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Vela-Amieva M, Alcántara-Ortigoza MA, González-del Angel A, Ibarra-González I, Fernández-Hernández L, Guillén-López S, López-Mejía L, Fernández-Lainez C. In Silico Structural Protein Evaluation of the Phenylalanine Hydroxylase p.(Tyr77His) Variant Associated with Benign Hyperphenylalaninemia as Identified through Mexican Newborn Screening. Children (Basel) 2023; 10:1865. [PMID: 38136067 PMCID: PMC10742057 DOI: 10.3390/children10121865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023]
Abstract
Hyperphenylalaninemia (HPA), which includes phenylketonuria (PKU), is a genetic autosomal recessive disorder arising from a deficiency in the enzyme named phenylalanine hydroxylase (PAH). Affected patients can experience severe and irreversible neurological impairments when phenylalanine (Phe) blood concentration exceeds 360 μmol/L (6 mg/dL). Here, we describe a female HPA patient who was born in Mexico to Cuban non-consanguineous parents and identified by newborn screening, and who bears the previously unreported PAH NM_000277.3(PAH):c.[229T>C];[1222C>T] or p.[Tyr77His];[Arg408Trp] genotype. At diagnosis, the patient showed a Phe blood level of 321 μmol/L (5.3 mg/dL), indicative of mild HPA. Neither of the PAH variants found in this patient had been previously reported in the mutational PAH spectrum of the Mexican population. The c.229T>C or p.(Tyr77His) PAH variant was previously related to mild HPA in the Swedish population. Our in silico structural analysis and molecular docking showed that mutated His 77 residue is located in the allosteric site of PAH at the interface of the two monomers. The PDBsum in silico tool predicted that this variant would cause minimal structural disturbance of the protein interface in the presence of Phe at the allosteric site. Docking studies revealed that these structural changes might be attenuated by the allosteric effect of Phe. Given the classic PKU phenotype conditioned by the "Celtic" or c.[1222C>T] or p.(Arg408Trp) PAH variant, which is the second variant in this patient, we propose that p.(Tyr77His) has a hypomorphic feature that could explain her mild HPA phenotype. Our results show the importance of following up on cases detected by NBS and the value of genetic studies and in silico tools that aid in the establishment of correct therapeutic strategies.
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Affiliation(s)
- Marcela Vela-Amieva
- Laboratorio de Errores Innatos del Metabolismo y Tamiz, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico; (M.V.-A.); (S.G.-L.); (L.L.-M.)
| | - Miguel Angel Alcántara-Ortigoza
- Laboratorio de Biología Molecular, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico; (M.A.A.-O.); (A.G.-d.A.); (L.F.-H.)
- Centro de Alta Especialidad en Genética Humana DNA-GEN S.C., Ciudad de México 14070, Mexico
| | - Ariadna González-del Angel
- Laboratorio de Biología Molecular, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico; (M.A.A.-O.); (A.G.-d.A.); (L.F.-H.)
- Centro de Alta Especialidad en Genética Humana DNA-GEN S.C., Ciudad de México 14070, Mexico
| | - Isabel Ibarra-González
- Unidad de Genética de la Nutrición, Instituto de Investigaciones Biomédicas UNAM, Ciudad de México 04510, Mexico;
| | - Liliana Fernández-Hernández
- Laboratorio de Biología Molecular, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico; (M.A.A.-O.); (A.G.-d.A.); (L.F.-H.)
| | - Sara Guillén-López
- Laboratorio de Errores Innatos del Metabolismo y Tamiz, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico; (M.V.-A.); (S.G.-L.); (L.L.-M.)
| | - Lizbeth López-Mejía
- Laboratorio de Errores Innatos del Metabolismo y Tamiz, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico; (M.V.-A.); (S.G.-L.); (L.L.-M.)
| | - Cynthia Fernández-Lainez
- Laboratorio de Errores Innatos del Metabolismo y Tamiz, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico; (M.V.-A.); (S.G.-L.); (L.L.-M.)
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2
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Fitzpatrick PF. The aromatic amino acid hydroxylases: Structures, catalysis, and regulation of phenylalanine hydroxylase, tyrosine hydroxylase, and tryptophan hydroxylase. Arch Biochem Biophys 2023; 735:109518. [PMID: 36639008 DOI: 10.1016/j.abb.2023.109518] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/01/2023] [Accepted: 01/06/2023] [Indexed: 01/12/2023]
Abstract
The aromatic amino acid hydroxylases phenylalanine hydroxylase, tyrosine hydroxylase, and tryptophan hydroxylase are non-heme iron enzymes that catalyze key physiological reactions. This review discusses the present understanding of the common catalytic mechanism of these enzymes and recent advances in understanding the relationship between their structures and their regulation.
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Affiliation(s)
- Paul F Fitzpatrick
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, 78229, USA.
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3
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Boulghobra A, Bonose M. Quantification of Monoamine Neurotransmitter Metabolites and Cofactors in Cerebrospinal Fluid: State-of-the-Art. Crit Rev Anal Chem 2022:1-16. [PMID: 36476251 DOI: 10.1080/10408347.2022.2151833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Inborn errors of monoamine neurotransmitter metabolism are rare diseases characterized by nonspecific neurological symptoms. These symptoms appear in early childhood and correspond to movement disorders, epilepsy, sleep disorders and/or mental disability. Cerebrospinal fluid biomarkers have been identified and validated to allow specific diagnosis of these diseases. Biomarkers of inborn errors of monoamine neurotransmitter metabolites are divided in two groups: monoamine neurotransmitter metabolites and pterins. Biomarkers quantification in cerebrospinal fluid is based on high-performance liquid chromatography separation coupled to electrochemical detection, fluorescence detection, or mass spectrometry. The following article reviews the advances in the proposed routine methods for the measurement of these analytes in cerebrospinal fluid. The purpose of this review is to compare the various proposed methods in terms of sample preparation, chromatographic conditions and detection modes. Despite the broad range of proposed methods, quantification of inborn errors of monoamine neurotransmitter biomarkers remains a great challenge, given the complexity of biological fluids and the low amounts of analytes that are present in cerebrospinal fluid.
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Affiliation(s)
- Ayoub Boulghobra
- Institut de Chimie Physique, Université Paris-Saclay, CNRS, UMR8000, 91405 Orsay, France
| | - Myriam Bonose
- Institut de Chimie Physique, Université Paris-Saclay, CNRS, UMR8000, 91405 Orsay, France
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4
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Meng D, Yang Q, Jeong MH, Curukovic A, Tiwary S, Melick CH, Lama-Sherpa TD, Wang H, Huerta-Rosario M, Urquhart G, Zacharias LG, Lewis C, DeBerardinis RJ, Jewell JL. SNAT7 regulates mTORC1 via macropinocytosis. Proc Natl Acad Sci U S A 2022; 119:e2123261119. [PMID: 35561222 PMCID: PMC9171778 DOI: 10.1073/pnas.2123261119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/13/2022] [Indexed: 11/30/2022] Open
Abstract
Mammalian target of rapamycin complex 1 (mTORC1) senses amino acids to control cell growth, metabolism, and autophagy. Some amino acids signal to mTORC1 through the Rag GTPase, whereas glutamine and asparagine activate mTORC1 through a Rag GTPase-independent pathway. Here, we show that the lysosomal glutamine and asparagine transporter SNAT7 activates mTORC1 after extracellular protein, such as albumin, is macropinocytosed. The N terminus of SNAT7 forms nutrient-sensitive interaction with mTORC1 and regulates mTORC1 activation independently of the Rag GTPases. Depletion of SNAT7 inhibits albumin-induced mTORC1 lysosomal localization and subsequent activation. Moreover, SNAT7 is essential to sustain KRAS-driven pancreatic cancer cell growth through mTORC1. Thus, SNAT7 links glutamine and asparagine signaling from extracellular protein to mTORC1 independently of the Rag GTPases and is required for macropinocytosis-mediated mTORC1 activation and pancreatic cancer cell growth.
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Affiliation(s)
- Delong Meng
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Qianmei Yang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Mi-Hyeon Jeong
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Adna Curukovic
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Shweta Tiwary
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Chase H. Melick
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Tshering D. Lama-Sherpa
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Huanyu Wang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Mariela Huerta-Rosario
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Greg Urquhart
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Lauren G. Zacharias
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Cheryl Lewis
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Ralph J. DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jenna L. Jewell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
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Lin C, Li Y, Zhang E, Feillet F, Zhang S, Blau N. Importance of the long non-coding RNA (lncRNA) transcript HULC for the regulation of phenylalanine hydroxylase and treatment of phenylketonuria. Mol Genet Metab 2022; 135:171-178. [PMID: 35101330 DOI: 10.1016/j.ymgme.2022.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/18/2022] [Accepted: 01/18/2022] [Indexed: 12/12/2022]
Abstract
More than 1280 variants in the phenylalanine hydroxylase (PAH) gene are responsible for a broad spectrum of phenylketonuria (PKU) phenotypes. While the genotype-phenotype correlation is reaching 88%, for some inconsistent phenotypes with the same genotype additional factors like tetrahydrobiopterin (BH4), the PAH co-chaperone DNAJC12, phosphorylation of the PAH residues or epigenetic factors may play an important role. Very recently an additional player, the long non-coding RNA (lncRNA) transcript HULC, was described to regulate PAH activity and enhance residual enzyme activity of some PAH variants (e.g., the most common p.R408W) by using HULC mimics. In this review we present an overview of the lncRNA function and in particular the interplay of the HUCL transcript with the PAH and discuss potential applications for the future treatment of some PKU patients.
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Affiliation(s)
- Chunru Lin
- Department of Molecular and Cellular Oncology, Division of Basic Science Research, The University of Texas, MD Anderson Cancer Center, Houston, TX, United States of America
| | - Yajuan Li
- Department of Molecular and Cellular Oncology, Division of Basic Science Research, The University of Texas, MD Anderson Cancer Center, Houston, TX, United States of America
| | - Eric Zhang
- Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, Houston, TX, United States of America
| | - François Feillet
- INSERM, U1256, NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy, France; Pediatric Department Reference Center for Inborn Errors of Metabolism Children University Hospital Nancy, Nancy, France
| | - Shuxing Zhang
- Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, Houston, TX, United States of America
| | - Nenad Blau
- Division of Metabolism, University Children's Hospital Zürich, Zurich, Switzerland.
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Chen P, Yang J, Wang R, Xiao B, Liu Q, Sun B, Wang X, Zhu L. Graphene oxide enhanced the endocrine disrupting effects of bisphenol A in adult male zebrafish: Integrated deep learning and metabolomics studies. Sci Total Environ 2022; 809:151103. [PMID: 34743883 DOI: 10.1016/j.scitotenv.2021.151103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/14/2021] [Accepted: 10/16/2021] [Indexed: 06/13/2023]
Abstract
In our previous studies, it was found that graphene oxide (GO) reduced the endocrine disruption of bisphenol A (BPA) in zebrafish embryo and larvae, but through different mechanisms. In this study, adult male zebrafish were selected to further understand the interactions between GO and BPA considering that adult zebrafish have different uptake pathways and metabolism from embryo and larvae. BPA was predicted to bind with the estrogen receptor α (ERα) with a probability of 98.1% by training a directed-message passing deep neural network model, and was confirmed by molecular docking analysis. The results were in accordance with the significantly increased vitellogenin (VTG) and estradiol (E2) levels, while decreased testosterone (T) and follicle-stimulating hormone (FSH) levels in the adult male zebrafish after 7 d exposure to 500 μg/L BPA. Compared to BPA single exposure group, the presence of GO led to significantly lower T and FSH levels and fewer spermatozoa, indicating that GO enhanced the endocrine disruption effects of BPA in the adult zebrafish. Metabolomics analysis revealed that 5 μg/L BPA could elicit changes in the metabolome, and the responses were correlated with BPA concentrations. Metabolic pathway analysis revealed more disturbance was caused by the mixture of GO and BPA compared to BPA alone, including three additional pathways and stronger perturbations on carbohydrate, lipid, and amino acid metabolism, fortifying that GO exaggerated the toxic effects of BPA. This was opposite to the depression effect observed in zebrafish embryo and larvae, magnifying that the joint effects of exposure to nanomaterials and endocrine disrupting chemicals are relevant to the life stages of organisms.
