1
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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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2
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Donlon J, Ryan P. Peptidylglycine monooxygenase activity of monomeric species of growth hormone. Heliyon 2019; 5:e02436. [PMID: 31528749 PMCID: PMC6739457 DOI: 10.1016/j.heliyon.2019.e02436] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 05/27/2019] [Accepted: 09/04/2019] [Indexed: 11/30/2022] Open
Abstract
C-terminal α-amidation of peptides is an important event in the course of pro-hormone and neuropeptide processing; it is a modification that contributes to the biological activity and stability of about 25 peptides in neural and endocrine systems. This laboratory has shown that bovine growth hormone (bGH) also has a catalytic function, i.e. peptidylglycine monooxygenase activity, which is the first step in the alpha-amidation of glycine-extended peptides. We report here that the peptidylglycine monooxygenase activity of monomeric bovine pituitary GH, in the presence of ascorbate, is stimulated by combination with oligomeric forms of bGH one of which is a hetero-oligomer with metallothionein. Three species of recombinant monomeric GH (bovine, human and chicken) also catalyze this monooxygenase reaction. Tetrahydrobiopterin also functions as a reductant - with a significantly greater turnover than achieved with ascorbate. These findings clarify the role of GH in peptidylglycine monooxygenation and provide an explanation for earlier observations that peptide amidation is not totally obliterated in the absence of ascorbate, in cultured pituitary cells or in vivo. The evolution of bifunctional GH is also discussed, as are some of the significances of the peptidylglycine monooxygenase activity of human GH in relation to peptides such as oxytocin, glucagon-like peptide-1 and peptide PYY.
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Affiliation(s)
- John Donlon
- Discipline of Biochemistry, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Patrick Ryan
- Discipline of Biochemistry, School of Natural Sciences, National University of Ireland, Galway, Ireland
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3
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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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4
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Xu J, Li Y, Lv Y, Bian C, You X, Endoh D, Teraoka H, Shi Q. Molecular Evolution of Tryptophan Hydroxylases in Vertebrates: A Comparative Genomic Survey. Genes (Basel) 2019; 10:E203. [PMID: 30857219 PMCID: PMC6470480 DOI: 10.3390/genes10030203] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/19/2019] [Accepted: 03/04/2019] [Indexed: 02/02/2023] Open
Abstract
Serotonin is a neurotransmitter involved in various physiological processes in the central and peripheral nervous systems. Serotonin is also a precursor for melatonin biosynthesis, which mainly occurs in the pineal gland of vertebrates. Tryptophan hydroxylase (TPH) acts as the rate-limiting enzyme in serotonin biosynthesis and is the initial enzyme involved in the synthesis of melatonin. Recently, two enzymes-TPH1 and TPH2-were reported to form the TPH family in vertebrates and to play divergent roles in serotonergic systems. Here, we examined the evolution of the TPH family from 70 vertebrate genomes. Based on the sequence similarity, we extracted 184 predicted tph homologs in the examined vertebrates. A phylogenetic tree, constructed on the basis of these protein sequences, indicated that tph genes could be divided into two main clades (tph1 and tph2), and that the two clades were further split into two subgroups of tetrapods and Actinopterygii. In tetrapods, and some basal non-teleost ray-finned fishes, only two tph isotypes exist. Notably, tph1 in most teleosts that had undergone the teleost-specific genome duplication could be further divided into tph1a and tph1b. Moreover, protein sequence comparisons indicated that TPH protein changes among vertebrates were concentrated at the NH₂-terminal. The tertiary structures of TPH1 and TPH2 revealed obvious differences in the structural elements. Five positively selected sites were characterized in TPH2 compared with TPH1; these sites may reflect the functional divergence in enzyme activity and substrate specificity. In summary, our current work provides novel insights into the evolution of tph genes in vertebrates from a comprehensive genomic perspective.
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Affiliation(s)
- Junmin Xu
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan.
| | - Yanping Li
- BGI-Shenzhen, Shenzhen 518083, China.
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Yunyun Lv
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
| | - Daiji Endoh
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan.
| | - Hiroki Teraoka
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan.
| | - Qiong Shi
- BGI-Shenzhen, Shenzhen 518083, China.
