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Carkaci-Salli N, Bewley MC, Tekin I, Flanagan JM, Vrana KE. The A328 V/E (rs2887147) polymorphisms in human tryptophan hydroxylase 2 compromise enzyme activity. Biochem Biophys Rep 2023; 35:101527. [PMID: 37608910 PMCID: PMC10440358 DOI: 10.1016/j.bbrep.2023.101527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/03/2023] [Accepted: 08/03/2023] [Indexed: 08/24/2023] Open
Abstract
Human tryptophan hydroxylase 2 (hTPH2) is the rate-limiting enzyme for serotonin biosynthesis in the brain. A number of naturally-occurring single nucleotide polymorphisms (SNPs) have been reported for hTPH2. We investigated the activity and kinetic characteristics of the most common missense polymorphism rs2887147 (A328 V/E; 0.92% allelic frequency for the two different reported SNPs at the same site) using bacterially expressed hTPH2. The recombinant full-length enzyme A328E had no measurable enzyme activity, but A328V displayed decreased enzyme activity (Vmax). A328V also displayed substrate inhibition and decreased stability compared to the wild-type enzyme. By contrast, in constructs lacking the N-terminal 150 amino acid regulatory domain, the A328V substitution had no effect; that is, there was no substrate inhibition, enzyme stabilities (for wild-type and A328V) were dramatically increased, and Vmax values were not different (while the A328E variant remained inactive). These findings, in combination with molecular modeling, suggest that substitutions at A328 affect catalytic activity by altering the conformational freedom of the regulatory domain. The reduced activity and substrate inhibition resulting from these polymorphisms may ultimately reduce serotonin synthesis and contribute to behavioral perturbations, emotional stress, and eating disorders.
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Affiliation(s)
- Nurgul Carkaci-Salli
- Departments of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Maria C. Bewley
- Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Izel Tekin
- Departments of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - John M. Flanagan
- Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Kent E. Vrana
- Departments of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
- Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
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2
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Nehela Y, Killiny N. Diaphorina citri Genome Possesses a Complete Melatonin Biosynthesis Pathway Differentially Expressed under the Influence of the Phytopathogenic Bacterium, Candidatus Liberibacter asiaticus. INSECTS 2021; 12:317. [PMID: 33916117 PMCID: PMC8065666 DOI: 10.3390/insects12040317] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/29/2021] [Accepted: 03/29/2021] [Indexed: 11/17/2022]
Abstract
Melatonin is synthesized from the amino acid L-tryptophan via the shikimic acid pathway and ubiquitously distributed in both prokaryotes and eukaryotes. Although most of melatonin biosynthesis genes were characterized in several plants and animal species including the insect model, Drosophila melanogaster, none of these enzymes have been identified from the Asian citrus psyllid, Diaphorina citri. We used comprehensive in silico analysis and gene expression techniques to identify the melatonin biosynthesis-related genes of D. citri and to evaluate the expression patterns of these genes within the adults of D. citri with gradient infection rates (0, 28, 34, 50, 58, and 70%) of the phytopathogenic bacterium Candidatus Liberibacter asiaticus and after the treatment with exogenous melatonin. We showed that the D. citri genome possesses six putative melatonin biosynthesis-related genes including two putative tryptophan 5-hydroxylase (DcT5H-1 and DcT5H-2), a putative aromatic amino acid decarboxylase (DcAADC), two putative arylalkylamine N-acetyltransferase (DcAANAT-1 and DcAANAT-2), and putative N-acetylserotonin O-methyltransferase (DcASMT). The infection with Ca. L. asiaticus decreased the transcript levels of all predicted genes in the adults of D. citri. Moreover, melatonin supplementation induced their expression levels in both healthy and Ca. L. asiaticus-infected psyllids. These findings confirm the association of these genes with the melatonin biosynthesis pathway.
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Affiliation(s)
- Yasser Nehela
- Citrus Research and Education Center, Department of Plant Pathology, University of Florida, 700 Experiment Station Rd., Lake Alfred, FL 33850, USA;
- Department of Agricultural Botany, Faculty of Agriculture, Tanta University, Tanta 31511, Egypt
| | - Nabil Killiny
- Citrus Research and Education Center, Department of Plant Pathology, University of Florida, 700 Experiment Station Rd., Lake Alfred, FL 33850, USA;
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Agarwal PK, Bernard DN, Bafna K, Doucet N. Enzyme dynamics: Looking beyond a single structure. ChemCatChem 2020; 12:4704-4720. [PMID: 33897908 PMCID: PMC8064270 DOI: 10.1002/cctc.202000665] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Indexed: 12/23/2022]
Abstract
Conventional understanding of how enzymes function strongly emphasizes the role of structure. However, increasing evidence clearly indicates that enzymes do not remain fixed or operate exclusively in or close to their native structure. Different parts of the enzyme (from individual residues to full domains) undergo concerted motions on a wide range of time-scales, including that of the catalyzed reaction. Information obtained on these internal motions and conformational fluctuations has so far uncovered and explained many aspects of enzyme mechanisms, which could not have been understood from a single structure alone. Although there is wide interest in understanding enzyme dynamics and its role in catalysis, several challenges remain. In addition to technical difficulties, the vast majority of investigations are performed in dilute aqueous solutions, where conditions are significantly different than the cellular milieu where a large number of enzymes operate. In this review, we discuss recent developments, several challenges as well as opportunities related to this topic. The benefits of considering dynamics as an integral part of the enzyme function can also enable new means of biocatalysis, engineering enzymes for industrial and medicinal applications.
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Affiliation(s)
- Pratul K. Agarwal
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, Oklahoma 74078
- Arium BioLabs, 2519 Caspian Drive, Knoxville, Tennessee 37932
| | - David N. Bernard
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, Quebec, H7V 1B7, Canada
| | - Khushboo Bafna
- Department of Chemistry and Chemical Biology, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, Quebec, H7V 1B7, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Structure, and Engineering, 1045 Avenue de la Médecine, Université Laval, Québec, QC, G1V 0A6, Canada
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4
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Tran ML, Génisson Y, Ballereau S, Dehoux C. Second-Generation Pharmacological Chaperones: Beyond Inhibitors. Molecules 2020; 25:molecules25143145. [PMID: 32660097 PMCID: PMC7397201 DOI: 10.3390/molecules25143145] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/29/2020] [Accepted: 07/05/2020] [Indexed: 02/06/2023] Open
Abstract
Protein misfolding induced by missense mutations is the source of hundreds of conformational diseases. The cell quality control may eliminate nascent misfolded proteins, such as enzymes, and a pathological loss-of-function may result from their early degradation. Since the proof of concept in the 2000s, the bioinspired pharmacological chaperone therapy became a relevant low-molecular-weight compound strategy against conformational diseases. The first-generation pharmacological chaperones were competitive inhibitors of mutant enzymes. Counterintuitively, in binding to the active site, these inhibitors stabilize the proper folding of the mutated protein and partially rescue its cellular function. The main limitation of the first-generation pharmacological chaperones lies in the balance between enzyme activity enhancement and inhibition. Recent research efforts were directed towards the development of promising second-generation pharmacological chaperones. These non-inhibitory ligands, targeting previously unknown binding pockets, limit the risk of adverse enzymatic inhibition. Their pharmacophore identification is however challenging and likely requires a massive screening-based approach. This review focuses on second-generation chaperones designed to restore the cellular activity of misfolded enzymes. It intends to highlight, for a selected set of rare inherited metabolic disorders, the strategies implemented to identify and develop these pharmacologically relevant small organic molecules as potential drug candidates.
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Affiliation(s)
| | | | | | - Cécile Dehoux
- Correspondence: (S.B.); (C.D.); Tel.: +33-5-6155-6127 (C.D.)