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Affiliation(s)
- Pengyu Chen
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering of Nankai University, Tianjin 300350, China; College of Oceanography, Hohai University, Nanjing 210098, China
| | - Jing Yang
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering of Nankai University, Tianjin 300350, China
| | - Ruihan Wang
- College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Bowen Xiao
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering of Nankai University, Tianjin 300350, China
| | - Qing Liu
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering of Nankai University, Tianjin 300350, China
| | - Binbin Sun
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering of Nankai University, Tianjin 300350, China
| | - Xiaolei Wang
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering of Nankai University, Tianjin 300350, China
| | - Lingyan Zhu
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering of Nankai University, Tianjin 300350, China.
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7
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Tomé CS, Lopes RR, Sousa PMF, Amaro MP, Leandro J, Mertens HDT, Leandro P, Vicente JB. Structure of full-length wild-type human phenylalanine hydroxylase by small angle X-ray scattering reveals substrate-induced conformational stability. Sci Rep 2019; 9:13615. [PMID: 31541188 PMCID: PMC6754429 DOI: 10.1038/s41598-019-49944-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/03/2019] [Indexed: 01/30/2023] Open
Abstract
Human phenylalanine hydroxylase (hPAH) hydroxylates L-phenylalanine (L-Phe) to L-tyrosine, a precursor for neurotransmitter biosynthesis. Phenylketonuria (PKU), caused by mutations in PAH that impair PAH function, leads to neurological impairment when untreated. Understanding the hPAH structural and regulatory properties is essential to outline PKU pathophysiological mechanisms. Each hPAH monomer comprises an N-terminal regulatory, a central catalytic and a C-terminal oligomerisation domain. To maintain physiological L-Phe levels, hPAH employs complex regulatory mechanisms. Resting PAH adopts an auto-inhibited conformation where regulatory domains block access to the active site. L-Phe-mediated allosteric activation induces a repositioning of the regulatory domains. Since a structure of activated wild-type hPAH is lacking, we addressed hPAH L-Phe-mediated conformational changes and report the first solution structure of the allosterically activated state. Our solution structures obtained by small-angle X-ray scattering support a tetramer with distorted P222 symmetry, where catalytic and oligomerisation domains form a core from which regulatory domains protrude, positioning themselves close to the active site entrance in the absence of L-Phe. Binding of L-Phe induces a large movement and dimerisation of regulatory domains, exposing the active site. Activated hPAH is more resistant to proteolytic cleavage and thermal denaturation, suggesting that the association of regulatory domains stabilises hPAH.
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Affiliation(s)
- Catarina S Tomé
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Raquel R Lopes
- Research Institute for Medicines (iMed.ULisboa) and Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Pedro M F Sousa
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Mariana P Amaro
- Research Institute for Medicines (iMed.ULisboa) and Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - João Leandro
- Research Institute for Medicines (iMed.ULisboa) and Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Paula Leandro
- Research Institute for Medicines (iMed.ULisboa) and Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal.
| | - João B Vicente
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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8
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Arturo EC, Gupta K, Hansen MR, Borne E, Jaffe EK. Biophysical characterization of full-length human phenylalanine hydroxylase provides a deeper understanding of its quaternary structure equilibrium. J Biol Chem 2019; 294:10131-10145. [PMID: 31076506 PMCID: PMC6664189 DOI: 10.1074/jbc.ra119.008294] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/09/2019] [Indexed: 11/06/2022] Open
Abstract
Dysfunction of human phenylalanine hydroxylase (hPAH, EC 1.14.16.1) is the primary cause of phenylketonuria, the most common inborn error of amino acid metabolism. The dynamic domain rearrangements of this multimeric protein have thwarted structural study of the full-length form for decades, until now. In this study, a tractable C29S variant of hPAH (C29S) yielded a 3.06 Å resolution crystal structure of the tetrameric resting-state conformation. We used size-exclusion chromatography in line with small-angle X-ray scattering (SEC-SAXS) to analyze the full-length hPAH solution structure both in the presence and absence of Phe, which serves as both substrate and allosteric activators. Allosteric Phe binding favors accumulation of an activated PAH tetramer conformation, which is biophysically distinct in solution. Protein characterization with enzyme kinetics and intrinsic fluorescence revealed that the C29S variant and hPAH are otherwise equivalent in their response to Phe, further supported by their behavior on various chromatography resins and by analytical ultracentrifugation. Modeling of resting-state and activated forms of C29S against SAXS data with available structural data created and evaluated several new models for the transition between the architecturally distinct conformations of PAH and highlighted unique intra- and inter-subunit interactions. Three best-fitting alternative models all placed the allosteric Phe-binding module 8-10 Å farther from the tetramer center than do all previous models. The structural insights into allosteric activation of hPAH reported here may help inform ongoing efforts to treat phenylketonuria with novel therapeutic approaches.
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Affiliation(s)
- Emilia C Arturo
- From the Molecular Therapeutics Program, Fox Chase Cancer Center, Temple University Health Systems, Philadelphia, Pennsylvania 19111
- the Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, and
| | - Kushol Gupta
- the Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Michael R Hansen
- From the Molecular Therapeutics Program, Fox Chase Cancer Center, Temple University Health Systems, Philadelphia, Pennsylvania 19111
| | - Elias Borne
- From the Molecular Therapeutics Program, Fox Chase Cancer Center, Temple University Health Systems, Philadelphia, Pennsylvania 19111
| | - Eileen K Jaffe
- From the Molecular Therapeutics Program, Fox Chase Cancer Center, Temple University Health Systems, Philadelphia, Pennsylvania 19111,
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9
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Pecimonova M, Kluckova D, Csicsay F, Reblova K, Krahulec J, Procházkova D, Skultety L, Kadasi L, Soltysova A. Structural and Functional Impact of Seven Missense Variants of Phenylalanine Hydroxylase. Genes (Basel) 2019; 10:E459. [PMID: 31208052 PMCID: PMC6628251 DOI: 10.3390/genes10060459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 11/17/2022] Open
Abstract
The molecular genetics of well-characterized inherited diseases, such as phenylketonuria (PKU) and hyperphenylalaninemia (HPA) predominantly caused by mutations in the phenylalanine hydroxylase (PAH) gene, is often complicated by the identification of many novel variants, often with no obvious impact on the associated disorder. To date, more than 1100 PAH variants have been identified of which a substantial portion have unknown clinical significance. In this work, we study the functionality of seven yet uncharacterized PAH missense variants p.Asn167Tyr, p.Thr200Asn, p.Asp229Gly, p.Gly239Ala, p.Phe263Ser, p.Ala342Pro, and p.Ile406Met first identified in the Czech PKU/HPA patients. From all tested variants, three of them, namely p.Asn167Tyr, p.Thr200Asn, and p.Ile406Met, exerted residual enzymatic activity in vitro similar to wild type (WT) PAH, however, when expressed in HepG2 cells, their protein level reached a maximum of 72.1% ± 4.9%, 11.2% ± 4.2%, and 36.6% ± 7.3% compared to WT PAH, respectively. Remaining variants were null with no enzyme activity and decreased protein levels in HepG2 cells. The chaperone-like effect of applied BH4 precursor increased protein level significantly for p.Asn167Tyr, p.Asp229Gly, p.Ala342Pro, and p.Ile406Met. Taken together, our results of functional characterization in combination with in silico prediction suggest that while p.Asn167Tyr, p.Thr200Asn, and p.Ile406Met PAH variants have a mild impact on the protein, p.Asp229Gly, p.Gly239Ala, p.Phe263Ser, and p.Ala342Pro severely affect protein structure and function.
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Affiliation(s)
- Martina Pecimonova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, Slovakia.
| | - Daniela Kluckova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, Slovakia.
| | - Frantisek Csicsay
- Insitute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia.
| | - Kamila Reblova
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic.
| | - Jan Krahulec
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, Slovakia.
| | - Dagmar Procházkova
- Department of Pediatrics, Medical Faculty of Masaryk University and University Hospital Brno, Černopolní 9, 625 00 Brno, Czech Republic.
| | - Ludovit Skultety
- Insitute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia.
| | - Ludevit Kadasi
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, Slovakia.
- Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia.
| | - Andrea Soltysova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, Slovakia.
- Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia.
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10
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Flydal MI, Alcorlo-Pagés M, Johannessen FG, Martínez-Caballero S, Skjærven L, Fernandez-Leiro R, Martinez A, Hermoso JA. Structure of full-length human phenylalanine hydroxylase in complex with tetrahydrobiopterin. Proc Natl Acad Sci U S A 2019; 116:11229-11234. [PMID: 31118288 PMCID: PMC6561269 DOI: 10.1073/pnas.1902639116] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Phenylalanine hydroxylase (PAH) is a key enzyme in the catabolism of phenylalanine, and mutations in this enzyme cause phenylketonuria (PKU), a genetic disorder that leads to brain damage and mental retardation if untreated. Some patients benefit from supplementation with a synthetic formulation of the cofactor tetrahydrobiopterin (BH4) that partly acts as a pharmacological chaperone. Here we present structures of full-length human PAH (hPAH) both unbound and complexed with BH4 in the precatalytic state. Crystal structures, solved at 3.18-Å resolution, show the interactions between the cofactor and PAH, explaining the negative regulation exerted by BH4 BH4 forms several H-bonds with the N-terminal autoregulatory tail but is far from the catalytic FeII Upon BH4 binding a polar and salt-bridge interaction network links the three PAH domains, explaining the stability conferred by BH4 Importantly, BH4 binding modulates the interaction between subunits, providing information about PAH allostery. Moreover, we also show that the cryo-EM structure of hPAH in absence of BH4 reveals a highly dynamic conformation for the tetramers. Structural analyses of the hPAH:BH4 subunits revealed that the substrate-induced movement of Tyr138 into the active site could be coupled to the displacement of BH4 from the precatalytic toward the active conformation, a molecular mechanism that was supported by site-directed mutagenesis and targeted molecular dynamics simulations. Finally, comparison of the rat and human PAH structures show that hPAH is more dynamic, which is related to amino acid substitutions that enhance the flexibility of hPAH and may increase the susceptibility to PKU-associated mutations.