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
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5
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Qi G, Zhang Y, Xu S, Li C, Wang D, Li H, Jin Y. Nucleus and Mitochondria Targeting Theranostic Plasmonic Surface-Enhanced Raman Spectroscopy Nanoprobes as a Means for Revealing Molecular Stress Response Differences in Hyperthermia Cell Death between Cancerous and Normal Cells. Anal Chem 2018; 90:13356-13364. [PMID: 30234969 DOI: 10.1021/acs.analchem.8b03034] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Metallic plasmonic nanoparticles have been intensively exploited as theranostic nanoprobes for plasmonic photothermal therapy (PPT) and surface-enhanced Raman spectroscopy (SERS) applications. But the underlying molecular mechanisms associated with PPT-induced apoptosis between cancerous and normal cells have remained largely unknown or disputed. In this study, we designed an organelle-targeting theranostic plasmonic SERS nanoprobe (CDs-Ag/Au NS) composed of porous Ag/Au nanoshell (p-Ag/Au NSs) and carbon dots (CDs) for nucleus and mitochondria targeted PPT of cells. The differences in molecular stress response in the PPT-induced hyperthermia cell death between cancerous HeLa and normal L929 and H8 cells have been revealed by site-specific single-cell SERS detection. The contents of tryptophan (Trp), phenylalanine (Phe), and tyrosine (Tyr) in HeLa cells were found more evidently increased than L929 and H8 cells during the PPT-induced cell-death process. And from the mitochondria point of view, we found that the PPT-induced cell apoptosis for HeLa cells mainly stems from (or is regulated through) cellular thermal stress-responsive proteins, while for L929 and H8 cells it seems more related to DNA. Understanding molecular stress response difference of the PPT-induced cell apoptosis between cancerous and normal cells is helpful for diagnosis and treatment of cancer, and the method will open an avenue for single-cell studies.
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Affiliation(s)
- Guohua Qi
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun 130022 , Jilin , People's Republic of China.,University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Ying Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun 130022 , Jilin , People's Republic of China.,University of Science and Technology of China , Hefei 230026 , People's Republic of China
| | - Shuping Xu
- State Key Laboratory of Supramolecular Structure and Materials , Jilin University , 2699 Qianjin Avenue , Changchun 130012 , People's Republic of China
| | - Chuanping Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun 130022 , Jilin , People's Republic of China.,University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Dandan Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun 130022 , Jilin , People's Republic of China.,University of Science and Technology of China , Hefei 230026 , People's Republic of China
| | - Haijuan Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun 130022 , Jilin , People's Republic of China
| | - Yongdong Jin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun 130022 , Jilin , People's Republic of China.,University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China.,University of Science and Technology of China , Hefei 230026 , People's Republic of China
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6
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Yang Y, Liu F, Liu A. Adapting to oxygen: 3-Hydroxyanthrinilate 3,4-dioxygenase employs loop dynamics to accommodate two substrates with disparate polarities. J Biol Chem 2018; 293:10415-10424. [PMID: 29784877 DOI: 10.1074/jbc.ra118.002698] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/18/2018] [Indexed: 11/06/2022] Open
Abstract
3-Hydroxyanthranilate 3,4-dioxygenase (HAO) is an iron-dependent protein that activates O2 and inserts both oxygen atoms into 3-hydroxyanthranilate (3-HAA). An intriguing question is how HAO can rapidly bind O2, even though local O2 concentrations and diffusion rates are relatively low. Here, a close inspection of the HAO structures revealed that substrate- and inhibitor-bound structures exhibit a closed conformation with three hydrophobic loop regions moving toward the catalytic iron center, whereas the ligand-free structure is open. We hypothesized that these loop movements enhance O2 binding to the binary complex of HAO and 3-HAA. We found that the carboxyl end of 3-HAA triggers changes in two loop regions and that the third loop movement appears to be driven by an H-bond interaction between Asn27 and Ile142 Mutational analyses revealed that N27A, I142A, and I142P variants cannot form a closed conformation, and steady-state kinetic assays indicated that these variants have a substantially higher Km for O2 than WT HAO. This observation suggested enhanced hydrophobicity at the iron center resulting from the concerted loop movements after the binding of the primary substrate, which is hydrophilic. Given that O2 is nonpolar, the increased hydrophobicity at the iron center of the binary complex appears to be essential for rapid O2 binding and activation, explaining the reason for the 3-HAA-induced loop movements. Because substrate binding-induced open-to-closed conformational changes are common, the results reported here may help further our understanding of how oxygen is enriched in nonheme iron-dependent dioxygenases.