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Study of the Potential of the Capsule Shell Based on Natural Polysaccharides in Targeted Delivery of the L-Phenylalanine Ammonia-Lyase Enzyme Preparation. Pharmaceuticals (Basel) 2020; 13:ph13040063. [PMID: 32283743 PMCID: PMC7243110 DOI: 10.3390/ph13040063] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/03/2020] [Accepted: 04/07/2020] [Indexed: 12/14/2022] Open
Abstract
The treatment of classical phenylketonuria is currently represented by many new methods of disease management. A promising method is the use of the enzyme L-phenylalanine ammonia-lyase (PAL) in various forms. The widespread use of enzyme preparations in therapy is limited by a lack of understanding of the mechanisms and systems of the targeted transport of PAL into certain organs and tissues as a result of the incorporation of a drug into the carrier. To ensure the stability of enzymes during the delivery process, encapsulation is preferable, which, as a rule, ensures the preservation of the qualitative characteristics of the enzymes orally applied to the environmental effects of the gastrointestinal tract (acidity, temperature, oxidation, etc.). Capsule preparations showed sufficient stability in the model gastric fluids and sustained release of the drug in the simulated intestinal fluid. Currently, there is a wide range of polymers used for encapsulation. The use of natural sources in the production technology of capsule systems improves bioavailability, controls the release, and prolongs the half-life of active substances. The advantage of this method is that the used enzyme is completely protected by the cell membranes of the capsules, which preserve its stability in the aggressive environment of the gastrointestinal tract. Capsules were obtained on the basis of compositions of hydrocolloids of plant origin. The potential of the developed capsules for targeted delivery of the enzyme preparation was studied. The degradation of the encapsulated form of the PAL enzyme preparation was studied in vitro in model bio-relevant media simulating the gastric and intestinal environment. The dynamics of the breakdown of the capsule shell allow us to expect that the release of L-phenylalanine ammonia-lyase from capsules based on plant hydrocolloids will occur no earlier than reaching the upper intestines, where the interaction with the protein components of the consumed food products to neutralize phenylalanine should occur.
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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] [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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7
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Chavez DE, Gronau I, Hains T, Kliver S, Koepfli KP, Wayne RK. Comparative genomics provides new insights into the remarkable adaptations of the African wild dog (Lycaon pictus). Sci Rep 2019; 9:8329. [PMID: 31171819 PMCID: PMC6554312 DOI: 10.1038/s41598-019-44772-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/22/2019] [Indexed: 12/02/2022] Open
Abstract
Within the Canidae, the African wild dog (Lycaon pictus) is the most specialized with regards to cursorial adaptations (specialized for running), having only four digits on their forefeet. In addition, this species is one of the few canids considered to be an obligate meat-eater, possessing a robust dentition for taking down large prey, and displays one of the most variable coat colorations amongst mammals. Here, we used comparative genomic analysis to investigate the evolutionary history and genetic basis for adaptations associated with cursoriality, hypercanivory, and coat color variation in African wild dogs. Genome-wide scans revealed unique amino acid deletions that suggest a mode of evolutionary digit loss through expanded apoptosis in the developing first digit. African wild dog-specific signals of positive selection also uncovered a putative mechanism of molar cusp modification through changes in genes associated with the sonic hedgehog (SHH) signaling pathway, required for spatial patterning of teeth, and three genes associated with pigmentation. Divergence time analyses suggest the suite of genomic changes we identified evolved ~1.7 Mya, coinciding with the diversification of large-bodied ungulates. Our results show that comparative genomics is a powerful tool for identifying the genetic basis of evolutionary changes in Canidae.
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Affiliation(s)
- Daniel E Chavez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, 90095, USA.
| | - Ilan Gronau
- Efi Arazi School of Computer Science, Herzliya Interdisciplinary Center (IDC), Herzliya, 46150, Israel
| | - Taylor Hains
- Environmental Science and Policy, Johns Hopkins University, Washington, D.C., 20036, USA
| | - Sergei Kliver
- Institute of Molecular and Cellular Biology, Novosibirsk, 630090, Russian Federation
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, D.C., 20008, USA
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, 90095, USA
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8
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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] [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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Levy HL, Sarkissian CN, Scriver CR. Phenylalanine ammonia lyase (PAL): From discovery to enzyme substitution therapy for phenylketonuria. Mol Genet Metab 2018; 124:223-229. [PMID: 29941359 DOI: 10.1016/j.ymgme.2018.06.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/06/2018] [Accepted: 06/07/2018] [Indexed: 01/17/2023]
Abstract
Phenylketonuria (PKU) is a genetic inborn error in metabolism that impacts many people globally, with profound individual and societal consequences when left untreated. The journey of phenylalanine ammonia lyase (PAL) from plant enzyme to enzyme substitution therapy for PKU is a fascinating story that illustrates the importance of collaboration between basic scientists and industry in the drug development process. The story begins with the curiosity of plant physiologists about the origin of lignin, a polymer involved in maintaining the rigidity of plants. They learned that the critical element in this synthesis was an intermediary enzyme that deaminates phenylalanine to cinnamic acid and ammonia (later called phenylalanine ammonia lyase or PAL). Recognition of this ability to metabolize phenylalanine led to subsequent consideration of PAL as a treatment for PKU. This was initially attempted as enteral therapy with extracted enzyme, but that showed only minimal efficacy. Crucially, further development of PAL as a therapy for PKU required quantities of enzyme that could only be obtained after successfully cloning the gene, expressing the enzyme in vitro and modifying the protein via PEGylation to enable parenteral administration of this non-mammalian enzyme. Ultimately, PEGylated PAL was developed as an enzyme substitution therapy for PKU now approved under the name "Palynziq." The multidisciplinary academic-industrial partnership engaged throughout this process has been key to the successful pursuit of this therapeutic possibility and serves as a model for the development of future innovative therapies.
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Affiliation(s)
- Harvey L Levy
- Division of Genetics and Genomics, Boston Children's Hospital, 1 Autumn St., Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
| | | | - Charles R Scriver
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 0C7, Canada.
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Parthasarathy A, Cross PJ, Dobson RCJ, Adams LE, Savka MA, Hudson AO. A Three-Ring Circus: Metabolism of the Three Proteogenic Aromatic Amino Acids and Their Role in the Health of Plants and Animals. Front Mol Biosci 2018; 5:29. [PMID: 29682508 PMCID: PMC5897657 DOI: 10.3389/fmolb.2018.00029] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 03/21/2018] [Indexed: 12/19/2022] Open
Abstract
Tyrosine, phenylalanine and tryptophan are the three aromatic amino acids (AAA) involved in protein synthesis. These amino acids and their metabolism are linked to the synthesis of a variety of secondary metabolites, a subset of which are involved in numerous anabolic pathways responsible for the synthesis of pigment compounds, plant hormones and biological polymers, to name a few. In addition, these metabolites derived from the AAA pathways mediate the transmission of nervous signals, quench reactive oxygen species in the brain, and are involved in the vast palette of animal coloration among others pathways. The AAA and metabolites derived from them also have integral roles in the health of both plants and animals. This review delineates the de novo biosynthesis of the AAA by microbes and plants, and the branching out of AAA metabolism into major secondary metabolic pathways in plants such as the phenylpropanoid pathway. Organisms that do not possess the enzymatic machinery for the de novo synthesis of AAA must obtain these primary metabolites from their diet. Therefore, the metabolism of AAA by the host animal and the resident microflora are important for the health of all animals. In addition, the AAA metabolite-mediated host-pathogen interactions in general, as well as potential beneficial and harmful AAA-derived compounds produced by gut bacteria are discussed. Apart from the AAA biosynthetic pathways in plants and microbes such as the shikimate pathway and the tryptophan pathway, this review also deals with AAA catabolism in plants, AAA degradation via the monoamine and kynurenine pathways in animals, and AAA catabolism via the 3-aryllactate and kynurenine pathways in animal-associated microbes. Emphasis will be placed on structural and functional aspects of several key AAA-related enzymes, such as shikimate synthase, chorismate mutase, anthranilate synthase, tryptophan synthase, tyrosine aminotransferase, dopachrome tautomerase, radical dehydratase, and type III CoA-transferase. The past development and current potential for interventions including the development of herbicides and antibiotics that target key enzymes in AAA-related pathways, as well as AAA-linked secondary metabolism leading to antimicrobials are also discussed.