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Affiliation(s)
| | - Martín Alcorlo-Pagés
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain
| | | | | | - Lars Skjærven
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
| | - Rafael Fernandez-Leiro
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway;
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain;
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11
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Khan CA, Meisburger SP, Ando N, Fitzpatrick PF. The phenylketonuria-associated substitution R68S converts phenylalanine hydroxylase to a constitutively active enzyme but reduces its stability. J Biol Chem 2019; 294:4359-4367. [PMID: 30674554 DOI: 10.1074/jbc.ra118.006477] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/15/2019] [Indexed: 11/06/2022] Open
Abstract
The naturally occurring R68S substitution of phenylalanine hydroxylase (PheH) causes phenylketonuria (PKU). However, the molecular basis for how the R68S variant leads to PKU remains unclear. Kinetic characterization of R68S PheH establishes that the enzyme is fully active in the absence of allosteric binding of phenylalanine, in contrast to the WT enzyme. Analytical ultracentrifugation establishes that the isolated regulatory domain of R68S PheH is predominantly monomeric in the absence of phenylalanine and dimerizes in its presence, similar to the regulatory domain of the WT enzyme. Fluorescence and small-angle X-ray scattering analyses establish that the overall conformation of the resting form of R68S PheH is different from that of the WT enzyme. The data are consistent with the substitution disrupting the interface between the catalytic and regulatory domains of the enzyme, shifting the equilibrium between the resting and activated forms ∼200-fold, so that the resting form of R68S PheH is ∼70% in the activated conformation. However, R68S PheH loses activity 2 orders of magnitude more rapidly than the WT enzyme at 37 °C and is significantly more sensitive to proteolysis. We propose that, even though this substitution converts the enzyme to a constitutively active enzyme, it results in PKU because of the decrease in protein stability.
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Affiliation(s)
- Crystal A Khan
- From the Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, Texas 78229 and
| | - Steve P Meisburger
- the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Nozomi Ando
- the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Paul F Fitzpatrick
- From the Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, Texas 78229 and
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12
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Khan CA, Fitzpatrick PF. Phosphorylation of Phenylalanine Hydroxylase Increases the Rate Constant for Formation of the Activated Conformation of the Enzyme. Biochemistry 2018; 57:6274-6277. [PMID: 30346142 DOI: 10.1021/acs.biochem.8b00919] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Liver phenylalanine hydroxylase (PheH) is an allosteric enzyme that is activated by phenylalanine. The enzyme is also phosphorylated by protein kinase A, but the effects of phosphorylation are unclear. Recent structural studies ( Meisburger et al. ( 2016 ) J. Amer. Chem. Soc. 138 , 6506 - 6516 ) support a model in which activation of the enzyme involves dimerization of the regulatory domains, creating the allosteric site for phenylalanine at the dimer interface. This conformational change also results in a change in the fluorescence of the protein that can be used to monitor activation. The kinetics of activation of PheH are biphasic over a range of phenylalanine concentrations. These data are well-described by a model involving an initial equilibrium between the resting form and the activated conformation, with a value of the equilibrium constant for formation of the activated conformation, L, equal to 0.007, followed by binding of two molecules of phenylalanine. Phosphorylation increases L 10-fold by increasing the rate constant for conversion of the resting form to the activated form. The results provide functional support for the previous structural model, identify the specific effect of phosphorylation on the enzyme, and rationalize the lack of change in the protein structure upon phosphorylation.
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Affiliation(s)
- Crystal A Khan
- Department of Biochemistry and Structural Biology , University of Texas Health Science Center , San Antonio , Texas 78229 , United States
| | - Paul F Fitzpatrick
- Department of Biochemistry and Structural Biology , University of Texas Health Science Center , San Antonio , Texas 78229 , United States
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13
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Ge Y, Borne E, Stewart S, Hansen MR, Arturo EC, Jaffe EK, Voelz VA. Simulations of the regulatory ACT domain of human phenylalanine hydroxylase (PAH) unveil its mechanism of phenylalanine binding. J Biol Chem 2018; 293:19532-19543. [PMID: 30287685 DOI: 10.1074/jbc.ra118.004909] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/17/2018] [Indexed: 12/20/2022] Open
Abstract
Phenylalanine hydroxylase (PAH) regulates phenylalanine (Phe) levels in mammals to prevent neurotoxicity resulting from high Phe concentrations as observed in genetic disorders leading to hyperphenylalaninemia and phenylketonuria. PAH senses elevated Phe concentrations by transient allosteric Phe binding to a protein-protein interface between ACT domains of different subunits in a PAH tetramer. This interface is present in an activated PAH (A-PAH) tetramer and absent in a resting-state PAH (RS-PAH) tetramer. To investigate this allosteric sensing mechanism, here we used the GROMACS molecular dynamics simulation suite on the Folding@home computing platform to perform extensive molecular simulations and Markov state model (MSM) analysis of Phe binding to ACT domain dimers. These simulations strongly implicated a conformational selection mechanism for Phe association with ACT domain dimers and revealed protein motions that act as a gating mechanism for Phe binding. The MSMs also illuminate a highly mobile hairpin loop, consistent with experimental findings also presented here that the PAH variant L72W does not shift the PAH structural equilibrium toward the activated state. Finally, simulations of ACT domain monomers are presented, in which spontaneous transitions between resting-state and activated conformations are observed, also consistent with a mechanism of conformational selection. These mechanistic details provide detailed insight into the regulation of PAH activation and provide testable hypotheses for the development of new allosteric effectors to correct structural and functional defects in PAH.
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Affiliation(s)
- Yunhui Ge
- From the Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Elias Borne
- Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania 19111, and
| | - Shannon Stewart
- Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania 19111, and
| | - Michael R Hansen
- Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania 19111, and
| | - Emilia C Arturo
- Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania 19111, and.,Drexel University College of Medicine, Philadelphia, Pennsylvania 19129
| | - Eileen K Jaffe
- Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania 19111, and
| | - Vincent A Voelz
- From the Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122,
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14
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Eichinger A, Danecka MK, Möglich T, Borsch J, Woidy M, Büttner L, Muntau AC, Gersting SW. Secondary BH4 deficiency links protein homeostasis to regulation of phenylalanine metabolism. Hum Mol Genet 2018; 27:1732-1742. [PMID: 29514280 DOI: 10.1093/hmg/ddy079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 02/28/2018] [Indexed: 01/01/2023] Open
Abstract
Metabolic control of phenylalanine concentrations in body fluids is essential for cognitive development and executive function. The hepatic phenylalanine hydroxylating system is regulated by the ratio of l-phenylalanine, which is substrate of phenylalanine hydroxylase (PAH), to the PAH cofactor tetrahydrobiopterin (BH4). Physiologically, phenylalanine availability is governed by nutrient intake, whereas liver BH4 is kept at constant level. In phenylketonuria, PAH deficiency leads to elevated blood phenylalanine and is often caused by PAH protein misfolding with loss of function. Here, we report secondary hepatic BH4 deficiency in Pah-deficient mice. Alterations in de novo synthesis and turnover of BH4 were ruled out as molecular causes. We demonstrate that kinetically instable and aggregation-prone variant Pah proteins trap BH4, shifting the pool of free BH4 towards bound BH4. Interference of PAH protein misfolding with metabolite-based control of l-phenylalanine turnover suggests a mechanistic link between perturbation of protein homeostasis and disturbed regulation of metabolic pathways.
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Affiliation(s)
- Anna Eichinger
- Molecular Pediatrics, Dr von Hauner Children's Hospital, Ludwig-Maximilians-Universität, Munich, Germany
| | | | - Tamara Möglich
- Molecular Pediatrics, Dr von Hauner Children's Hospital, Ludwig-Maximilians-Universität, Munich, Germany
| | - Julia Borsch
- Molecular Pediatrics, Dr von Hauner Children's Hospital, Ludwig-Maximilians-Universität, Munich, Germany
| | - Mathias Woidy
- University Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lars Büttner
- Molecular Pediatrics, Dr von Hauner Children's Hospital, Ludwig-Maximilians-Universität, Munich, Germany
| | - Ania C Muntau
- University Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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15
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Huber KL, Serrano BP, Hardy JA. Caspase-9 CARD : core domain interactions require a properly formed active site. Biochem J 2018; 475:1177-96. [PMID: 29500231 DOI: 10.1042/BCJ20170913] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/27/2018] [Accepted: 03/01/2018] [Indexed: 12/20/2022]
Abstract
Caspase-9 is a critical factor in the initiation of apoptosis and as a result is tightly regulated by many mechanisms. Caspase-9 contains a Caspase Activation and Recruitment Domain (CARD), which enables caspase-9 to form a tight interaction with the apoptosome, a heptameric activating platform. The caspase-9 CARD has been thought to be principally involved in recruitment to the apoptosome, but its roles outside this interaction have yet to be uncovered. In this work, we show that the CARD is involved in physical interactions with the catalytic core of caspase-9 in the absence of the apoptosome; this interaction requires a properly formed caspase-9 active site. The active sites of caspases are composed of four extremely mobile loops. When the active-site loops are not properly ordered, the CARD and core domains of caspase-9 do not interact and behave independently, like loosely tethered beads. When the active-site loop bundle is properly ordered, the CARD domain interacts with the catalytic core, forming a single folding unit. Taken together, these findings provide mechanistic insights into a new level of caspase-9 regulation, prompting speculation that the CARD may also play a role in the recruitment or recognition of substrate.
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16
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Leandro J, Stokka AJ, Teigen K, Andersen OA, Flatmark T. Substituting Tyr 138 in the active site loop of human phenylalanine hydroxylase affects catalysis and substrate activation. FEBS Open Bio 2017; 7:1026-1036. [PMID: 28680815 PMCID: PMC5494296 DOI: 10.1002/2211-5463.12243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/27/2017] [Accepted: 05/10/2017] [Indexed: 11/22/2022] Open
Abstract
Mammalian phenylalanine hydroxylase (PAH) is a key enzyme in l‐phenylalanine (l‐Phe) metabolism and is active as a homotetramer. Biochemical and biophysical work has demonstrated that it cycles between two states with a variably low and a high activity, and that the substrate l‐Phe is the key player in this transition. X‐ray structures of the catalytic domain have shown mobility of a partially intrinsically disordered Tyr138‐loop to the active site in the presence of l‐Phe. The mechanism by which the loop dynamics are coupled to substrate binding at the active site in tetrameric PAH is not fully understood. We have here conducted functional studies of four Tyr138 point mutants. A high linear correlation (r2 = 0.99) was observed between their effects on the catalytic efficiency of the catalytic domain dimers and the corresponding effect on the catalytic efficiency of substrate‐activated full‐length tetramers. In the tetramers, a correlation (r2 = 0.96) was also observed between the increase in catalytic efficiency (activation) and the global conformational change (surface plasmon resonance signal response) at the same l‐Phe concentration. The new data support a similar functional importance of the Tyr138‐loop in the catalytic domain and the full‐length enzyme homotetramer.
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Affiliation(s)
- João Leandro
- Department of Biomedicine University of Bergen Norway.,Metabolism and Genetics Group Research Institute for Medicines (iMed.ULisboa) Faculty of Pharmacy University of Lisbon Portugal.,Present address: Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai 1425 Madison Avenue, Box 1498 New York NY 10029 USA
| | - Anne J Stokka
- Department of Biomedicine University of Bergen Norway.,The Biotechnology Centre of Oslo University of Oslo Norway
| | - Knut Teigen
- Department of Biomedicine University of Bergen Norway
| | - Ole A Andersen
- Department of Biomedicine University of Bergen Norway.,Evotec (UK) Ltd .Abingdon UK
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17
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Abstract
X-ray scattering is uniquely suited to the study of disordered systems and thus has the potential to provide insight into dynamic processes where diffraction methods fail. In particular, while X-ray crystallography has been a staple of structural biology for more than half a century and will continue to remain so, a major limitation of this technique has been the lack of dynamic information. Solution X-ray scattering has become an invaluable tool in structural and mechanistic studies of biological macromolecules where large conformational changes are involved. Such systems include allosteric enzymes that play key roles in directing metabolic fluxes of biochemical pathways, as well as large, assembly-line type enzymes that synthesize secondary metabolites with pharmaceutical applications. Furthermore, crystallography has the potential to provide information on protein dynamics via the diffuse scattering patterns that are overlaid with Bragg diffraction. Historically, these patterns have been very difficult to interpret, but recent advances in X-ray detection have led to a renewed interest in diffuse scattering analysis as a way to probe correlated motions. Here, we will review X-ray scattering theory and highlight recent advances in scattering-based investigations of protein solutions and crystals, with a particular focus on complex enzymes.