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Affiliation(s)
- Yu Yang
- From the Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249 and
| | - Fange Liu
- the Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Aimin Liu
- From the Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249 and
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7
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Tidemand KD, Peters GH, Harris P, Stensgaard E, Christensen HEM. Isoform-Specific Substrate Inhibition Mechanism of Human Tryptophan Hydroxylase. Biochemistry 2017; 56:6155-6164. [PMID: 29035515 DOI: 10.1021/acs.biochem.7b00763] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tryptophan hydroxylase (TPH) catalyzes the initial and rate-limiting step in the biosynthesis of serotonin, which is associated with a variety of disorders such as depression and irritable bowel syndrome. TPH exists in two isoforms: TPH1 and TPH2. TPH1 catalyzes the initial step in the synthesis of serotonin in the peripheral tissues, while TPH2 catalyzes this step in the brain. In this study, the steady-state kinetic mechanism for the catalytic domain of human TPH1 has been determined. Varying substrate tryptophan (Trp) and tetrahydrobiopterin (BH4) results in a hybrid Ping Pong-ordered mechanism in which the reaction can either occur through a Ping Pong or a sequential mechanism depending on the concentration of tryptophan. The catalytic domain of TPH1 shares a sequence identity of 81% with TPH2. Despite the high sequence identity, differences in the kinetic parameters of the isoforms have been identified; i.e., only TPH1 displays substrate tryptophan inhibition. This study demonstrates that the difference can be traced to an active site loop which displays different properties in the TPH isoforms. Steady-state kinetic results of the isoforms, and variants with point mutations in a loop lining the active site, show that the kinetic parameters of only TPH1 are significantly changed upon mutations. Mutations in the active site loop of TPH1 result in an increase in the substrate inhibition constant, Ki, and therefore turnover rate. Molecular dynamics simulations reveal that this substrate inhibition mechanism occurs through a closure of the cosubstrate, BH4, binding pocket, which is induced by Trp binding.
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Affiliation(s)
- Kasper D Tidemand
- Department of Chemistry, Technical University of Denmark , Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Günther H Peters
- Department of Chemistry, Technical University of Denmark , Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Pernille Harris
- Department of Chemistry, Technical University of Denmark , Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Eva Stensgaard
- Department of Chemistry, Technical University of Denmark , Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Hans E M Christensen
- Department of Chemistry, Technical University of Denmark , Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
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8
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Hayakawa D, Yamaotsu N, Nakagome I, Ozawa SI, Yoshida T, Hirono S. In silico analyses of the effects of a point mutation and a pharmacological chaperone on the thermal fluctuation of phenylalanine hydroxylase. Biophys Chem 2017; 228:47-54. [DOI: 10.1016/j.bpc.2017.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 06/28/2017] [Accepted: 06/28/2017] [Indexed: 10/19/2022]
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9
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Jaffe EK. New protein structures provide an updated understanding of phenylketonuria. Mol Genet Metab 2017; 121:289-296. [PMID: 28645531 PMCID: PMC5549558 DOI: 10.1016/j.ymgme.2017.06.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 06/08/2017] [Indexed: 11/16/2022]
Abstract
Phenylketonuria (PKU) and less severe hyperphenylalaninemia (HPA) constitute the most common inborn error of amino acid metabolism, and is most often caused by defects in phenylalanine hydroxylase (PAH) function resulting in accumulation of Phe to neurotoxic levels. Despite the success of dietary intervention in preventing permanent neurological damage, individuals living with PKU clamor for additional non-dietary therapies. The bulk of disease-associated mutations are PAH missense variants, which occur throughout the entire 452 amino acid human PAH protein. While some disease-associated mutations affect protein structure (e.g. truncations) and others encode catalytically dead variants, most have been viewed as defective in protein folding/stability. Here we refine this view to address how PKU-associated missense variants can perturb the equilibrium among alternate native PAH structures (resting-state PAH and activated PAH), thus shifting the tipping point of this equilibrium to a neurotoxic Phe concentration. This refined view of PKU introduces opportunities for the design or discovery of therapeutic pharmacological chaperones that can help restore the tipping point to healthy Phe levels and how such a therapeutic might work with or without the inhibitory pharmacological chaperone BH4. Dysregulation of an equilibrium of architecturally distinct native PAH structures departs from the concept of "misfolding", provides an updated understanding of PKU, and presents an enhanced foundation for understanding genotype/phenotype relationships.