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Affiliation(s)
- Anutthaman Parthasarathy
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Penelope J. Cross
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
| | - Lily E. Adams
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Michael A. Savka
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
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11
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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] [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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12
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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] [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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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] [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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Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
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15
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Briggs GD, Bulley J, Dickson PW. Catalytic domain surface residues mediating catecholamine inhibition in tyrosine hydroxylase. J Biochem 2013; 155:183-93. [DOI: 10.1093/jb/mvt110] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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16
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Glu434 is an important amino acid residue for the activity, structure and stability of tyrosine hydroxylase of the silkworm, Bombyx mori. Process Biochem 2013. [DOI: 10.1016/j.procbio.2013.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Structural and thermodynamic insight into phenylalanine hydroxylase from the human pathogen Legionella pneumophila. FEBS Open Bio 2013; 3:370-8. [PMID: 24251098 PMCID: PMC3821034 DOI: 10.1016/j.fob.2013.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 08/12/2013] [Accepted: 08/12/2013] [Indexed: 11/20/2022] Open
Abstract
Phenylalanine hydroxylase from Legionella pneumophila (lpPAH) has a major functional role in the synthesis of the pigment pyomelanin, which is a potential virulence factor. We present here the crystal structure of lpPAH, which is a dimeric enzyme that shows high thermostability, with a midpoint denaturation temperature of 79 °C, and low substrate affinity. The structure revealed a dimerization motif that includes ionic interactions and a hydrophobic core, composed of both β-structure and a C-terminal region, with the specific residues (P255, P256, Y257 and F258) interacting with the same residues from the adjacent subunit within the dimer. This unique dimerization interface, together with a number of aromatic clusters, appears to contribute to the high thermal stability of lpPAH. The crystal structure also explains the increased aggregation of the enzyme in the presence of salt. Moreover, the low affinity for substrate l-Phe could be explained from three consecutive glycine residues (G181, 182, 183) located at the substrate-binding site. This is the first structure of a dimeric bacterial PAH and provides a framework for interpreting the molecular and kinetic properties of lpPAH and for further investigating the regulation of the enzyme. The structure Legionella pneumophila PAH (lpPAH) has been resolved The Tm of lpPAH at 79 °C is explained by structure The unique dimer interface of lpPAH comprises aromatic and ionic interactions Tyr257 seems important for dimerization This is the first structure of a dimeric bacterial PAH
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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] [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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Roberts KM, Pavon JA, Fitzpatrick PF. Kinetic mechanism of phenylalanine hydroxylase: intrinsic binding and rate constants from single-turnover experiments. Biochemistry 2013; 52:1062-73. [PMID: 23327364 DOI: 10.1021/bi301675e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phenylalanine hydroxylase (PheH) catalyzes the key step in the catabolism of dietary phenylalanine, its hydroxylation to tyrosine using tetrahydrobiopterin (BH(4)) and O(2). A complete kinetic mechanism for PheH was determined by global analysis of single-turnover data in the reaction of PheHΔ117, a truncated form of the enzyme lacking the N-terminal regulatory domain. Formation of the productive PheHΔ117-BH(4)-phenylalanine complex begins with the rapid binding of BH(4) (K(d) = 65 μM). Subsequent addition of phenylalanine to the binary complex to form the productive ternary complex (K(d) = 130 μM) is approximately 10-fold slower. Both substrates can also bind to the free enzyme to form inhibitory binary complexes. O(2) rapidly binds to the productive ternary complex; this is followed by formation of an unidentified intermediate, which can be detected as a decrease in absorbance at 340 nm, with a rate constant of 140 s(-1). Formation of the 4a-hydroxypterin and Fe(IV)O intermediates is 10-fold slower and is followed by the rapid hydroxylation of the amino acid. Product release is the rate-determining step and largely determines k(cat). Similar reactions using 6-methyltetrahydropterin indicate a preference for the physiological pterin during hydroxylation.
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Affiliation(s)
- Kenneth M Roberts
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
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Fuchs JE, Huber RG, von Grafenstein S, Wallnoefer HG, Spitzer GM, Fuchs D, Liedl KR. Dynamic regulation of phenylalanine hydroxylase by simulated redox manipulation. PLoS One 2012; 7:e53005. [PMID: 23300845 PMCID: PMC3534100 DOI: 10.1371/journal.pone.0053005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 11/26/2012] [Indexed: 01/06/2023] Open
Abstract
Recent clinical studies revealed increased phenylalanine levels and phenylalanine to tyrosine ratios in patients suffering from infection, inflammation and general immune activity. These data implicated down-regulation of activity of phenylalanine hydroxylase by oxidative stress upon in vivo immune activation. Though the structural damage of oxidative stress is expected to be comparably small, a structural rationale for this experimental finding was lacking. Hence, we investigated the impact of side chain oxidation at two vicinal cysteine residues on local conformational flexibility in the protein by comparative molecular dynamics simulations. Analysis of backbone dynamics revealed a highly flexible loop region (Tyr138-loop) in proximity to the active center of phenylalanine hydroxylase. We observed elevated loop dynamics in connection with a loop movement towards the active site in the oxidized state, thereby partially blocking access for the substrate phenylalanine. These findings were confirmed by extensive replica exchange molecular dynamics simulations and serve as a first structural explanation for decreased enzyme turnover in situations of oxidative stress.
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Affiliation(s)
- Julian E. Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Roland G. Huber
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Susanne von Grafenstein
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Hannes G. Wallnoefer
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Gudrun M. Spitzer
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Dietmar Fuchs
- Division of Biological Chemistry, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
- * E-mail:
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Flydal MI, Chatfield CH, Zheng H, Gunderson FF, Aubi O, Cianciotto NP, Martinez A. Phenylalanine hydroxylase from Legionella pneumophila is a thermostable enzyme with a major functional role in pyomelanin synthesis. PLoS One 2012; 7:e46209. [PMID: 23049981 PMCID: PMC3458870 DOI: 10.1371/journal.pone.0046209] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 08/29/2012] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Legionella pneumophila is a pathogenic bacterium that can cause Legionnaires' disease and other non-pneumonic infections in humans. This bacterium produces a pyomelanin pigment, a potential virulence factor with ferric reductase activity. In this work, we have investigated the role of phenylalanine hydroxylase from L. pneumophila (lpPAH), the product of the phhA gene, in the synthesis of the pyomelanin pigment and the growth of the bacterium in defined compositions. METHODOLOGY/PRINCIPAL FINDINGS Comparative studies of wild-type and phhA mutant corroborate that lpPAH provides the excess tyrosine for pigment synthesis. phhA and letA (gacA) appear transcriptionally linked when bacteria were grown in buffered yeast extract medium at 37°C. phhA is expressed in L. pneumophila growing in macrophages. We also cloned and characterized lpPAH, which showed many characteristics of other PAHs studied so far, including Fe(II) requirement for activity. However, it also showed many particular properties such as dimerization, a high conformational thermal stability, with a midpoint denaturation temperature (T(m)) = 79 ± 0.5°C, a high specific activity at 37°C (10.2 ± 0.3 µmol L-Tyr/mg/min) and low affinity for the substrate (K(m) (L-Phe) = 735 ± 50 µM. CONCLUSIONS/SIGNIFICANCE lpPAH has a major functional role in the synthesis of pyomelanin and promotes growth in low-tyrosine media. The high thermal stability of lpPAH might reflect the adaptation of the enzyme to withstand relatively high survival temperatures.