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Affiliation(s)
- Steve P Meisburger
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - William C Thomas
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Maxwell B Watkins
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Nozomi Ando
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
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18
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Ye W, Qian T, Liu H, Luo R, Chen HF. Allosteric Autoinhibition Pathway in Transcription Factor ERG: Dynamics Network and Mutant Experimental Evaluations. J Chem Inf Model 2017; 57:1153-1165. [PMID: 28425706 DOI: 10.1021/acs.jcim.7b00073] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Allosteric autoinhibition exists in many transcription factors. The ERG proteins exhibit autoinhibition on DNA binding by the C-terminal and N-terminal inhibitory domains (CID and NID). However, the autoinhibition mechanism and allosteric pathway of ERG are unknown. In this study we intend to elucidate the residue-level allosteric mechanism and pathway via a combined approach of computational and experimental analyses. Specifically computational residue-level fluctuation correlation data was analyzed to reveal detailed dynamics signatures in the allosteric autoinhibition process. A hypothesis of "NID/CID binding induced allostery" is proposed to link similar structures and different protein functions, which is subsequently validated by perturbation and mutation analyses in both computation and experiment. Two possible allosteric autoinhibition pathways of L286-L382-A379-G377-I360-Y355-R353 and L286-L382-A379-G377-I360-Y355- A351-K347-R350 were identified computationally and were confirmed by the computational and experimental mutations. Specifically we identified two mutation sites on the allosteric inhibition pathways, L286P/Q383P (NID/CID binding site) and I360G (pathway junction), which completely restore the wild type DNA binding affinity. These results suggest that the putative protein structure-function relationship may be augmented with a general relationship of protein "structure/fluctuation-correlation/function" for more thorough analyses of protein functions.
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Affiliation(s)
- Wei Ye
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai, 200240, China
| | - Tianle Qian
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai, 200240, China
| | - Hao Liu
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai, 200240, China
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical Engineering and Materials Science, and Biomedical Engineering, University of California , Irvine, California 92697-3900, United States
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai, 200240, China.,Shanghai Center for Bioinformation Technology , 1278 Keyuan Road, Shanghai, 200235, China
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19
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Leandro J, Saraste J, Leandro P, Flatmark T. PKU mutation p.G46S prevents the stereospecific binding of l-phenylalanine to the dimer of human phenylalanine hydroxylase regulatory domain. FEBS Open Bio 2017; 7:195-203. [PMID: 28174686 PMCID: PMC5292662 DOI: 10.1002/2211-5463.12175] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 12/01/2016] [Accepted: 12/03/2016] [Indexed: 11/23/2022] Open
Abstract
Mammalian phenylalanine hydroxylase (PAH) has a potential allosteric regulatory binding site for l‐phenylalanine (l‐Phe), in addition to its catalytic site. This arrangement is supported by a crystal structure of a homodimeric truncated form of the regulatory domain of human PAH (hPAH‐RD1–118/19–118) [Patel D et al. (2016) Sci Rep doi: 10.1038/srep23748]. In this study, a fusion protein of the domain (MBP‐(pepXa)‐hPAH‐RD1–120) was overexpressed and recovered in a metastable and soluble state, which allowed the isolation of a dimeric and a monomeric fusion protein. When cleaved from MBP, hPAH‐RD forms aggregates which are stereospecifically inhibited by l‐Phe (> 95%) at low physiological concentrations. Aggregation of the cleaved dimer of the mutant form hPAH‐G46S‐RD was not inhibited by l‐Phe, which is compatible with structurally/conformationally changed βαββαβ ACT domain folds in the mutant.
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Affiliation(s)
- João Leandro
- Department of Biomedicine University of Bergen Norway; Metabolism and Genetics Group Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL) Faculty of Pharmacy University of Lisbon Portugal
| | | | - Paula Leandro
- Metabolism and Genetics Group Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL) Faculty of Pharmacy University of Lisbon Portugal
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20
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Gai Z, Wang Q, Yang C, Wang L, Deng W, Wu G. Structural mechanism for the arginine sensing and regulation of CASTOR1 in the mTORC1 signaling pathway. Cell Discov 2016; 2:16051. [PMID: 28066558 PMCID: PMC5187391 DOI: 10.1038/celldisc.2016.51] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/12/2016] [Indexed: 12/12/2022] Open
Abstract
The mTOR complex I (mTORC1) signaling pathway controls many metabolic processes and is regulated by amino acid signals, especially arginine. CASTOR1 has been identified as the cytosolic arginine sensor for the mTORC1 pathway, but the molecular mechanism of how it senses arginine is elusive. Here, by determining the crystal structure of human CASTOR1 in complex with arginine, we found that an exquisitely tailored pocket, carved between the NTD and the CTD domains of CASTOR1, is employed to recognize arginine. Mutation of critical residues in this pocket abolished or diminished arginine binding. By comparison with structurally similar aspartate kinases, a surface patch of CASTOR1-NTD on the opposite side of the arginine-binding site was identified to mediate direct physical interaction with its downstream effector GATOR2, via GATOR2 subunit Mios. Mutation of this surface patch disrupted CASTOR1’s recognition and inhibition of GATOR2, revealed by in vitro pull-down assay. Normal mode (NM) analysis revealed an ‘open’-to-‘closed’ conformational change for CASTOR1, which is correlated to the switching between the exposing and concealing of its GATOR2-binding residues, and is most likely related to arginine binding. Interestingly, the GATOR2-binding sites on the two protomers of CASTOR1 dimer face the same direction, which prompted us to propose a model for how dimerization of CASTOR1 relieves the inhibition of GATOR1 by GATOR2. Our study thus provides a thorough analysis on how CASTOR1 recognizes arginine, and describes a possible mechanism of how arginine binding induces the inter-domain movement of CASTOR1 to affect its association with GATOR2.
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Affiliation(s)
- Zhongchao Gai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University , Shanghai, China
| | - Qian Wang
- National Center for Protein Science Shanghai , Shanghai, China
| | - Can Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University , Shanghai, China
| | - Lei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University , Shanghai, China
| | - Wei Deng
- National Center for Protein Science Shanghai , Shanghai, China
| | - Geng Wu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University , Shanghai, China
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21
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Tidemand KD, Christensen HEM, Hoeck N, Harris P, Boesen J, Peters GH. Stabilization of tryptophan hydroxylase 2 by l-phenylalanine-induced dimerization. FEBS Open Bio 2016; 6:987-999. [PMID: 27761358 PMCID: PMC5055035 DOI: 10.1002/2211-5463.12100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 06/20/2016] [Accepted: 06/29/2016] [Indexed: 12/12/2022] Open
Abstract
Tryptophan hydroxylase 2 (TPH2) catalyses the initial and rate‐limiting step in the biosynthesis of serotonin, which is associated with a variety of disorders such as depression, obsessive compulsive disorder, and schizophrenia. Full‐length TPH2 is poorly characterized due to low purification quantities caused by its inherent instability. Three truncated variants of human TPH2 (rchTPH2; regulatory and catalytic domain, NΔ47‐rchTPH2; truncation of 47 residues in the N terminus of rchTPH2, and chTPH2; catalytic domain) were expressed, purified, and examined for changes in transition temperature, inactivation rate, and oligomeric state. chTPH2 displayed 14‐ and 11‐fold higher half‐lives compared to rchTPH2 and NΔ47‐rchTPH2, respectively. Differential scanning calorimetry experiments demonstrated that this is caused by premature unfolding of the less stable regulatory domain. By differential scanning fluorimetry, the unfolding transitions of rchTPH2 and NΔ47‐rchTPH2 are found to shift from polyphasic to apparent two‐state by the addition of l‐Trp or l‐Phe. Analytical gel filtration revealed that rchTPH2 and NΔ47‐rchTPH2 reside in a monomer–dimer equilibrium which is significantly shifted toward dimer in the presence of l‐Phe. The dimerizing effect induced by l‐Phe is accompanied by a stabilizing effect, which resulted in a threefold increase in half‐lives of rchTPH2 and NΔ47‐rchTPH2. Addition of l‐Phe to the purification buffer significantly increases the purification yields, which will facilitate characterization of hTPH2.
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Affiliation(s)
- Kasper D Tidemand
- Department of Chemistry Technical University of Denmark Kongens Lyngby Denmark
| | | | - Niclas Hoeck
- Department of Chemistry Technical University of Denmark Kongens Lyngby Denmark
| | - Pernille Harris
- Department of Chemistry Technical University of Denmark Kongens Lyngby Denmark
| | - Jane Boesen
- Department of Chemistry Technical University of Denmark Kongens Lyngby Denmark
| | - Günther H Peters
- Department of Chemistry Technical University of Denmark Kongens Lyngby Denmark
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22
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Koshiba S, Motoike I, Kojima K, Hasegawa T, Shirota M, Saito T, Saigusa D, Danjoh I, Katsuoka F, Ogishima S, Kawai Y, Yamaguchi-Kabata Y, Sakurai M, Hirano S, Nakata J, Motohashi H, Hozawa A, Kuriyama S, Minegishi N, Nagasaki M, Takai-Igarashi T, Fuse N, Kiyomoto H, Sugawara J, Suzuki Y, Kure S, Yaegashi N, Tanabe O, Kinoshita K, Yasuda J, Yamamoto M. The structural origin of metabolic quantitative diversity. Sci Rep 2016; 6:31463. [PMID: 27528366 PMCID: PMC4985752 DOI: 10.1038/srep31463] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/18/2016] [Indexed: 12/21/2022] Open
Abstract
Relationship between structural variants of enzymes and metabolic phenotypes in human population was investigated based on the association study of metabolite quantitative traits with whole genome sequence data for 512 individuals from a population cohort. We identified five significant associations between metabolites and non-synonymous variants. Four of these non-synonymous variants are located in enzymes involved in metabolic disorders, and structural analyses of these moderate non-synonymous variants demonstrate that they are located in peripheral regions of the catalytic sites or related regulatory domains. In contrast, two individuals with larger changes of metabolite levels were also identified, and these individuals retained rare variants, which caused non-synonymous variants located near the catalytic site. These results are the first demonstrations that variant frequency, structural location, and effect for phenotype correlate with each other in human population, and imply that metabolic individuality and susceptibility for diseases may be elicited from the moderate variants and much more deleterious but rare variants.