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Affiliation(s)
- Eileen K Jaffe
- Fox Chase Cancer Center - Temple University Health System, 333 Cottman Ave, Philadelphia, PA 19111, USA.
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10
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Leandro J, Stokka AJ, Teigen K, Andersen OA, Flatmark T. Substituting Tyr 138 in the active site loop of human phenylalanine hydroxylase affects catalysis and substrate activation. FEBS Open Bio 2017; 7:1026-1036. [PMID: 28680815 PMCID: PMC5494296 DOI: 10.1002/2211-5463.12243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/27/2017] [Accepted: 05/10/2017] [Indexed: 11/22/2022] Open
Abstract
Mammalian phenylalanine hydroxylase (PAH) is a key enzyme in l‐phenylalanine (l‐Phe) metabolism and is active as a homotetramer. Biochemical and biophysical work has demonstrated that it cycles between two states with a variably low and a high activity, and that the substrate l‐Phe is the key player in this transition. X‐ray structures of the catalytic domain have shown mobility of a partially intrinsically disordered Tyr138‐loop to the active site in the presence of l‐Phe. The mechanism by which the loop dynamics are coupled to substrate binding at the active site in tetrameric PAH is not fully understood. We have here conducted functional studies of four Tyr138 point mutants. A high linear correlation (r2 = 0.99) was observed between their effects on the catalytic efficiency of the catalytic domain dimers and the corresponding effect on the catalytic efficiency of substrate‐activated full‐length tetramers. In the tetramers, a correlation (r2 = 0.96) was also observed between the increase in catalytic efficiency (activation) and the global conformational change (surface plasmon resonance signal response) at the same l‐Phe concentration. The new data support a similar functional importance of the Tyr138‐loop in the catalytic domain and the full‐length enzyme homotetramer.
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Affiliation(s)
- João Leandro
- Department of Biomedicine University of Bergen Norway.,Metabolism and Genetics Group Research Institute for Medicines (iMed.ULisboa) Faculty of Pharmacy University of Lisbon Portugal.,Present address: Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai 1425 Madison Avenue, Box 1498 New York NY 10029 USA
| | - Anne J Stokka
- Department of Biomedicine University of Bergen Norway.,The Biotechnology Centre of Oslo University of Oslo Norway
| | - Knut Teigen
- Department of Biomedicine University of Bergen Norway
| | - Ole A Andersen
- Department of Biomedicine University of Bergen Norway.,Evotec (UK) Ltd .Abingdon UK
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11
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Subedi BP, Fitzpatrick PF. Kinetic Mechanism and Intrinsic Rate Constants for the Reaction of a Bacterial Phenylalanine Hydroxylase. Biochemistry 2016; 55:6848-6857. [DOI: 10.1021/acs.biochem.6b01012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bishnu P. Subedi
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio Texas 78229, United States
| | - Paul F. Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio Texas 78229, United States
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12
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McCracken J, Eser BE, Mannikko D, Krzyaniak MD, Fitzpatrick PF. HYSCORE Analysis of the Effects of Substrates on Coordination of Water to the Active Site Iron in Tyrosine Hydroxylase. Biochemistry 2015; 54:3759-71. [DOI: 10.1021/acs.biochem.5b00363] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- John McCracken
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Bekir E. Eser
- Department
of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229, United States
| | - Donald Mannikko
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Matthew D. Krzyaniak
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Paul F. Fitzpatrick
- Department
of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229, United States
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13
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Ronau J, Paul LN, Fuchs JE, Liedl K, Abu-Omar MM, Das C. A conserved acidic residue in phenylalanine hydroxylase contributes to cofactor affinity and catalysis. Biochemistry 2014; 53:6834-48. [PMID: 25295853 PMCID: PMC4222540 DOI: 10.1021/bi500734h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 09/22/2014] [Indexed: 01/19/2023]
Abstract