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Affiliation(s)
- Marte I. Flydal
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Christa H. Chatfield
- Department of Microbiology-Immunology, Northwestern University Medical School, Chicago, Illinois, United States of America
| | - Huaixin Zheng
- Department of Microbiology-Immunology, Northwestern University Medical School, Chicago, Illinois, United States of America
| | - Felizza F. Gunderson
- Department of Microbiology-Immunology, Northwestern University Medical School, Chicago, Illinois, United States of America
| | - Oscar Aubi
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Nicholas P. Cianciotto
- Department of Microbiology-Immunology, Northwestern University Medical School, Chicago, Illinois, United States of America
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Bergen, Norway
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Dictyostelium
phenylalanine hydroxylase is activated by its substrate phenylalanine. FEBS Lett 2012; 586:3596-600. [DOI: 10.1016/j.febslet.2012.09.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 09/08/2012] [Accepted: 09/10/2012] [Indexed: 11/20/2022]
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23
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Torreblanca R, Lira-Navarrete E, Sancho J, Hurtado-Guerrero R. Structural and mechanistic basis of the interaction between a pharmacological chaperone and human phenylalanine hydroxylase. Chembiochem 2012; 13:1266-9. [PMID: 22549968 DOI: 10.1002/cbic.201200188] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Indexed: 01/15/2023]
Abstract
Not without a chaperone: Pharmacological chaperones are designed to bind and ideally stabilise their target protein. Here, we elucidate the molecular mechanism of a potential pharmacological chaperone to treat phenylketonuria. The crystal structure of human phenylalanine hydroxylase with compound IV may help in the rational design of more efficient compounds to treat this disease.
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Affiliation(s)
- Renzo Torreblanca
- Department of Biochemistry and Molecular and Cellular Biology, Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Pedro Cerbuna 12, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Spain
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Mijovilovich A, Hayashi H, Kawamura N, Osawa H, Bruijnincx PCA, Klein Gebbink RJM, de Groot FMF, Weckhuysen BM. Kβ Detected High-Resolution XANES of FeII and FeIII Models of the 2-His-1-Carboxylate Motif: Analysis of the Carboxylate Binding Mode. Eur J Inorg Chem 2012. [DOI: 10.1002/ejic.201101075] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Underhaug J, Aubi O, Martinez A. Phenylalanine hydroxylase misfolding and pharmacological chaperones. Curr Top Med Chem 2012; 12:2534-45. [PMID: 23339306 PMCID: PMC3664513 DOI: 10.2174/1568026611212220008] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 08/28/2012] [Accepted: 08/29/2012] [Indexed: 12/15/2022]
Abstract
Phenylketonuria (PKU) is a loss-of-function inborn error of metabolism. As many other inherited diseases the main pathologic mechanism in PKU is an enhanced tendency of the mutant phenylalanine hydroxylase (PAH) to misfold and undergo ubiquitin-dependent degradation. Recent alternative approaches with therapeutic potential for PKU aim at correcting the PAH misfolding, and in this respect pharmacological chaperones are the focus of increasing interest. These compounds, which often resemble the natural ligands and show mild competitive inhibition, can rescue the misfolded proteins by stimulating their renaturation in vivo. For PKU, a few studies have proven the stabilization of PKU-mutants in vitro, in cells, and in mice by pharmacological chaperones, which have been found either by using the tetrahydrobiopterin (BH(4)) cofactor as query structure for shape-focused virtual screening or by high-throughput screening of small compound libraries. Both approaches have revealed a number of compounds, most of which bind at the iron-binding site, competitively with respect to BH(4). Furthermore, PAH shares a number of ligands, such as BH(4), amino acid substrates and inhibitors, with the other aromatic amino acid hydroxylases: the neuronal/neuroendocrine enzymes tyrosine hydroxylase (TH) and the tryptophan hydroxylases (TPHs). Recent results indicate that the PAH-targeted pharmacological chaperones should also be tested on TH and the TPHs, and eventually be derivatized to avoid unwanted interactions with these other enzymes. After derivatization and validation in animal models, the PAH-chaperoning compounds represent novel possibilities in the treatment of PKU.
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Affiliation(s)
| | | | - Aurora Martinez
- Department of Biomedicine, and K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
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Cerreto M, Cavaliere P, Carluccio C, Amato F, Zagari A, Daniele A, Salvatore F. Natural phenylalanine hydroxylase variants that confer a mild phenotype affect the enzyme's conformational stability and oligomerization equilibrium. BIOCHIMICA ET BIOPHYSICA ACTA 2011; 1812:1435-45. [PMID: 21820508 DOI: 10.1016/j.bbadis.2011.07.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 07/19/2011] [Accepted: 07/20/2011] [Indexed: 11/26/2022]
Abstract
Hyperphenylalaninemias are genetic diseases prevalently caused by mutations in the phenylalanine hydroxylase (PAH) gene. The wild-type PAH enzyme is a homotetramer regulated by its substrate, cofactor and phosphorylation. We reproduced a full-length wild-type protein and seven natural full-length PAH variants, p.I65M, p.N223Y, p.R297L, p.F382L, p.K398N, p.A403V, and p.Q419R, and analyzed their biochemical and biophysical behavior. All mutants exhibited reduced enzymatic activity, namely from 38% to 69% of wild-type activity. Biophysical characterization was performed by size-exclusion chromatography, light scattering and circular dichroism. In the purified wild-type PAH, we identified the monomer in equilibrium with the dimer and tetramer. In most mutants, the equilibrium shifted toward the dimer and most tended to form aggregates. All PAH variants displayed different biophysical behaviors due to loss of secondary structure and thermal destabilization. Specifically, p.F382L was highly unstable at physiological temperature. Moreover, using confocal microscopy with the number and brightness technique, we studied the effect of BH4 addition directly in living human cells expressing wild-type PAH or p.A403V, a mild mutant associated with BH4 responsiveness in vivo. Our results demonstrate that BH4 addition promotes re-establishment of the oligomerization equilibrium, thus indicating that the dimer-to-tetramer shift in pA403V plays a key role in BH4 responsiveness. In conclusion, we show that the oligomerization process and conformational stability are altered by mutations that could affect the physiological behavior of the enzyme. This endorses the hypothesis that oligomerization and folding defects of PAH variants are the most common causes of HPAs, particularly as regards mild human phenotypes.