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Affiliation(s)
- Seizo Koshiba
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Ikuko Motoike
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8579 Japan
| | - Kaname Kojima
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Takanori Hasegawa
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Matsuyuki Shirota
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Tomo Saito
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Daisuke Saigusa
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Inaho Danjoh
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Fumiki Katsuoka
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Soichi Ogishima
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Yosuke Kawai
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Yumi Yamaguchi-Kabata
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Miyuki Sakurai
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Sachiko Hirano
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Junichi Nakata
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Hozumi Motohashi
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Institute of Development, Aging and Cancer, Tohoku University, 4-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Masao Nagasaki
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8579 Japan
| | - Takako Takai-Igarashi
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Hideyasu Kiyomoto
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Junichi Sugawara
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Yoichi Suzuki
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Shigeo Kure
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Nobuo Yaegashi
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Osamu Tanabe
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8579 Japan.,Institute of Development, Aging and Cancer, Tohoku University, 4-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Jun Yasuda
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
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23
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Bezem MT, Baumann A, Skjærven L, Meyer R, Kursula P, Martinez A, Flydal MI. Stable preparations of tyrosine hydroxylase provide the solution structure of the full-length enzyme. Sci Rep 2016; 6:30390. [PMID: 27462005 DOI: 10.1038/srep30390] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/30/2016] [Indexed: 01/22/2023] Open
Abstract
Tyrosine hydroxylase (TH) catalyzes the rate-limiting step in the biosynthesis of catecholamine neurotransmitters. TH is a highly complex enzyme at mechanistic, structural, and regulatory levels, and the preparation of kinetically and conformationally stable enzyme for structural characterization has been challenging. Here, we report on improved protocols for purification of recombinant human TH isoform 1 (TH1), which provide large amounts of pure, stable, active TH1 with an intact N-terminus. TH1 purified through fusion with a His-tagged maltose-binding protein on amylose resin was representative of the iron-bound functional enzyme, showing high activity and stabilization by the natural feedback inhibitor dopamine. TH1 purified through fusion with a His-tagged ZZ domain on TALON is remarkably stable, as it was partially inhibited by resin-derived cobalt. This more stable enzyme preparation provided high-quality small-angle X-ray scattering (SAXS) data and reliable structural models of full-length tetrameric TH1. The SAXS-derived model reveals an elongated conformation (Dmax = 20 nm) for TH1, different arrangement of the catalytic domains compared with the crystal structure of truncated forms, and an N-terminal region with an unstructured tail that hosts the phosphorylation sites and a separated Ala-rich helical motif that may have a role in regulation of TH by interacting with binding partners.
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24
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Neira JL, Hornos F, Bacarizo J, Cámara-Artigás A, Gómez J. The Monomeric Species of the Regulatory Domain of Tyrosine Hydroxylase Has a Low Conformational Stability. Biochemistry 2016; 55:3418-31. [PMID: 27224548 DOI: 10.1021/acs.biochem.6b00135] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tyrosine hydroxylase (TyrH) catalyzes the hydroxylation of tyrosine to form 3,4-dihydroxyphenylalanine, the first step in the synthesis of catecholamine neurotransmitters. The protein contains a 159-residue regulatory domain (RD) at its N-terminus that forms dimers in solution; the N-terminal region of RDTyrH (residues 1-71) is absent in the solution structure of the domain. We have characterized the conformational stability of two species of RDTyrH (one containing the N-terminal region and another lacking the first 64 residues) to clarify how that N-terminal region modulates the conformational stability of RD. Under the conditions used in this study, the RD species lacking the first 64 residues is a monomer at pH 7.0, with a small conformational stability at 25 °C (4.7 ± 0.8 kcal mol(-1)). On the other hand, the entire RDTyrH is dimeric at physiological pH, with an estimated dissociation constant of 1.6 μM, as determined by zonal gel filtration chromatography; dimer dissociation was spectroscopically silent to circular dichroism but not to fluoresecence. Both RD species were disordered below physiological pH, but the acquisition of secondary native-like structure occurs at pHs lower than those measured for the attainment of tertiary native- and compactness-like arrangements.
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Affiliation(s)
- José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández , 03202 Elche (Alicante), Spain.,Biocomputation and Complex Systems Physics Institute , 50009 Zaragoza, Spain
| | - Felipe Hornos
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández , 03202 Elche (Alicante), Spain
| | - Julio Bacarizo
- Department of Physical Chemistry, Biochemistry and Inorganic Chemistry, University of Almería , Agrifood Campus of International Excellence (ceiA3), Almería, Spain
| | - Ana Cámara-Artigás
- Department of Physical Chemistry, Biochemistry and Inorganic Chemistry, University of Almería , Agrifood Campus of International Excellence (ceiA3), Almería, Spain
| | - Javier Gómez
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández , 03202 Elche (Alicante), Spain
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25
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Zhang S, Hinck CS, Fitzpatrick PF. The regulatory domain of human tryptophan hydroxylase 1 forms a stable dimer. Biochem Biophys Res Commun 2016; 476:457-61. [PMID: 27255998 DOI: 10.1016/j.bbrc.2016.05.144] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 05/27/2016] [Indexed: 02/06/2023]
Abstract
The three eukaryotic aromatic amino acid hydroxylases phenylalanine hydroxylase, tyrosine hydroxylase, and tryptophan hydroxylase have essentially identical catalytic domains and discrete regulatory domains. The regulatory domains of phenylalanine hydroxylase form ACT domain dimers when phenylalanine is bound to an allosteric site. In contrast the regulatory domains of tyrosine hydroxylase form a stable ACT dimer that does not bind the amino acid substrate. The regulatory domain of isoform 1 of human tryptophan hydroxylase was expressed and purified; mutagenesis of Cys64 was required to prevent formation of disulfide-linked dimers. The resulting protein behaved as a dimer upon gel filtration and in analytical ultracentrifugation. The sw value of the protein was unchanged from 2.7 to 35 μM, a concentration range over which the regulatory domain of phenylalanine hydroxylase forms both monomers and dimers, consistent with the regulatory domain of tryptophan hydroxylase 1 forming a stable dimer stable that does not undergo a monomer-dimer equilibrium. Addition of phenylalanine, a good substrate for the enzyme, had no effect on the sw value, consistent with there being no allosteric site for the amino acid substrate.
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26
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Meisburger SP, Taylor AB, Khan CA, Zhang S, Fitzpatrick PF, Ando N. Domain Movements upon Activation of Phenylalanine Hydroxylase Characterized by Crystallography and Chromatography-Coupled Small-Angle X-ray Scattering. J Am Chem Soc 2016; 138:6506-16. [PMID: 27145334 PMCID: PMC4896396 DOI: 10.1021/jacs.6b01563] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mammalian phenylalanine hydroxylase (PheH) is an allosteric enzyme that catalyzes the first step in the catabolism of the amino acid phenylalanine. Following allosteric activation by high phenylalanine levels, the enzyme catalyzes the pterin-dependent conversion of phenylalanine to tyrosine. Inability to control elevated phenylalanine levels in the blood leads to increased risk of mental disabilities commonly associated with the inherited metabolic disorder, phenylketonuria. Although extensively studied, structural changes associated with allosteric activation in mammalian PheH have been elusive. Here, we examine the complex allosteric mechanisms of rat PheH using X-ray crystallography, isothermal titration calorimetry (ITC), and small-angle X-ray scattering (SAXS). We describe crystal structures of the preactivated state of the PheH tetramer depicting the regulatory domains docked against the catalytic domains and preventing substrate binding. Using SAXS, we further describe the domain movements involved in allosteric activation of PheH in solution and present the first demonstration of chromatography-coupled SAXS with Evolving Factor Analysis (EFA), a powerful method for separating scattering components in a model-independent way. Together, these results support a model for allostery in PheH in which phenylalanine stabilizes the dimerization of the regulatory domains and exposes the active site for substrate binding and other structural changes needed for activity.
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Affiliation(s)
- Steve P. Meisburger
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Alexander B. Taylor
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229, USA
| | - Crystal A. Khan
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229, USA
| | - Shengnan Zhang
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229, USA
| | - Paul F. Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229, USA
| | - Nozomi Ando
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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27
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Patel D, Kopec J, Fitzpatrick F, McCorvie TJ, Yue WW. Structural basis for ligand-dependent dimerization of phenylalanine hydroxylase regulatory domain. Sci Rep 2016; 6:23748. [PMID: 27049649 PMCID: PMC4822156 DOI: 10.1038/srep23748] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 03/08/2016] [Indexed: 02/01/2023] Open
Abstract
The multi-domain enzyme phenylalanine hydroxylase (PAH) catalyzes the hydroxylation of dietary I-phenylalanine (Phe) to I-tyrosine. Inherited mutations that result in PAH enzyme deficiency are the genetic cause of the autosomal recessive disorder phenylketonuria. Phe is the substrate for the PAH active site, but also an allosteric ligand that increases enzyme activity. Phe has been proposed to bind, in addition to the catalytic domain, a site at the PAH N-terminal regulatory domain (PAH-RD), to activate the enzyme via an unclear mechanism. Here we report the crystal structure of human PAH-RD bound with Phe at 1.8 Å resolution, revealing a homodimer of ACT folds with Phe bound at the dimer interface. This work delivers the structural evidence to support previous solution studies that a binding site exists in the RD for Phe, and that Phe binding results in dimerization of PAH-RD. Consistent with our structural observation, a disease-associated PAH mutant impaired in Phe binding disrupts the monomer:dimer equilibrium of PAH-RD. Our data therefore support an emerging model of PAH allosteric regulation, whereby Phe binds to PAH-RD and mediates the dimerization of regulatory modules that would bring about conformational changes to activate the enzyme.
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Affiliation(s)
- Dipali Patel
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, UK OX3 7DQ
| | - Jolanta Kopec
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, UK OX3 7DQ
| | - Fiona Fitzpatrick
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, UK OX3 7DQ
| | - Thomas J McCorvie
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, UK OX3 7DQ
| | - Wyatt W Yue
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, UK OX3 7DQ
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28
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Chantranupong L, Scaria SM, Saxton RA, Gygi MP, Shen K, Wyant GA, Wang T, Harper JW, Gygi SP, Sabatini DM. The CASTOR Proteins Are Arginine Sensors for the mTORC1 Pathway. Cell 2016; 165:153-164. [PMID: 26972053 DOI: 10.1016/j.cell.2016.02.035] [Citation(s) in RCA: 541] [Impact Index Per Article: 67.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/31/2016] [Accepted: 02/17/2016] [Indexed: 12/12/2022]
Abstract
Amino acids signal to the mTOR complex I (mTORC1) growth pathway through the Rag GTPases. Multiple distinct complexes regulate the Rags, including GATOR1, a GTPase activating protein (GAP), and GATOR2, a positive regulator of unknown molecular function. Arginine stimulation of cells activates mTORC1, but how it is sensed is not well understood. Recently, SLC38A9 was identified as a putative lysosomal arginine sensor required for arginine to activate mTORC1 but how arginine deprivation represses mTORC1 is unknown. Here, we show that CASTOR1, a previously uncharacterized protein, interacts with GATOR2 and is required for arginine deprivation to inhibit mTORC1. CASTOR1 homodimerizes and can also heterodimerize with the related protein, CASTOR2. Arginine disrupts the CASTOR1-GATOR2 complex by binding to CASTOR1 with a dissociation constant of ~30 μM, and its arginine-binding capacity is required for arginine to activate mTORC1 in cells. Collectively, these results establish CASTOR1 as an arginine sensor for the mTORC1 pathway.
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Affiliation(s)
- Lynne Chantranupong
- Department of Biology, Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge MA 02142, USA
| | - Sonia M Scaria
- Department of Biology, Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge MA 02142, USA
| | - Robert A Saxton
- Department of Biology, Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge MA 02142, USA
| | - Melanie P Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Kuang Shen
- Department of Biology, Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge MA 02142, USA
| | - Gregory A Wyant
- Department of Biology, Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge MA 02142, USA
| | - Tim Wang
- Department of Biology, Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge MA 02142, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - David M Sabatini
- Department of Biology, Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge MA 02142, USA.