The catalytic domains of aromatic amino acid hydroxylases (AAAHs) contain a non-heme iron coordinated to a 2-His-1-carboxylate facial triad and two water molecules. Asp139 from Chromobacterium violaceum PAH (cPAH) resides within the second coordination sphere and contributes key hydrogen bonds with three active site waters that mediate its interaction with an oxidized form of the cofactor, 7,8-dihydro-l-biopterin, in crystal structures. To determine the catalytic role of this residue, various point mutants were prepared and characterized. Our isothermal titration calorimetry (ITC) analysis of iron binding implies that polarity at position 139 is not the sole criterion for metal affinity, as binding studies with D139E suggest that the size of the amino acid side chain also appears to be important. High-resolution crystal structures of the mutants reveal that Asp139 may not be essential for holding the bridging water molecules together, because many of these waters are retained even in the Ala mutant. However, interactions via the bridging waters contribute to cofactor binding at the active site, interactions for which charge of the residue is important, as the D139N mutant shows a 5-fold decrease in its affinity for pterin as revealed by ITC (compared to a 16-fold loss of affinity in the case of the Ala mutant). The Asn and Ala mutants show a much more pronounced defect in their kcat values, with nearly 16- and 100-fold changes relative to that of the wild type, respectively, indicating a substantial role of this residue in stabilization of the transition state by aligning the cofactor in a productive orientation, most likely through direct binding with the cofactor, supported by data from molecular dynamics simulations of the complexes. Our results indicate that the intervening water structure between the cofactor and the acidic residue masks direct interaction between the two, possibly to prevent uncoupled hydroxylation of the cofactor before the arrival of phenylalanine. It thus appears that the second-coordination sphere Asp residue in cPAH, and, by extrapolation, the equivalent residue in other AAAHs, plays a role in fine-tuning pterin affinity in the ground state via deformable interactions with bridging waters and assumes a more significant role in the transition state by aligning the cofactor through direct hydrogen bonding.
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Affiliation(s)
- Judith
A. Ronau
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University, 266
Whitney Avenue, New Haven, Connecticut 06520, United States
| | - Lake N. Paul
- Bindley
Biosciences Center, Purdue University, West Lafayette, Indiana 47907, United States
| | - Julian E. Fuchs
- Institute
of General, Inorganic and Theoretical Chemistry and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, Innrain
80/82, 6020 Innsbruck, Austria
- Centre
for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Klaus
R. Liedl
- Institute
of General, Inorganic and Theoretical Chemistry and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, Innrain
80/82, 6020 Innsbruck, Austria
| | - Mahdi M. Abu-Omar
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Chittaranjan Das
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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14
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Baisya SS, Roy PS. Crystal structure of (2-amino-7-methyl-4-oxido-pteridine-6-carboxyl-ato-κ(3) O (4),N (5),O (6))aqua-(1,10-phenanthroline-κ(2) N,N')copper(II) trihydrate. Acta Crystallogr Sect E Struct Rep Online 2014; 70:348-51. [PMID: 25484742 PMCID: PMC4257256 DOI: 10.1107/s1600536814022302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 10/09/2014] [Indexed: 11/23/2022]
Abstract
In a hydrated copper(II) complex, 2-amino-7-methyl-4-oxidopteridine-6-carboxylate and 1,10-phenanthroline ligands chelate the CuII cation while a water molecule further coordinates to the CuII cation to complete the elongated distorted octahedral coordination geometry. In the title compound, [Cu(C8H5N5O3)(C12H8N2)(H2O)]·3H2O, the CuII cation is O,N,O′-chelated by the 2-amino-7-methyl-4-oxidopteridine-6-carboxylate anion and N,N′-chelated by the 1,10-phenanthroline (phen) ligand. A water molecule further coordinates to the CuII cation to complete the elongated distorted octahedral coordination geometry. In the molecule, the pteridine ring system is essentially planar [maximum deviation = 0.055 (4) Å], and its mean plane is nearly perpendicular to the phen ring system [dihedral angle = 85.97 (3)°]. In the crystal, N—H⋯O, O—H⋯N and O—H⋯·O hydrogen bonds, as well as weak C—H⋯O hydrogen bonds and C—H⋯π interactions, link the complex molecules and lattice water molecules into a three-dimensional supramolecular architecture. Extensive π–π stacking between nearly parallel aromatic rings of adjacent molecules are also observed, the centroid-to-centroid distances being 3.352 (2), 3.546 (3), 3.706 (3) and 3.744 (3) Å.