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Leandro J, Leandro P, Flatmark T. Heterotetrameric forms of human phenylalanine hydroxylase: Co-expression of wild-type and mutant forms in a bicistronic system. Biochim Biophys Acta Mol Basis Dis 2011; 1812:602-12. [DOI: 10.1016/j.bbadis.2011.02.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 01/19/2011] [Accepted: 02/03/2011] [Indexed: 11/28/2022]
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Briggs GD, Gordon SL, Dickson PW. Mutational Analysis of Catecholamine Binding in Tyrosine Hydroxylase. Biochemistry 2011; 50:1545-55. [DOI: 10.1021/bi101455b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Gabrielle D. Briggs
- The School of Biomedical Sciences and Pharmacy and The Hunter Medical Research Institute, Faculty of Health, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Sarah L. Gordon
- The School of Biomedical Sciences and Pharmacy and The Hunter Medical Research Institute, Faculty of Health, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Phillip W. Dickson
- The School of Biomedical Sciences and Pharmacy and The Hunter Medical Research Institute, Faculty of Health, The University of Newcastle, Callaghan, New South Wales 2308, Australia
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Leandro J, Simonsen N, Saraste J, Leandro P, Flatmark T. Phenylketonuria as a protein misfolding disease: The mutation pG46S in phenylalanine hydroxylase promotes self-association and fibril formation. Biochim Biophys Acta Mol Basis Dis 2010; 1812:106-20. [PMID: 20937381 DOI: 10.1016/j.bbadis.2010.09.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 09/02/2010] [Accepted: 09/21/2010] [Indexed: 10/19/2022]
Abstract
The missense mutation pG46S in the regulatory (R) domain of human phenylalanine hydroxylase (hPAH), associated with a severe form of phenylketonuria, generates a misfolded protein which is rapidly degraded on expression in HEK293 cells. When overexpressed as a MBP-G46S fusion protein, soluble and fully active tetrameric/dimeric forms are assembled and recovered in a metastable conformational state. When MBP is cleaved off, G46S undergoes a conformational change and self-associates with a lag phase and an autocatalytic growth phase (tetramers≫dimers), as determined by light scattering. The self-association is controlled by pH, ionic strength, temperature, protein concentration and the phosphorylation state of Ser16; the net charge of the protein being a main modulator of the process. A superstoichiometric amount of WT dimers revealed a 2-fold enhancement of the rate of G46S dimer self-association. Electron microscopy demonstrates the formation of higher-order oligomers and linear polymers of variable length, partly as a branching network, and partly as individual long and twisted fibrils (diameter ~145-300Å). The heat-shock proteins Hsp70/Hsp40, Hsp90 and a proposed pharmacological PAH chaperone (3-amino-2-benzyl-7-nitro-4-(2-quinolyl)-1,2-dihydroisoquinolin-1-one) partly inhibit the self-association process. Our data indicate that the G46S mutation results in a N-terminal extension of α-helix 1 which perturbs the wild-type α-β sandwich motif in the R-domain and promotes new intermolecular contacts, self-association and non-amyloid fibril formation. The metastable conformational state of G46S as a MBP fusion protein, and its self-association propensity when released from MBP, may represent a model system for the study of other hPAH missense mutations characterized by misfolded proteins.
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Affiliation(s)
- João Leandro
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway
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Li J, Ilangovan U, Daubner SC, Hinck AP, Fitzpatrick PF. Direct evidence for a phenylalanine site in the regulatory domain of phenylalanine hydroxylase. Arch Biochem Biophys 2010; 505:250-5. [PMID: 20951114 DOI: 10.1016/j.abb.2010.10.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Revised: 10/05/2010] [Accepted: 10/11/2010] [Indexed: 10/18/2022]
Abstract
The hydroxylation of phenylalanine to tyrosine by the liver enzyme phenylalanine hydroxylase is regulated by the level of phenylalanine. Whether there is a distinct allosteric binding site for phenylalanine outside of the active site has been unclear. The enzyme contains an N-terminal regulatory domain that extends through Thr117. The regulatory domain of rat phenylalanine hydroxylase was expressed in Escherichia coli. The purified protein behaves as a dimer on a gel filtration column. In the presence of phenylalanine, the protein elutes earlier from the column, consistent with a conformational change in the presence of the amino acid. No change in elution is seen in the presence of the non-activating amino acid proline. ¹H-¹⁵N HSQC NMR spectra were obtained of the ¹⁵N-labeled protein alone and in the presence of phenylalanine or proline. A subset of the peaks in the spectrum exhibits chemical shift perturbation in the presence of phenylalanine, consistent with binding of phenylalanine at a specific site. No change in the NMR spectrum is seen in the presence of proline. These results establish that the regulatory domain of phenylalanine hydroxylase can bind phenylalanine, consistent with the presence of an allosteric site for the amino acid.
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Affiliation(s)
- Jun Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, 77843-2128, United States
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Podtetenieff J, Taglieber A, Bill E, Reijerse EJ, Reetz MT. An Artificial Metalloenzyme: Creation of a Designed Copper Binding Site in a Thermostable Protein. Angew Chem Int Ed Engl 2010; 49:5151-5. [PMID: 20572232 DOI: 10.1002/anie.201002106] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- John Podtetenieff
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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Podtetenieff J, Taglieber A, Bill E, Reijerse E, Reetz M. An Artificial Metalloenzyme: Creation of a Designed Copper Binding Site in a Thermostable Protein. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201002106] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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33
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Li J, Dangott LJ, Fitzpatrick PF. Regulation of phenylalanine hydroxylase: conformational changes upon phenylalanine binding detected by hydrogen/deuterium exchange and mass spectrometry. Biochemistry 2010; 49:3327-35. [PMID: 20307070 DOI: 10.1021/bi1001294] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Phenylalanine acts as an allosteric activator of the tetrahydropterin-dependent enzyme phenylalanine hydroxylase. Hydrogen/deuterium exchange monitored by mass spectrometry has been used to gain insight into local conformational changes accompanying activation of rat phenylalanine hydroxylase by phenylalanine. Peptides in the regulatory and catalytic domains that lie in the interface between these two domains show large increases in the extent of deuterium incorporation from solvent in the presence of phenylalanine. In contrast, the effects of phenylalanine on the exchange kinetics of a mutant enzyme lacking the regulatory domain are limited to peptides surrounding the binding site for the amino acid substrate. These results support a model in which the N-terminus of the protein acts as an inhibitory peptide, with phenylalanine binding causing a conformational change in the regulatory domain that alters the interaction between the catalytic and regulatory domains.
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Affiliation(s)
- Jun Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station,Texas 77843-2128, USA
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34
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Cianchetta G, Stouch T, Yu W, Shi ZC, Tari LW, Swanson RV, Hunter MJ, Hoffman ID, Liu Q. Mechanism of Inhibition of Novel Tryptophan Hydroxylase Inhibitors Revealed by Co-crystal Structures and Kinetic Analysis. CURRENT CHEMICAL GENOMICS 2010; 4:19-26. [PMID: 20556201 PMCID: PMC2885594 DOI: 10.2174/1875397301004010019] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Revised: 02/26/2010] [Accepted: 02/26/2010] [Indexed: 11/22/2022]
Abstract
Trytophan Hydroxylase Type I (TPH1), most abundantly expressed in the gastrointestinal tract, initiates the synthesis of serotonin by catalyzing hydroxylation of tryptophan in the presence of biopterin and oxygen. We have previously described three series of novel, periphery-specific TPH1 inhibitors that selectively deplete serotonin in the gastrointestinal tract. We have now determined co-crystal structures of TPH1 with three of these inhibitors at high resolution. Analysis of the structural data showed that each of the three inhibitors fills the tryptophan binding pocket of TPH1 without reaching into the binding site of the cofactor pterin, and induces major conformational changes of the enzyme. The enzyme-inhibitor complexes assume a compact conformation that is similar to the one in tryptophan complex. Kinetic analysis showed that all three inhibitors are competitive versus the substrate tryptophan, consistent with the structural data that the compounds occupy the tryptophan binding site. On the other hand, all three inhibitors appear to be uncompetitive versus the cofactor 6-methyltetrahydropterin, which is not only consistent with the structural data but also indicate that the hydroxylation reaction follows an ordered binding mechanism in which a productive complex is formed only if tryptophan binds only after pterin, similar to the kinetic mechanisms of tyrosine and phenylalanine hydroxylase.