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29
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Nakabayashi M, Shibata N, Ishido-Nakai E, Kanagawa M, Iio Y, Komori H, Ueda Y, Nakagawa N, Kuramitsu S, Higuchi Y. Crystal structure of a hypothetical protein, TTHA0829 from Thermus thermophilus HB8, composed of cystathionine-β-synthase (CBS) and aspartate-kinase chorismate-mutase tyrA (ACT) domains. Extremophiles 2016; 20:275-82. [DOI: 10.1007/s00792-016-0817-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 02/14/2016] [Indexed: 01/01/2023]
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30
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Arturo EC, Gupta K, Héroux A, Stith L, Cross PJ, Parker EJ, Loll PJ, Jaffe EK. First structure of full-length mammalian phenylalanine hydroxylase reveals the architecture of an autoinhibited tetramer. Proc Natl Acad Sci U S A 2016; 113:2394-9. [PMID: 26884182 DOI: 10.1073/pnas.1516967113] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Improved understanding of the relationship among structure, dynamics, and function for the enzyme phenylalanine hydroxylase (PAH) can lead to needed new therapies for phenylketonuria, the most common inborn error of amino acid metabolism. PAH is a multidomain homo-multimeric protein whose conformation and multimerization properties respond to allosteric activation by the substrate phenylalanine (Phe); the allosteric regulation is necessary to maintain Phe below neurotoxic levels. A recently introduced model for allosteric regulation of PAH involves major domain motions and architecturally distinct PAH tetramers [Jaffe EK, Stith L, Lawrence SH, Andrake M, Dunbrack RL, Jr (2013) Arch Biochem Biophys 530(2):73-82]. Herein, we present, to our knowledge, the first X-ray crystal structure for a full-length mammalian (rat) PAH in an autoinhibited conformation. Chromatographic isolation of a monodisperse tetrameric PAH, in the absence of Phe, facilitated determination of the 2.9 Å crystal structure. The structure of full-length PAH supersedes a composite homology model that had been used extensively to rationalize phenylketonuria genotype-phenotype relationships. Small-angle X-ray scattering (SAXS) confirms that this tetramer, which dominates in the absence of Phe, is different from a Phe-stabilized allosterically activated PAH tetramer. The lack of structural detail for activated PAH remains a barrier to complete understanding of phenylketonuria genotype-phenotype relationships. Nevertheless, the use of SAXS and X-ray crystallography together to inspect PAH structure provides, to our knowledge, the first complete view of the enzyme in a tetrameric form that was not possible with prior partial crystal structures, and facilitates interpretation of a wealth of biochemical and structural data that was hitherto impossible to evaluate.
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31
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Zhang S, Fitzpatrick PF. Identification of the Allosteric Site for Phenylalanine in Rat Phenylalanine Hydroxylase. J Biol Chem 2016; 291:7418-25. [PMID: 26823465 DOI: 10.1074/jbc.m115.709998] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Indexed: 11/06/2022] Open
Abstract
Liver phenylalanine hydroxylase (PheH) is an allosteric enzyme that requires activation by phenylalanine for full activity. The location of the allosteric site for phenylalanine has not been established. NMR spectroscopy of the isolated regulatory domain (RDPheH(25-117) is the regulatory domain of PheH lacking residues 1-24) of the rat enzyme in the presence of phenylalanine is consistent with formation of a side-by-side ACT dimer. Six residues in RDPheH(25-117) were identified as being in the phenylalanine-binding site on the basis of intermolecular NOEs between unlabeled phenylalanine and isotopically labeled protein. The location of these residues is consistent with two allosteric sites per dimer, with each site containing residues from both monomers. Site-specific variants of five of the residues (E44Q, A47G, L48V, L62V, and H64N) decreased the affinity of RDPheH(25-117) for phenylalanine based on the ability to stabilize the dimer. Incorporation of the A47G, L48V, and H64N mutations into the intact protein increased the concentration of phenylalanine required for activation. The results identify the location of the allosteric site as the interface of the regulatory domain dimer formed in activated PheH.
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Affiliation(s)
- Shengnan Zhang
- From the Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229
| | - Paul F Fitzpatrick
- From the Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229
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32
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Aubi O, Flydal MI, Zheng H, Skjærven L, Rekand I, Leiros HKS, Haug BE, Cianciotto NP, Martinez A, Underhaug J. Discovery of a Specific Inhibitor of Pyomelanin Synthesis in Legionella pneumophila. J Med Chem 2015; 58:8402-12. [DOI: 10.1021/acs.jmedchem.5b01589] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Oscar Aubi
- Department
of Biomedicine, University of Bergen, Bergen, Norway
| | - Marte I. Flydal
- Department
of Biomedicine, University of Bergen, Bergen, Norway
| | - Huaixin Zheng
- Department
of Microbiology and Immunology, Northwestern University Medical School, Chicago, Illinois 60611, United States
| | - Lars Skjærven
- Department
of Biomedicine, University of Bergen, Bergen, Norway
| | - Illimar Rekand
- Department
of Chemistry and Centre for Pharmacy, University of Bergen, Bergen, Norway
| | - Hanna-Kirsti S. Leiros
- The
Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway, Tromsø, Norway
| | - Bengt Erik Haug
- Department
of Chemistry and Centre for Pharmacy, University of Bergen, Bergen, Norway
| | - Nicholas P. Cianciotto
- Department
of Microbiology and Immunology, Northwestern University Medical School, Chicago, Illinois 60611, United States
| | - Aurora Martinez
- Department
of Biomedicine, University of Bergen, Bergen, Norway
| | - Jarl Underhaug
- Department
of Biomedicine, University of Bergen, Bergen, Norway
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33
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Carluccio C, Fraternali F, Salvatore F, Fornili A, Zagari A. Towards the identification of the allosteric Phe-binding site in phenylalanine hydroxylase. J Biomol Struct Dyn 2015; 34:497-507. [PMID: 26479306 DOI: 10.1080/07391102.2015.1052016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The enzyme phenylalanine hydroxylase (PAH) is defective in the inherited disorder phenylketonuria. PAH, a tetrameric enzyme, is highly regulated and displays positive cooperativity for its substrate, Phe. Whether Phe binds to an allosteric site is a matter of debate, despite several studies worldwide. To address this issue, we generated a dimeric model for Phe-PAH interactions, by performing molecular docking combined with molecular dynamics simulations on human and rat wild-type sequences and also on a human G46S mutant. Our results suggest that the allosteric Phe-binding site lies at the dimeric interface between the regulatory and the catalytic domains of two adjacent subunits. The structural and dynamical features of the site were characterized in depth and described. Interestingly, our findings provide evidence for lower allosteric Phe-binding ability of the G46S mutant than the human wild-type enzyme. This also explains the disease-causing nature of this mutant.
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Affiliation(s)
- Carla Carluccio
- a CEINGE-Biotecnologie Avanzate , S.c. a r.l., Napoli , Italy
| | - Franca Fraternali
- b Randall Division of Cell and Molecular Biophysics , King's College London , London , UK
| | - Francesco Salvatore
- a CEINGE-Biotecnologie Avanzate , S.c. a r.l., Napoli , Italy.,c SDN-Istituto di Ricerca Diagnostica e Nucleare , Napoli , Italy
| | - Arianna Fornili
- b Randall Division of Cell and Molecular Biophysics , King's College London , London , UK
| | - Adriana Zagari
- a CEINGE-Biotecnologie Avanzate , S.c. a r.l., Napoli , Italy
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34
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Zhang S, Hinck AP, Fitzpatrick PF. The Amino Acid Specificity for Activation of Phenylalanine Hydroxylase Matches the Specificity for Stabilization of Regulatory Domain Dimers. Biochemistry 2015; 54:5167-74. [PMID: 26252467 PMCID: PMC4551101 DOI: 10.1021/acs.biochem.5b00616] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Liver
phenylalanine hydroxylase is allosterically activated by
phenylalanine. The structural changes that accompany activation have
not been identified, but recent studies of the effects of phenylalanine
on the isolated regulatory domain of the enzyme support a model in
which phenylalanine binding promotes regulatory domain dimerization.
Such a model predicts that compounds that stabilize the regulatory
domain dimer will also activate the enzyme. Nuclear magnetic resonance
spectroscopy and analytical ultracentrifugation were used to determine
the ability of different amino acids and phenylalanine analogues to
stabilize the regulatory domain dimer. The abilities of these compounds
to activate the enzyme were analyzed by measuring their effects on
the fluorescence change that accompanies activation and on the activity
directly. At concentrations of 10–50 mM, d-phenylalanine, l-methionine, l-norleucine, and (S)-2-amino-3-phenyl-1-propanol were able to activate the enzyme to
the same extent as 1 mM l-phenylalanine. Lower levels of
activation were seen with l-4-aminophenylalanine, l-leucine, l-isoleucine, and 3-phenylpropionate. The ability
of these compounds to stabilize the regulatory domain dimer agreed
with their ability to activate the enzyme. These results support a
model in which allosteric activation of phenylalanine hydroxylase
is linked to dimerization of regulatory domains.
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Affiliation(s)
- Shengnan Zhang
- Department of Biochemistry, University of Texas Health Science Center , San Antonio, Texas 78229, United States
| | - Andrew P Hinck
- Department of Biochemistry, University of Texas Health Science Center , San Antonio, Texas 78229, United States
| | - Paul F Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center , San Antonio, Texas 78229, United States
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35
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Fitzpatrick PF. Structural insights into the regulation of aromatic amino acid hydroxylation. Curr Opin Struct Biol 2015; 35:1-6. [PMID: 26241318 DOI: 10.1016/j.sbi.2015.07.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 06/30/2015] [Accepted: 07/15/2015] [Indexed: 11/30/2022]
Abstract
The aromatic amino acid hydroxylases phenylalanine hydroxylase, tyrosine hydroxylase, and tryptophan hydroxylase are homotetramers, with each subunit containing a homologous catalytic domain and a divergent regulatory domain. The solution structure of the regulatory domain of tyrosine hydroxylase establishes that it contains a core ACT domain similar to that in phenylalanine hydroxylase. The isolated regulatory domain of tyrosine hydroxylase forms a stable dimer, while that of phenylalanine hydroxylase undergoes a monomer-dimer equilibrium, with phenylalanine stabilizing the dimer. These solution properties are consistent with the regulatory mechanisms of the two enzymes, in that phenylalanine hydroxylase is activated by phenylalanine binding to an allosteric site, while tyrosine hydroxylase is regulated by binding of catecholamines in the active site.
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Affiliation(s)
- Paul F Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, United States.
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36
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Réblová K, Kulhánek P, Fajkusová L. Computational study of missense mutations in phenylalanine hydroxylase. J Mol Model 2015; 21:70. [PMID: 25750018 DOI: 10.1007/s00894-015-2620-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 02/15/2015] [Indexed: 10/23/2022]
Abstract
Hyperphenylalaninemia (HPA) is one of the most common metabolic disorders. HPA, which is transmitted by an autosomal recessive mode of inheritance, is caused by mutations of the phenylalanine hydroxylase gene. Most mutations are missense and lead to reduced protein stability and/or impaired catalytic function. The impact of such mutations varies, ranging from classical phenylketonuria (PKU), mild PKU, to non-PKU HPA phenotypes. Despite the fact that HPA is a monogenic disease, clinical data show that one PKU genotype can be associated with more in vivo phenotypes, which indicates the role of other (still unknown) factors. To better understand the phenotype-genotype relationships, we analyzed computationally the impact of missense mutations in homozygotes stored in the BIOPKU database. A total of 34 selected homozygous genotypes was divided into two main groups according to their phenotypes: (A) genotypes leading to non-PKU HPA or combined phenotype non-PKU HPA/mild PKU and (B) genotypes leading to classical PKU, mild PKU or combined phenotype mild PKU/classical PKU. Combining in silico analysis and molecular dynamics simulations (in total 3 μs) we described the structural impact of the mutations, which allowed us to separate 32 out of 34 mutations between groups A and B. Testing the simulation conditions revealed that the outcome of mutant simulations can be modulated by the ionic strength. We also employed programs SNPs3D, Polyphen-2, and SIFT but based on the predictions performed we were not able to discriminate mutations with mild and severe PKU phenotypes.