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Affiliation(s)
- Siddhartha S Baisya
- Department of Chemistry, University of North Bengal, Siliguri 734 013, India
| | - Parag S Roy
- Department of Chemistry, University of North Bengal, Siliguri 734 013, India
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15
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Chadha N, Tiwari AK, Kumar V, Milton MD, Mishra AK. In silico thermodynamics stability change analysis involved in BH4 responsive mutations in phenylalanine hydroxylase: QM/MM and MD simulations analysis. J Biomol Struct Dyn 2014; 33:573-83. [PMID: 24628256 DOI: 10.1080/07391102.2014.897258] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The mammalian tetrahydrobiopterin (BH4)-dependent phenylalanine hydroxylases (PAH), involved in important metabolic pathways of phenylalanine, belong to non-heme iron-containing aromatic acid hydroxylases' enzyme (AAH) family. AAHs utilize BH4 as protein co-factor and thus promote hydroxylation reactions of their substrates. Any alterations in BH4 -mediated AAH's pathway or mutations in these enzymes are responsible for various disorders, and thus highlights the importance of mutational analysis to assess the effect on their biosynthetic pathways. Our present studies are aimed at single-site mutations in PAH that lead to thermodynamic stability change upon folding and further validation of designed non-reduced BH2 designed co-factors. We have presented single-site mutational analysis of PAH where single-site mutations have been identified from known literature. Further, in silico studies with the PAH, in silico mutant PAH, and crystallized known mutant A313T forms, involved QM/MM and Molecular Dynamics (MD) simulations analysis. The modified co-factor A showed high affinity with PAH and all mutant PAH with high G-score of -14.851. The best pose high affinity co-factor A subjected to QM/MM optimization which leads to square-pyramidal coordination of non-heme active site. The structural and energetic information obtained from the production phase of 20 ns MD simulation of co-factor-metalloprotein complex results helped to understand the binding mode and involvement of three molecules throughout the reaction pathways' catalysis of PAH. The free energies of binding (dG) of A were found to be -68.181 kcal/mol and -72.249 for 1DMW and 1TDW for A313T mutant. Binding of Co-factor A do not perturb the coordination environment of iron at the active site which resides in 2-Histdine and 1-Glutamate triad, and may enhance the percentage response towards co-factor-mediated therapy.