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Affiliation(s)
- Giovanni Cianchetta
- Department of Medicinal Chemistry, Lexicon Pharmaceuticals, Inc., 350 Carter Rd., Princeton, New Jersey, USA
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35
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Zhuang N, Seo KH, Chen C, Kim HL, Park YS, Lee KH. Purification, crystallization and crystallographic analysis of Dictyostelium discoideum phenylalanine hydroxylase in complex with dihydrobiopterin and FeIII. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:463-6. [PMID: 20383023 PMCID: PMC2852345 DOI: 10.1107/s1744309110007220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 02/25/2010] [Indexed: 11/11/2022]
Abstract
Dictyostelium discoideum phenylalanine hydroxylase (DicPAH; residues 1-415) was expressed in Escherichia coli and purified for structural analysis. Apo DicPAH and DicPAH complexed with dihydrobiopterin (BH(2)) and Fe(III) were crystallized using 0.06 M PIPES pH 7.0, 26%(w/v) PEG 2000 by the hanging-drop vapour-diffusion method. Crystals of apo DicPAH and the DicPAH-BH(2)-Fe(III) complex diffracted to 2.6 and 2.07 A resolution, respectively, and belonged to space group P2(1), with unit-cell parameters a = 70.02, b = 85.43, c = 74.86 A, beta = 110.12 degrees and a = 70.97, b = 85.33, c = 74.89 A, beta = 110.23 degrees , respectively. There were two molecules in the asymmetric unit. The structure of DicPAH has been solved by molecular replacement.
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Affiliation(s)
- Ningning Zhuang
- Division of Applied Life Science (BK21 Program), Gyeongsang National University, Jinju 660-701, Republic of Korea
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
- Environmental Biotechnology National Core Research Center (EB-NCRC), Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Kyung Hey Seo
- Division of Applied Life Science (BK21 Program), Gyeongsang National University, Jinju 660-701, Republic of Korea
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
- Environmental Biotechnology National Core Research Center (EB-NCRC), Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Cong Chen
- Division of Applied Life Science (BK21 Program), Gyeongsang National University, Jinju 660-701, Republic of Korea
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
- Environmental Biotechnology National Core Research Center (EB-NCRC), Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Hye-Lim Kim
- FIRST Rearch Group, School of Biological Sciences, Inje University, Kimhae 621-749, Republic of Korea
| | - Young Shik Park
- FIRST Rearch Group, School of Biological Sciences, Inje University, Kimhae 621-749, Republic of Korea
| | - Kon Ho Lee
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
- Environmental Biotechnology National Core Research Center (EB-NCRC), Gyeongsang National University, Jinju 660-701, Republic of Korea
- Department of Microbiology, School of Medicine, Gyeongsang National University, Jinju 660-751, Republic of Korea
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Hsieh TJ, Yen TJ, Lin TS, Chang HT, Huang SY, Hsu CH, Farh L, Chan NL. Twisting of the DNA-binding surface by a beta-strand-bearing proline modulates DNA gyrase activity. Nucleic Acids Res 2010; 38:4173-81. [PMID: 20215433 PMCID: PMC2896533 DOI: 10.1093/nar/gkq153] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
DNA gyrase is the only topoisomerase capable of introducing (-) supercoils into relaxed DNA. The C-terminal domain of the gyrase A subunit (GyrA-CTD) and the presence of a gyrase-specific 'GyrA-box' motif within this domain are essential for this unique (-) supercoiling activity by allowing gyrase to wrap DNA around itself. Here we report the crystal structure of Xanthomonas campestris GyrA-CTD and provide the first view of a canonical GyrA-box motif. This structure resembles the GyrA-box-disordered Escherichia coli GyrA-CTD, both adopting a non-planar beta-pinwheel fold composed of six seemingly spirally arranged beta-sheet blades. Interestingly, structural analysis revealed that the non-planar architecture mainly stems from the tilted packing seen between blades 1 and 2, with the packing geometry likely being defined by a conserved and unusual beta-strand-bearing proline. Consequently, the GyrA-box-containing blade 1 is placed at an angled spatial position relative to the other DNA-binding blades, and an abrupt bend is introduced into the otherwise flat DNA-binding surface. Mutagenesis studies support that the proline-induced structural twist contributes directly to gyrase's (-) supercoiling activity. To our knowledge, this is the first demonstration that a beta-strand-bearing proline may impact protein function. Potential relevance of beta-strand-bearing proline to disease phenylketonuria is also noted.
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Affiliation(s)
- Tung-Ju Hsieh
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei City 100, Taiwan
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37
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Kang TS, Stevens RC. Structural aspects of therapeutic enzymes to treat metabolic disorders. Hum Mutat 2010; 30:1591-610. [PMID: 19790257 DOI: 10.1002/humu.21111] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein therapeutics represents a niche subset of pharmacological agents that is rapidly gaining importance in medicine. In addition to the exceptional specificity that is characteristic of protein therapeutics, several classes of proteins have also been effectively utilized for treatment of conditions that would otherwise lack effective pharmacotherapeutic options. A particularly striking class of protein therapeutics is exogenous enzymes administered for replacement therapy in patients afflicted with metabolic disorders. To date, at least 11 enzymes have either been approved for use, or are in clinical trials for the treatment of selected inherited metabolic disorders. With the recent advancement in structural biology, a significantly larger amount of structural information for several of these enzymes is now available. This article is an overview of the correlation between structural perturbations of these enzymes with the clinical presentation of the respective metabolic conditions, as well as a discussion of the relevant structural modification strategies engaged in improving these enzymes for replacement therapies.
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Affiliation(s)
- Tse Siang Kang
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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38
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Kino K, Hara R, Nozawa A. Enhancement of L-tryptophan 5-hydroxylation activity by structure-based modification of L-phenylalanine 4-hydroxylase from Chromobacterium violaceum. J Biosci Bioeng 2010; 108:184-9. [PMID: 19664549 DOI: 10.1016/j.jbiosc.2009.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2008] [Revised: 04/02/2009] [Accepted: 04/03/2009] [Indexed: 10/20/2022]
Abstract
The objective of this study was to enhance l-tryptophan hydroxylation activity of l-phenylalanine 4-hydroxylase. It had been known that l-phenylalanine 4-hydroxylase from Chromobacterium violaceum could convert l-tryptophan to 5-hydroxy-l-tryptophan and l-phenylalanine to l-tyrosine; however, the activity for l-tryptophan was extremely low compared to l-phenylalanine activity levels. We used the information on the crystal structures of aromatic amino acid hydroxylases to generate C. violaceuml-phenylalanine 4-hydroxylase with high l-tryptophan hydroxylating activity. In silico structural modeling analysis suggested that hydrophobic and/or stacking interactions with the substrate and cofactor at L101 and W180 in C. violaceuml-phenylalanine 4-hydroxylase would increase hydroxylation activity. Based on this hypothesis, we introduced a saturation mutagenesis towards these sites followed by the evaluation of 5-hydroxy-l-tryptophan productivity using a modified Gibbs assay. Three and nine positive mutants were obtained from the L101 and W180 mutant libraries, respectively. Among the mutants, L101Y and W180F showed the highest l-tryptophan hydroxylation activity at the respective residues. Steady-state kinetic analysis revealed that k(cat) values for l-tryptophan hydroxylation were increased from 0.40 (wild-type) to 1.02 (L101Y) and 0.51 s(-1) (W180F). In addition, the double mutant (L101Y-W180F) displayed higher l-tryptophan hydroxylation activity than the wild-type and the W180F and L101Y mutants. The k(cat) value of L101Y-W180F increased to 2.08 s(-1), showing a 5.2-fold increase compared to wild-type enzyme levels.
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Affiliation(s)
- Kuniki Kino
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan.