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Affiliation(s)
- Kamila Réblová
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic,
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37
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Roberts KM, Khan CA, Hinck CS, Fitzpatrick PF. Activation of phenylalanine hydroxylase by phenylalanine does not require binding in the active site. Biochemistry 2014; 53:7846-53. [PMID: 25453233 PMCID: PMC4270383 DOI: 10.1021/bi501183x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
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Phenylalanine
hydroxylase (PheH), a liver enzyme that catalyzes
the hydroxylation of excess phenylalanine in the diet to tyrosine,
is activated by phenylalanine. The lack of activity at low levels
of phenylalanine has been attributed to the N-terminus of the protein’s
regulatory domain acting as an inhibitory peptide by blocking substrate
access to the active site. The location of the site at which phenylalanine
binds to activate the enzyme is unknown, and both the active site
in the catalytic domain and a separate site in the N-terminal regulatory
domain have been proposed. Binding of catecholamines to the active-site
iron was used to probe the accessibility of the active site. Removal
of the regulatory domain increases the rate constants for association
of several catecholamines with the wild-type enzyme by ∼2-fold.
Binding of phenylalanine in the active site is effectively abolished
by mutating the active-site residue Arg270 to lysine. The kcat/Kphe value is
down 104 for the mutant enzyme, and the Km value for phenylalanine for the mutant enzyme is >0.5
M. Incubation of the R270K enzyme with phenylalanine also results
in a 2-fold increase in the rate constants for catecholamine binding.
The change in the tryptophan fluorescence emission spectrum seen in
the wild-type enzyme upon activation by phenylalanine is also seen
with the R270K mutant enzyme in the presence of phenylalanine. Both
results establish that activation of PheH by phenylalanine does not
require binding of the amino acid in the active site. This is consistent
with a separate allosteric site, likely in the regulatory domain.
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Affiliation(s)
- Kenneth M Roberts
- Department of Biochemistry, University of Texas Health Science Center , San Antonio, Texas 78229, United States
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38
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Lang EJM, Cross PJ, Mittelstädt G, Jameson GB, Parker EJ. Allosteric ACTion: the varied ACT domains regulating enzymes of amino-acid metabolism. Curr Opin Struct Biol 2014; 29:102-11. [PMID: 25543886 DOI: 10.1016/j.sbi.2014.10.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 10/28/2014] [Indexed: 11/29/2022]
Abstract
Allosteric regulation of enzyme activity plays important metabolic roles. Here we review the allostery of enzymes of amino-acid metabolism conferred by a discrete domain known as the ACT domain. This domain of 60-70 residues has a βαββαβ topology leading to a four-stranded β4β1β3β2 antiparallel sheet with two antiparallel helices on one face. Extensive sequence variation requires a combined sequence/structure/function analysis for identification of the ACT domain. Common features include highly varied modes of self-association of ACT domains, ligand binding at domain interfaces, and transmittal of allosteric signals through conformational changes and/or the manipulation of quaternary equilibria. A recent example illustrates the relatively facile adoption of this versatile module of allostery by gene fusion.
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Affiliation(s)
- Eric J M Lang
- Maurice Wilkins Centre, Biomolecular Interaction Centre, Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - Penelope J Cross
- Maurice Wilkins Centre, Biomolecular Interaction Centre, Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - Gerd Mittelstädt
- Maurice Wilkins Centre, Biomolecular Interaction Centre, Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - Geoffrey B Jameson
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Emily J Parker
- Maurice Wilkins Centre, Biomolecular Interaction Centre, Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
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39
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Abstract
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Analytical ultracentrifugation has
been used to analyze the oligomeric
structure of the isolated regulatory domain of phenylalanine hydroxylase.
The protein exhibits a monomer–dimer equilibrium with a dissociation
constant of ∼46 μM; this value is unaffected by the removal
of the 24 N-terminal residues or by phosphorylation of Ser16. In contrast,
phenylalanine binding (Kd = 8 μM)
stabilizes the dimer. These results suggest that dimerization of the
regulatory domain of phenylalanine hydroxylase is linked to allosteric
activation of the enzyme.
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Affiliation(s)
- Shengnan Zhang
- Department of Biochemistry, University of Texas Health Science Center at San Antonio , San Antonio, Texas 78229, United States
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40
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Kobayashi K, Katz A, Rajkovic A, Ishii R, Branson OE, Freitas MA, Ishitani R, Ibba M, Nureki O. The non-canonical hydroxylase structure of YfcM reveals a metal ion-coordination motif required for EF-P hydroxylation. Nucleic Acids Res 2014; 42:12295-305. [PMID: 25274739 PMCID: PMC4231759 DOI: 10.1093/nar/gku898] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
EF-P is a bacterial tRNA-mimic protein, which accelerates the ribosome-catalyzed polymerization of poly-prolines. In Escherichia coli, EF-P is post-translationally modified on a conserved lysine residue. The post-translational modification is performed in a two-step reaction involving the addition of a β-lysine moiety and the subsequent hydroxylation, catalyzed by PoxA and YfcM, respectively. The β-lysine moiety was previously shown to enhance the rate of poly-proline synthesis, but the role of the hydroxylation is poorly understood. We solved the crystal structure of YfcM and performed functional analyses to determine the hydroxylation mechanism. In addition, YfcM appears to be structurally distinct from any other hydroxylase structures reported so far. The structure of YfcM is similar to that of the ribonuclease YbeY, even though they do not share sequence homology. Furthermore, YfcM has a metal ion-coordinating motif, similar to YbeY. The metal ion-coordinating motif of YfcM resembles a 2-His-1-carboxylate motif, which coordinates an Fe(II) ion and forms the catalytic site of non-heme iron enzymes. Our findings showed that the metal ion-coordinating motif of YfcM plays an essential role in the hydroxylation of the β-lysylated lysine residue of EF-P. Taken together, our results suggested the potential catalytic mechanism of hydroxylation by YfcM.
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Affiliation(s)
- Kan Kobayashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan Global Research Cluster, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Assaf Katz
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Andrei Rajkovic
- Molecular, Cell, and Developmental Biology Program, Ohio State University, Columbus, OH 43210, USA
| | - Ryohei Ishii
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan Global Research Cluster, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Owen E Branson
- Department of Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Michael A Freitas
- Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA Department of Molecular Virology, Immunology and Medical Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan Global Research Cluster, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Michael Ibba
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA Ohio State Biochemistry Program, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan Global Research Cluster, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
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41
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Abstract
Detection of individuals with phenylketonuria (PKU), an autosomal recessively inherited disorder in phenylalanine degradation, is straightforward and efficient due to newborn screening programs. A recent introduction of the pharmacological treatment option emerged rapid development of molecular testing. However, variants responsible for PKU do not all suppress enzyme activity to the same extent. A spectrum of over 850 variants, gives rise to a continuum of hyperphenylalaninemia from very mild, requiring no intervention, to severe classical PKU, requiring urgent intervention. Locus-specific and genotypes database are today an invaluable resource of information for more efficient classification and management of patients. The high-tech molecular methods allow patients' genotype to be obtained in a few days, especially if each laboratory develops a panel for the most frequent variants in the corresponding population.
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Affiliation(s)
- Nenad Blau
- Division of Inborn Metabolic Diseases, University Children's Hospital, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
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42
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Ganesan A, Mohammadi N, Wang F. From building blocks of proteins to drugs: a quantum chemical study on structure–property relationships of phenylalanine, tyrosine and dopa. RSC Adv 2014. [DOI: 10.1039/c3ra47364c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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43
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Zhang S, Huang T, Ilangovan U, Hinck AP, Fitzpatrick PF. The solution structure of the regulatory domain of tyrosine hydroxylase. J Mol Biol 2013; 426:1483-97. [PMID: 24361276 DOI: 10.1016/j.jmb.2013.12.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 11/13/2013] [Accepted: 12/10/2013] [Indexed: 11/19/2022]
Abstract
Tyrosine hydroxylase (TyrH) catalyzes the hydroxylation of tyrosine to form 3,4-dihydroxyphenylalanine in the biosynthesis of the catecholamine neurotransmitters. The activity of the enzyme is regulated by phosphorylation of serine residues in a regulatory domain and by binding of catecholamines to the active site. Available structures of TyrH lack the regulatory domain, limiting the understanding of the effect of regulation on structure. We report the use of NMR spectroscopy to analyze the solution structure of the isolated regulatory domain of rat TyrH. The protein is composed of a largely unstructured N-terminal region (residues 1-71) and a well-folded C-terminal portion (residues 72-159). The structure of a truncated version of the regulatory domain containing residues 65-159 has been determined and establishes that it is an ACT domain. The isolated domain is a homodimer in solution, with the structure of each monomer very similar to that of the core of the regulatory domain of phenylalanine hydroxylase. Two TyrH regulatory domain monomers form an ACT domain dimer composed of a sheet of eight strands with four α-helices on one side of the sheet. Backbone dynamic analyses were carried out to characterize the conformational flexibility of TyrH65-159. The results provide molecular details critical for understanding the regulatory mechanism of TyrH.
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Affiliation(s)
- Shengnan Zhang
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Tao Huang
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Udayar Ilangovan
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Andrew P Hinck
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Paul F Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA.
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44
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Carluccio C, Fraternali F, Salvatore F, Fornili A, Zagari A. Structural features of the regulatory ACT domain of phenylalanine hydroxylase. PLoS One 2013; 8:e79482. [PMID: 24244510 DOI: 10.1371/journal.pone.0079482] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 09/22/2013] [Indexed: 11/30/2022] Open
Abstract
Phenylalanine hydroxylase (PAH) catalyzes the conversion of L-Phe to L-Tyr. Defects in PAH activity, caused by mutations in the human gene, result in the autosomal recessively inherited disease hyperphenylalaninemia. PAH activity is regulated by multiple factors, including phosphorylation and ligand binding. In particular, PAH displays positive cooperativity for L-Phe, which is proposed to bind the enzyme on an allosteric site in the N-terminal regulatory domain (RD), also classified as an ACT domain. This domain is found in several proteins and is able to bind amino acids. We used molecular dynamics simulations to obtain dynamical and structural insights into the isolated RD of PAH. Here we show that the principal motions involve conformational changes leading from an initial open to a final closed domain structure. The global intrinsic motions of the RD are correlated with exposure to solvent of a hydrophobic surface, which corresponds to the ligand binding-site of the ACT domain. Our results strongly suggest a relationship between the Phe-binding function and the overall dynamic behaviour of the enzyme. This relationship may be affected by structure-disturbing mutations. To elucidate the functional implications of the mutations, we investigated the structural effects on the dynamics of the human RD PAH induced by six missense hyperphenylalaninemia-causing mutations, namely p.G46S, p.F39C, p.F39L, p.I65S, p.I65T and p.I65V. These studies showed that the alterations in RD hydrophobic interactions induced by missense mutations could affect the functionality of the whole enzyme.
