Molecular Biosciences Unit, BioSIM – Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
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Pina AF, Sousa SF, Cerqueira NMFSA. The Catalytic Mechanism of Pdx2 Glutaminase Driven by a Cys-His-Glu Triad: A Computational Study. Chembiochem 2021; 23:e202100555. [PMID: 34762772 DOI: 10.1002/cbic.202100555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/10/2021] [Indexed: 11/08/2022]
Abstract
The catalytic mechanism of Pdx2 was studied with atomic detail employing the computational ONIOM hybrid QM/MM methodology. Pdx2 employs a Cys-His-Glu catalytic triad to deaminate glutamine to glutamate and ammonia - the source of the nitrogen of pyridoxal 5'-phosphate (PLP). This enzyme is, therefore, a rate-limiting step in the PLP biosynthetic pathway of Malaria and Tuberculosis pathogens that rely on this mechanism to obtain PLP. For this reason, Pdx2 is considered a novel and promising drug target to treat these diseases. The results obtained show that the catalytic mechanism of Pdx2 occurs in six steps that can be divided into four stages: (i) activation of Cys87 , (ii) deamination of glutamine with the formation of the glutamyl-thioester intermediate, (iii) hydrolysis of the formed intermediate, and (iv) enzymatic turnover. The kinetic data available in the literature (19.1-19.5 kcal mol-1 ) agree very well with the calculated free energy barrier of the hydrolytic step (18.2 kcal.mol-11 ), which is the rate-limiting step of the catalytic process when substrate is readily available in the active site. This catalytic mechanism differs from other known amidases in three main points: i) it requires the activation of the nucleophile Cys87 to a thiolate; ii) the hydrolysis occurs in a single step and therefore does not require the formation of a second tetrahedral reaction intermediate, as it is proposed, and iii) Glu198 does not have a direct role in the catalytic process. Together, these results can be used for the synthesis of new transition state analogue inhibitors capable of inhibiting Pdx2 and impair diseases like Malaria and Tuberculosis.
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Affiliation(s)
- André F Pina
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
| | - Sérgio F Sousa
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
| | - Nuno M F S A Cerqueira
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
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