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The Aromatic Amino Acid Hydroxylase Mechanism: A Perspective From Computational Chemistry. ADVANCES IN INORGANIC CHEMISTRY 2010. [DOI: 10.1016/s0898-8838(10)62011-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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40
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Haahr LT, Jensen KP, Boesen J, Christensen HEM. Experimentally calibrated computational chemistry of tryptophan hydroxylase: trans influence, hydrogen-bonding, and 18-electron rule govern O2-activation. J Inorg Biochem 2009; 104:136-45. [PMID: 19939457 DOI: 10.1016/j.jinorgbio.2009.10.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Revised: 10/09/2009] [Accepted: 10/16/2009] [Indexed: 10/20/2022]
Abstract
Insight into the nature of oxygen activation in tryptophan hydroxylase has been obtained from density functional computations. Conformations of O(2)-bound intermediates have been studied with oxygen trans to glutamate and histidine, respectively. An O(2)-adduct with O(2)trans to histidine (O(his)) and a peroxo intermediate with peroxide trans to glutamate (P(glu)) were found to be consistent (0.57-0.59mm/s) with experimental Mössbauer isomer shifts (0.55mm/s) and had low computed free energies. The weaker trans influence of histidine is shown to give rise to a bent O(2) coordination mode with O(2) pointing towards the cofactor and a more activated O-O bond (1.33A) than in O(glu) (1.30A). It is shown that the cofactor can hydrogen bond to O(2) and activate the O-O bond further (from 1.33 to 1.38A). The O(his) intermediate leads to a ferryl intermediate (F(his)) with an isomer shift of 0.34mm/s, also consistent with the experimental value (0.25mm/s) which we propose as the structure of the hydroxylating intermediate, with the tryptophan substrate well located for further reaction 3.5A from the ferryl group. Based on the optimized transition states, the activation barriers for the two paths (glu and his) are similar, so a two-state scenario involving O(his) and P(glu) is possible. A structure of the activated deoxy state which is high-spin implies that the valence electron count has been lowered from 18 to 16 (glutamate becomes bidentate), giving a "green light" that invites O(2)-binding. Our mechanism of oxygen activation in tryptophan hydroxylase does not require inversion of spin, which may be an important observation.
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Affiliation(s)
- Laerke T Haahr
- Technical University of Denmark, DTU Chemistry, Kemitorvet 207, 2800 Kgs. Lyngby, DK, Denmark
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41
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Molecular Diagnosis of Phenylketonuria: From Defective Protein to Disease-Causing Gene Mutation. J Med Biochem 2009. [DOI: 10.2478/v10011-009-0021-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular Diagnosis of Phenylketonuria: From Defective Protein to Disease-Causing Gene MutationPhenylketonuria (PKU) is the most common inborn error of amino acid metabolism, with an average incidence of 1/10000 in Caucasians. PKU is caused by more than 500 mutations in the phenylalanine hydroxylase gene (PAH) which result in phenylalanine hydroxylase (PAH) enzyme deficiency. Two approaches, in vitro expression analysis of mutant PAH and genotype-phenotype correlation study, are used for the assessment of severity ofPAHmutations. It has been shown that there is a significant correlation between mutantPAHgenotypes and PKU phenotypes. As a result, the molecular diagnosis is completely shifted toward the detection of mutations in the phenylalanine hydroxylase gene. The study of the molecular basis of PKU in Serbia included identification of the spectrum and frequency ofPAHmutations in Serbian PKU patients and genotype-phenotype correlation analysis. By using both PCR-RFLP and »broad range« DGGE/DNA sequencing analysis, the mutation detection rate reached 97%. Thus, the base for molecular diagnosis, genetic counseling and selection of BH4-responsive PKU patients in Serbia was created.
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42
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Wang S, Sura GR, Dangott LJ, Fitzpatrick PF. Identification by hydrogen/deuterium exchange of structural changes in tyrosine hydroxylase associated with regulation. Biochemistry 2009; 48:4972-9. [PMID: 19371093 PMCID: PMC2730116 DOI: 10.1021/bi9004254] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The activity of tyrosine hydroxylase is regulated by reversible phosphorylation of serine residues in an N-terminal regulatory domain and catecholamine inhibition at the active site. Catecholamines such as dopamine bind very tightly to the resting enzyme; phosphorylation of Ser40 decreases the affinity for catecholamines by 3 orders of magnitude. The effects of dopamine binding and phosphorylation of Ser40 on the kinetics of deuterium incorporation into peptide bonds were examined by mass spectrometry. When dopamine is bound, three peptic peptides show significantly slower deuterium incorporation, 35-41 and 42-71 in the regulatory domain and 295-299 in the catalytic domain. In the phosphorylated enzyme, peptide 295-299 shows more rapid incorporation of deuterium, while 35-41 and 42-71 can not be detected. These results are consistent with tyrosine hydroxylase existing in two different conformations. In the closed conformation, the regulatory domain lies across the active site loop containing residues 295-298; this is stabilized when dopamine is bound in the active site. In the open conformation, the regulatory domain has moved out of the active site, allowing substrate access; this conformation is favored by phosphorylation of Ser40.
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Affiliation(s)
- Shanzhi Wang
- Departments of Biochemistry and Biophysics Texas A&M University, College Station TX 77843-2128
| | - Giri R. Sura
- Departments of Biochemistry and Biophysics Texas A&M University, College Station TX 77843-2128
| | - Lawrence J. Dangott
- Protein Chemistry Laboratory Texas A&M University, College Station TX 77843-2128
| | - Paul F. Fitzpatrick
- Departments of Biochemistry and Biophysics Texas A&M University, College Station TX 77843-2128
- Department of Chemistry Texas A&M University, College Station TX 77843-2128
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43
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44
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Pavon JA, Fitzpatrick PF. Demonstration of a peroxide shunt in the tetrahydropterin-dependent aromatic amino acid monooxygenases. J Am Chem Soc 2009; 131:4582-3. [PMID: 19281164 PMCID: PMC2676924 DOI: 10.1021/ja900128m] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The nonheme iron enzyme phenylalanine hydroxylase, tyrosine hydroxylase, and tryptophan hydroxylase catalyze the hydroxylation of their aromatic amino acid substrates using a tetrahydropterin as the source of electrons. The hydroxylating intermediate is proposed to be an Fe(IV)O species. We report here that all three enzymes will catalyze hydroxylation reactions using H(2)O(2) in place of tetrahydropterin and oxygen, forming tyrosine and 3-hydroxyphenylalanine from phenylalanine, 4-HOCH(2)-phenylalanine from 4-CH(3)-phenylalanine, and hydroxycyclohexylalanine from 3-cyclohexylalanine. No peroxide-dependent reaction is seen with active site mutants of TyrH and PheH in which the stability or reactivity of the iron center is compromised. These results provide further support for an Fe(IV)O hydroxylating intermediate.
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Affiliation(s)
- Jorge Alex Pavon
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
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45
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Windahl MS, Petersen CR, Christensen HEM, Harris P. Crystal structure of tryptophan hydroxylase with bound amino acid substrate. Biochemistry 2008; 47:12087-94. [PMID: 18937498 DOI: 10.1021/bi8015263] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tryptophan hydroxylase (TPH) is a mononuclear non-heme iron enzyme, which catalyzes the reaction between tryptophan, O 2, and tetrahydrobiopterin (BH 4) to produce 5-hydroxytryptophan and 4a-hydroxytetrahydrobiopterin. This is the first and rate-limiting step in the biosynthesis of the neurotransmitter and hormone serotonin (5-hydroxytryptamine). We have determined the 1.9 A resolution crystal structure of the catalytic domain (Delta1-100/Delta415-445) of chicken TPH isoform 1 (TPH1) in complex with the tryptophan substrate and an iron-bound imidazole. This is the first structure of any aromatic amino acid hydroxylase with bound natural amino acid substrate. The iron coordination can be described as distorted trigonal bipyramidal coordination with His273, His278, and Glu318 (partially bidentate) and one imidazole as ligands. The tryptophan stacks against Pro269 with a distance of 3.9 A between the iron and the tryptophan Czeta3 atom that is hydroxylated. The binding of tryptophan and maybe the imidazole has caused the structural changes in the catalytic domain compared to the structure of the human TPH1 without tryptophan. The structure of chicken TPH1 is more compact, and the loops of residues Leu124-Asp139 and Ile367-Thr369 close around the active site. Similar structural changes are seen in the catalytic domain of phenylalanine hydroxylase (PAH) upon binding of substrate analogues norleucine and thienylalanine to the PAH.BH 4 complex. In fact, the chicken TPH1.Trp.imidazole structure resembles the PAH.BH 4.thienylalanine structure more (root-mean-square deviation for Calpha atoms of 0.90 A) than the human TPH1 structure (root-mean-square deviation of 1.47 A).