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45
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Bashyam MD, Chaudhary AK, Kiran M, Nagarajaram HA, Devi RR, Ranganath P, Dalal A, Bashyam L, Gupta N, Kabra M, Muranjan M, Puri RD, Verma IC, Nampoothiri S, Kadandale JS. Splice, insertion-deletion and nonsense mutations that perturb the phenylalanine hydroxylase transcript cause phenylketonuria in India. J Cell Biochem 2013; 115:566-74. [PMID: 24130151 DOI: 10.1002/jcb.24692] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 10/10/2013] [Indexed: 01/20/2023]
Abstract
Phenylketonuria (PKU) is an autosomal recessive metabolic disorder caused by mutational inactivation of the phenylalanine hydroxylase (PAH) gene. Missense mutations are the most common PAH mutation type detected in PKU patients worldwide. We performed PAH mutation analysis in 27 suspected Indian PKU families (including 7 from our previous study) followed by structure and function analysis of specific missense and splice/insertion-deletion/nonsense mutations, respectively. Of the 27 families, disease-causing mutations were detected in 25. A total of 20 different mutations were identified of which 7 "unique" mutations accounted for 13 of 25 mutation positive families. The unique mutations detected exclusively in Indian PKU patients included three recurrent mutations detected in three families each. The 20 mutations included only 5 missense mutations in addition to 5 splice, 4 each nonsense and insertion-deletion mutations, a silent variant in coding region and a 3'UTR mutation. One deletion and two nonsense mutations were characterized to confirm significant reduction in mutant transcript levels possibly through activation of nonsense mediated decay. All missense mutations affected conserved amino acid residues and sequence and structure analysis suggested significant perturbations in the enzyme activity of respective mutant proteins. This is probably the first report of identification of a significantly low proportion of missense PAH mutations from PKU families and together with the presence of a high proportion of splice, insertion-deletion, and nonsense mutations, points to a unique PAH mutation profile in Indian PKU patients.
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Affiliation(s)
- Murali D Bashyam
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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Jaffe EK. Impact of quaternary structure dynamics on allosteric drug discovery. Curr Top Med Chem 2013; 13:55-63. [PMID: 23409765 DOI: 10.2174/1568026611313010006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 11/29/2012] [Accepted: 11/30/2012] [Indexed: 11/22/2022]
Abstract
The morpheein model of allosteric regulation draws attention to proteins that can exist as an equilibrium of functionally distinct assemblies where: one subunit conformation assembles into one multimer; a different subunit conformation assembles into a different multimer; and the various multimers are in a dynamic equilibrium whose position can be modulated by ligands that bind to a multimer-specific ligand binding site. The case study of porphobilinogen synthase (PBGS) illustrates how such an equilibrium holds lessons for disease mechanisms, drug discovery, understanding drug side effects, and identifying proteins wherein drug discovery efforts might focus on quaternary structure dynamics. The morpheein model of allostery has been proposed as applicable for a wide assortment of disease-associated proteins (Selwood, T., Jaffe, E., (2012) Arch. Bioch. Biophys, 519:131-143). Herein we discuss quaternary structure dynamics aspects to drug discovery for the disease-associated putative morpheeins phenylalanine hydroxylase, HIV integrase, pyruvate kinase, and tumor necrosis factor α. Also highlighted is the quaternary structure equilibrium of transthyretin and successful drug discovery efforts focused on controlling its quaternary structure dynamics.
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Affiliation(s)
- Eileen K Jaffe
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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Ronau JA, Paul LN, Fuchs JE, Corn IR, Wagner KT, Liedl KR, Abu-Omar MM, Das C. An additional substrate binding site in a bacterial phenylalanine hydroxylase. Eur Biophys J 2013; 42:691-708. [PMID: 23860686 PMCID: PMC3972754 DOI: 10.1007/s00249-013-0919-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 06/20/2013] [Accepted: 06/26/2013] [Indexed: 01/07/2023]
Abstract
Phenylalanine hydroxylase (PAH) is a non-heme iron enzyme that catalyzes oxidation of phenylalanine to tyrosine, a reaction that must be kept under tight regulatory control. Mammalian PAH has a regulatory domain in which binding of the substrate leads to allosteric activation of the enzyme. However, the existence of PAH regulation in evolutionarily distant organisms, for example some bacteria in which it occurs, has so far been underappreciated. In an attempt to crystallographically characterize substrate binding by PAH from Chromobacterium violaceum, a single-domain monomeric enzyme, electron density for phenylalanine was observed at a distal site 15.7 Å from the active site. Isothermal titration calorimetry (ITC) experiments revealed a dissociation constant of 24 ± 1.1 μM for phenylalanine. Under the same conditions, ITC revealed no detectable binding for alanine, tyrosine, or isoleucine, indicating the distal site may be selective for phenylalanine. Point mutations of amino acid residues in the distal site that contact phenylalanine (F258A, Y155A, T254A) led to impaired binding, consistent with the presence of distal site binding in solution. Although kinetic analysis revealed that the distal site mutants suffer discernible loss of their catalytic activity, X-ray crystallographic analysis of Y155A and F258A, the two mutants with the most noticeable decrease in activity, revealed no discernible change in the structure of their active sites, suggesting that the effect of distal binding may result from protein dynamics in solution.
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Affiliation(s)
- Judith A. Ronau
- Brown Laboratory of Chemistry, Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN-47907, USA
| | - Lake N. Paul
- Bindley Biosciences Center, Purdue University, West Lafayette, IN 47907, USA
| | - Julian E. Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Isaac R. Corn
- Brown Laboratory of Chemistry, Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN-47907, USA
| | - Kyle T. Wagner
- Brown Laboratory of Chemistry, Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN-47907, USA
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Mahdi M. Abu-Omar
- Brown Laboratory of Chemistry, Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN-47907, USA
| | - Chittaranjan Das
- Brown Laboratory of Chemistry, Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN-47907, USA,To whom correspondence should be addressed: Chittaranjan Das, Brown Laboratory of Chemistry, 560 Oval Drive, West Lafayette, IN, 47907, (765)-494-5478, Fax: (765)-494-0239,
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Heintz C, Cotton RGH, Blau N. Tetrahydrobiopterin, its mode of action on phenylalanine hydroxylase, and importance of genotypes for pharmacological therapy of phenylketonuria. Hum Mutat 2013; 34:927-36. [PMID: 23559577 DOI: 10.1002/humu.22320] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 03/20/2013] [Accepted: 03/20/2013] [Indexed: 11/11/2022]
Abstract
In about 20%-30% of phenylketonuria (PKU) patients (all phenotypes of PAH deficiency), Phe levels may be controlled through phenylalanine hydroxylase cofactor tetrahydrobiopterin therapy. These patients can be diagnosed by an oral tetrahydrobiopterin challenge and are characterized by mutations coding for proteins with substantial residual PAH activity. They can be treated with a commercially available synthetic form of tetrahydrobiopterin, either as a monotherapy or as adjunct to the diet. This review article summarizes molecular and metabolic bases of PKU and the importance of the tetrahydrobiopterin loading test used for PKU patients. On the basis of in vitro residual PAH activity, more than 1,200 genotypes from patients challenged with tetrahydrobiopterin were categorized as predictive for tetrahydrobiopterin responsiveness or non-responsiveness and correlated with the loading test, phenotype, and residual in vitro PAH activity. The coexpression of two distinct PAH mutant alleles revealed possible dominance effects (positive or negative) by one of the mutations on residual activity as result of interallelic complementation. The treatment of the transfected cells with tetrahydrobiopterin showed an increase in residual PAH activity with several mutations coexpressed.
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Wang H, Chen H, Hao G, Yang B, Feng Y, Wang Y, Feng L, Zhao J, Song Y, Zhang H, Chen YQ, Wang L, Chen W. Role of the phenylalanine-hydroxylating system in aromatic substance degradation and lipid metabolism in the oleaginous fungus Mortierella alpina. Appl Environ Microbiol 2013; 79:3225-33. [PMID: 23503309 PMCID: PMC3685260 DOI: 10.1128/aem.00238-13] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 03/05/2013] [Indexed: 11/20/2022] Open
Abstract
Mortierella alpina is a filamentous fungus commonly found in soil that is able to produce lipids in the form of triacylglycerols that account for up to 50% of its dry weight. Analysis of the M. alpina genome suggests that there is a phenylalanine-hydroxylating system for the catabolism of phenylalanine, which has never been found in fungi before. We characterized the phenylalanine-hydroxylating system in M. alpina to explore its role in phenylalanine metabolism and its relationship to lipid biosynthesis. Significant changes were found in the profile of fatty acids in M. alpina grown on medium containing an inhibitor of the phenylalanine-hydroxylating system compared to M. alpina grown on medium without inhibitor. Genes encoding enzymes involved in the phenylalanine-hydroxylating system (phenylalanine hydroxylase [PAH], pterin-4α-carbinolamine dehydratase, and dihydropteridine reductase) were expressed heterologously in Escherichia coli, and the resulting proteins were purified to homogeneity. Their enzymatic activity was investigated by high-performance liquid chromatography (HPLC) or visible (Vis)-UV spectroscopy. Two functional PAH enzymes were observed, encoded by distinct gene copies. A novel role for tetrahydrobiopterin in fungi as a cofactor for PAH, which is similar to its function in higher life forms, is suggested. This study establishes a novel scheme for the fungal degradation of an aromatic substance (phenylalanine) and suggests that the phenylalanine-hydroxylating system is functionally significant in lipid metabolism.
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Affiliation(s)
- Hongchao Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Haiqin Chen
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Guangfei Hao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Bo Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Yun Feng
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
| | - Yu Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Lu Feng
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
| | - Jianxin Zhao
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Yuanda Song
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Hao Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Yong Q. Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Lei Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
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Pan YH, Zhang Y, Cui J, Liu Y, McAllan BM, Liao CC, Zhang S. Adaptation of phenylalanine and tyrosine catabolic pathway to hibernation in bats. PLoS One 2013; 8:e62039. [PMID: 23620802 PMCID: PMC3631164 DOI: 10.1371/journal.pone.0062039] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 02/24/2013] [Indexed: 11/19/2022] Open
Abstract
Some mammals hibernate in response to harsh environments. Although hibernating mammals may metabolize proteins, the nitrogen metabolic pathways commonly activated during hibernation are not fully characterized. In contrast to the hypothesis of amino acid preservation, we found evidence of amino acid metabolism as three of five key enzymes, including phenylalanine hydroxylase (PAH), homogentisate 1,2-dioxygenase (HGD), fumarylacetoacetase (FAH), involved in phenylalanine and tyrosine catabolism were co-upregulated during hibernation in two distantly related species of bats, Myotis ricketti and Rhinolophus ferrumequinum. In addition, the levels of phenylalanine in the livers of these bats were significantly decreased during hibernation. Because phenylalanine and tyrosine are both glucogenic and ketogenic, these results indicate the role of this catabolic pathway in energy supply. Since any deficiency in the catabolism of these two amino acids can cause accumulations of toxic metabolites, these results also suggest the detoxification role of these enzymes during hibernation. A higher selective constraint on PAH, HPD, and HGD in hibernators than in non-hibernators was observed, and hibernators had more conserved amino acid residues in each of these enzymes than non-hibernators. These conserved amino acid residues are mostly located in positions critical for the structure and activity of the enzymes. Taken together, results of this work provide novel insights in nitrogen metabolism and removal of harmful metabolites during bat hibernation.
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Affiliation(s)
- Yi-Hsuan Pan
- Laboratory of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
| | - Yijian Zhang
- Laboratory of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
| | - Jie Cui
- Laboratory of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
| | - Yang Liu
- Laboratory of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
| | - Bronwyn M. McAllan
- Discipline of Physiology and Bosch Institute, School of Medical Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Chen-Chung Liao
- Proteomic Research Center, National Yang-Ming University, Taipei, Taiwan
- * E-mail: (SZ); (CL)
| | - Shuyi Zhang
- Laboratory of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
- * E-mail: (SZ); (CL)
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