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Affiliation(s)
- Nidhi Chadha
- a Division of Cyclotron and Radiopharmaceutical Sciences , Institute of Nuclear Medicine and Allied Sciences , Brig. S. K. Mazumdar Road, Delhi 110054 , India
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16
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Wang H, Chen H, Hao G, Yang B, Feng Y, Wang Y, Feng L, Zhao J, Song Y, Zhang H, Chen YQ, Wang L, Chen W. Role of the phenylalanine-hydroxylating system in aromatic substance degradation and lipid metabolism in the oleaginous fungus Mortierella alpina. Appl Environ Microbiol 2013; 79:3225-33. [PMID: 23503309 PMCID: PMC3685260 DOI: 10.1128/aem.00238-13] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 03/05/2013] [Indexed: 11/20/2022] Open
Abstract
Mortierella alpina is a filamentous fungus commonly found in soil that is able to produce lipids in the form of triacylglycerols that account for up to 50% of its dry weight. Analysis of the M. alpina genome suggests that there is a phenylalanine-hydroxylating system for the catabolism of phenylalanine, which has never been found in fungi before. We characterized the phenylalanine-hydroxylating system in M. alpina to explore its role in phenylalanine metabolism and its relationship to lipid biosynthesis. Significant changes were found in the profile of fatty acids in M. alpina grown on medium containing an inhibitor of the phenylalanine-hydroxylating system compared to M. alpina grown on medium without inhibitor. Genes encoding enzymes involved in the phenylalanine-hydroxylating system (phenylalanine hydroxylase [PAH], pterin-4α-carbinolamine dehydratase, and dihydropteridine reductase) were expressed heterologously in Escherichia coli, and the resulting proteins were purified to homogeneity. Their enzymatic activity was investigated by high-performance liquid chromatography (HPLC) or visible (Vis)-UV spectroscopy. Two functional PAH enzymes were observed, encoded by distinct gene copies. A novel role for tetrahydrobiopterin in fungi as a cofactor for PAH, which is similar to its function in higher life forms, is suggested. This study establishes a novel scheme for the fungal degradation of an aromatic substance (phenylalanine) and suggests that the phenylalanine-hydroxylating system is functionally significant in lipid metabolism.
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Affiliation(s)
- Hongchao Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Haiqin Chen
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Guangfei Hao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Bo Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Yun Feng
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
| | - Yu Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Lu Feng
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
| | - Jianxin Zhao
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Yuanda Song
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Hao Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Yong Q. Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Lei Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
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17
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Daubner SC, Avila A, Bailey JO, Barrera D, Bermudez JY, Giles DH, Khan CA, Shaheen N, Thompson JW, Vasquez J, Oxley SP, Fitzpatrick PF. Mutagenesis of a specificity-determining residue in tyrosine hydroxylase establishes that the enzyme is a robust phenylalanine hydroxylase but a fragile tyrosine hydroxylase. Biochemistry 2013; 52:1446-55. [PMID: 23368961 PMCID: PMC3584195 DOI: 10.1021/bi400031n] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The aromatic amino acid hydroxylases tyrosine hydroxylase (TyrH) and phenylalanine hydroxylase (PheH) have essentially identical active sites; however, PheH is nearly incapable of hydroxylating tyrosine, while TyrH can readily hydroxylate both tyrosine and phenylalanine. Previous studies have indicated that Asp425 of TyrH is important in determining the substrate specificity of that enzyme [Daubner, S. C., Melendez, J., and Fitzpatrick, P. F. (2000) Biochemistry 39, 9652-9661]. Alanine-scanning mutagenesis of amino acids 423-427, a mobile loop containing Asp425, shows that only mutagenesis of Asp425 alters the activity of the enzyme significantly. Saturation mutagenesis of Asp425 results in large (up to 10(4)) decreases in the V(max) and V(max)/K(tyr) values for tyrosine hydroxylation, but only small decreases or even increases in the V(max) and V(max)/K(phe) values for phenylalanine hydroxylation. The decrease in the tyrosine hydroxylation activity of the mutant proteins is due to an uncoupling of tetrahydropterin oxidation from amino acid hydroxylation with tyrosine as the amino acid substrate. In contrast, with the exception of the D425W mutant, the extent of coupling of tetrahydropterin oxidation and amino acid hydroxylation is unaffected or increases with phenylalanine as the amino acid substrate. The decrease in the V(max) value with tyrosine as the substrate shows a negative correlation with the hydrophobicity of the amino acid residue at position 425. The results are consistent with a critical role of Asp425 being to prevent a hydrophobic interaction that results in a restricted active site in which hydroxylation of tyrosine does not occur.