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Affiliation(s)
- Michael S Windahl
- Department of Basic Sciences and Environment, Faculty of Life Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
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46
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Song G, Li Y, Cheng C, Zhao Y, Gao A, Zhang R, Joachimiak A, Shaw N, Liu ZJ. Structural insight into acute intermittent porphyria. FASEB J 2008; 23:396-404. [PMID: 18936296 DOI: 10.1096/fj.08-115469] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Acute intermittent porphyria (AIP), an inherited disease of heme biosynthesis, is one of the most common types of porphyria. Reduced activity of the enzyme porphobilinogen deaminase (PBGD), which catalyzes the sequential condensation of 4 molecules of porphobilinogen to yield preuroporphyrinogen, has been linked to the symptoms of AIP. We have determined the 3-dimensional structure of human PBGD at 2.2 A resolution. Analysis of the structure revealed a dipyrromethane cofactor molecule covalently linked to C261, sitting in a positively charged cleft region. In addition to the critical catalytic D99, a number of other residues are seen hydrogen bonded to the cofactor and play a role in catalysis. Sequential entry of 4 pyrrole molecules into the active site is accomplished by movement of the domains around the hinges. H120P mutation resulted in an inactive enzyme, supporting the role of H120 as a hinge residue. Interestingly, some of the mutations of the human PBGD documented in patients suffering from AIP are located far away from the active site. The structure provides insights into the mechanism of action of PBGD at the molecular level and could aid the development of potential drugs for the up-regulation of PBGD activity in AIP.
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Affiliation(s)
- Gaojie Song
- National Laboratory of Biomacromolecules, Institute of Biophysics, 15 Datun Lu, Beijing 100101, China
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47
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Kasnauskienė J, Cimbalistienė L, Kučinskas V. Predicting a clinical/biochemical phenotype for PKU/MHP patients with PAH gene mutations. RUSS J GENET+ 2008. [DOI: 10.1134/s1022795408100116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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48
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Mijovilovich A. XANES Study of the Carboxylate Binding Mode in Two Pterin Hydroxylases. Chem Biodivers 2008; 5:2131-2139. [DOI: 10.1002/cbdv.200890194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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49
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Panay AJ, Fitzpatrick PF. Kinetic isotope effects on aromatic and benzylic hydroxylation by Chromobacterium violaceum phenylalanine hydroxylase as probes of chemical mechanism and reactivity. Biochemistry 2008; 47:11118-24. [PMID: 18817418 DOI: 10.1021/bi801295w] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phenylalanine hydroxylase from Chromobacterium violaceum (CvPheH) is a non-heme iron monooxygenase that catalyzes the hydroxylation of phenylalanine to tyrosine. In this study, we used deuterium kinetic isotope effects to probe the chemical mechanisms of aromatic and benzylic hydroxylation to compare the reactivities of bacterial and eukaryotic aromatic amino acid hydroxylases. The (D) k cat value for the reaction of CvPheH with [(2)H 5]phenylalanine is 1.2 with 6-methyltetrahydropterin and 1.4 with 6,7-dimethyltetrahydropterin. With the mutant enzyme I234D, the (D) k cat value decreases to 0.9 with the latter pterin; this is likely to be the intrinsic effect for addition of oxygen to the amino acid. The isotope effect on the subsequent tautomerization of a dienone intermediate was determined to be 5.1 by measuring the retention of deuterium in tyrosine produced from partially deuterated phenylalanine; this large isotope effect is responsible for the normal effect on k cat. The isotope effect for hydroxylation of the methyl group of 4-CH 3-phenylalanine, obtained from the partitioning of benzylic and aromatic hydroxylation products, is 10. The temperature dependence of this isotope effect establishes the contribution of hydrogen tunneling to benzylic hydroxylation by this enzyme. The results presented here provide evidence that the reactivities of the prokaryotic and eukaryotic hydroxylases are similar and further define the reactivity of the iron center for the family of aromatic amino acid hydroxylases.
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Affiliation(s)
- Aram J Panay
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, USA
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50
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Gersting SW, Kemter KF, Staudigl M, Messing DD, Danecka MK, Lagler FB, Sommerhoff CP, Roscher AA, Muntau AC. Loss of function in phenylketonuria is caused by impaired molecular motions and conformational instability. Am J Hum Genet 2008; 83:5-17. [PMID: 18538294 PMCID: PMC2443833 DOI: 10.1016/j.ajhg.2008.05.013] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Revised: 05/09/2008] [Accepted: 05/17/2008] [Indexed: 11/21/2022] Open
Abstract
A significant share of patients with phenylalanine hydroxylase (PAH) deficiency benefits from pharmacological doses of tetrahydrobiopterin (BH(4)), the natural PAH cofactor. Phenylketonuria (PKU) is hypothesized to be a conformational disease, with loss of function due to protein destabilization, and the restoration of enzyme function that is observed in BH(4) treatment might be transmitted by correction of protein misfolding. To elucidate the molecular basis of functional impairment in PAH deficiency, we investigated the impact of ten PAH gene mutations identified in patients with BH(4)-responsiveness on enzyme kinetics, stability, and conformation of the protein (F55L, I65S, H170Q, P275L, A300S, S310Y, P314S, R408W, Y414C, Y417H). Residual enzyme activity was generally high, but allostery was disturbed in almost all cases and pointed to altered protein conformation. This was confirmed by reduced proteolytic stability, impaired tetramer assembly or aggregation, increased hydrophobicity, and accelerated thermal unfolding--with particular impact on the regulatory domain--observed in most variants. Three-dimensional modeling revealed the involvement of functionally relevant amino acid networks that may communicate misfolding throughout the protein. Our results substantiate the view that PAH deficiency is a protein-misfolding disease in which global conformational changes hinder molecular motions essential for physiological enzyme function. Thus, PKU has evolved from a model of a genetic disease that leads to severe neurological impairment to a model of a treatable protein-folding disease with loss of function.
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Affiliation(s)
- Søren W. Gersting
- Department of Molecular Pediatrics, Children's Research Center, Dr. von Hauner Children's Hospital, Ludwig Maximilians University, 80337 Munich, Germany
| | - Kristina F. Kemter
- Department of Molecular Pediatrics, Children's Research Center, Dr. von Hauner Children's Hospital, Ludwig Maximilians University, 80337 Munich, Germany
| | - Michael Staudigl
- Department of Molecular Pediatrics, Children's Research Center, Dr. von Hauner Children's Hospital, Ludwig Maximilians University, 80337 Munich, Germany
| | - Dunja D. Messing
- Department of Molecular Pediatrics, Children's Research Center, Dr. von Hauner Children's Hospital, Ludwig Maximilians University, 80337 Munich, Germany
| | - Marta K. Danecka
- Department of Molecular Pediatrics, Children's Research Center, Dr. von Hauner Children's Hospital, Ludwig Maximilians University, 80337 Munich, Germany
| | - Florian B. Lagler
- Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - Christian P. Sommerhoff
- Department of Clinical Chemistry and Clinical Biochemistry, Surgical Clinic, Ludwig Maximilians University, 80337 Munich, Germany
| | - Adelbert A. Roscher
- Department of Molecular Pediatrics, Children's Research Center, Dr. von Hauner Children's Hospital, Ludwig Maximilians University, 80337 Munich, Germany
| | - Ania C. Muntau
- Department of Molecular Pediatrics, Children's Research Center, Dr. von Hauner Children's Hospital, Ludwig Maximilians University, 80337 Munich, Germany
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