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Affiliation(s)
- S. Colette Daubner
- Department of Biological Sciences, St. Mary’s University, San Antonio TX 78228
| | - Audrey Avila
- Department of Biological Sciences, St. Mary’s University, San Antonio TX 78228
| | - Johnathan O. Bailey
- Department of Biochemistry and Biophysics, Texas A&M University, College Station TX 77840
| | - Dimitrios Barrera
- Department of Chemistry and Biochemistry, St. Mary’s University, San Antonio TX 78228
| | - Jaclyn Y. Bermudez
- Department of Biological Sciences, St. Mary’s University, San Antonio TX 78228
| | - David H. Giles
- Department of Biochemistry, University of Texas Health Science Center San Antonio, San Antonio TX 78229
| | - Crystal A. Khan
- Department of Biochemistry, University of Texas Health Science Center San Antonio, San Antonio TX 78229
| | - Noel Shaheen
- Department of Biological Sciences, St. Mary’s University, San Antonio TX 78228
| | - Janie Womac Thompson
- Department of Biochemistry and Biophysics, Texas A&M University, College Station TX 77840
| | - Jessica Vasquez
- Department of Biochemistry and Biophysics, Texas A&M University, College Station TX 77840
| | - Susan P. Oxley
- Department of Chemistry and Biochemistry, St. Mary’s University, San Antonio TX 78228
| | - Paul F. Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center San Antonio, San Antonio TX 78229
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18
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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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19
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Zhang W, Ames BD, Walsh CT. Identification of phenylalanine 3-hydroxylase for meta-tyrosine biosynthesis. Biochemistry 2011; 50:5401-3. [PMID: 21615132 DOI: 10.1021/bi200733c] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phenylalanine hydroxylase (PheH) is an iron(II)-dependent enzyme that catalyzes the hydroxylation of aromatic amino acid l-phenylalanine (L-Phe) to l-tyrosine (L-Tyr). The enzymatic modification has been demonstrated to be highly regiospecific, forming proteinogenic para-Tyr (p-Tyr) exclusively. Here we biochemically characterized the first example of a phenylalanine 3-hydroxylase (Phe3H) that catalyzes the synthesis of meta-Tyr (m-Tyr) from Phe. Subsequent mutagenesis studies revealed that two residues in the active site of Phe3H (Cys187 and Thr202) contribute to C-3 rather than C-4 hydroxylation of the phenyl ring. This work sets the stage for the mechanistic and structural study of regiospecific control of the substrate hydroxylation by PheH.
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Affiliation(s)
- Wenjun Zhang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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20
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Gersting SW, Staudigl M, Truger MS, Messing DD, Danecka MK, Sommerhoff CP, Kemter KF, Muntau AC. Activation of phenylalanine hydroxylase induces positive cooperativity toward the natural cofactor. J Biol Chem 2010; 285:30686-97. [PMID: 20667834 PMCID: PMC2945563 DOI: 10.1074/jbc.m110.124016] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Revised: 06/29/2010] [Indexed: 11/06/2022] Open
Abstract
Protein misfolding with loss-of-function of the enzyme phenylalanine hydroxylase (PAH) is the molecular basis of phenylketonuria in many individuals carrying missense mutations in the PAH gene. PAH is complexly regulated by its substrate L-Phenylalanine and its natural cofactor 6R-L-erythro-5,6,7,8-tetrahydrobiopterin (BH(4)). Sapropterin dihydrochloride, the synthetic form of BH(4), was recently approved as the first pharmacological chaperone to correct the loss-of-function phenotype. However, current knowledge about enzyme function and regulation in the therapeutic setting is scarce. This illustrates the need for comprehensive analyses of steady state kinetics and allostery beyond single residual enzyme activity determinations to retrace the structural impact of missense mutations on the phenylalanine hydroxylating system. Current standard PAH activity assays are either indirect (NADH) or discontinuous due to substrate and product separation before detection. We developed an automated fluorescence-based continuous real-time PAH activity assay that proved to be faster and more efficient but as precise and accurate as standard methods. Wild-type PAH kinetic analyses using the new assay revealed cooperativity of activated PAH toward BH(4), a previously unknown finding. Analyses of structurally preactivated variants substantiated BH(4)-dependent cooperativity of the activated enzyme that does not rely on the presence of l-Phenylalanine but is determined by activating conformational rearrangements. These findings may have implications for an individualized therapy, as they support the hypothesis that the patient's metabolic state has a more significant effect on the interplay of the drug and the conformation and function of the target protein than currently appreciated.
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Affiliation(s)
- Søren W. Gersting
- From the Department of Molecular Pediatrics, Dr. von Hauner Children's Hospital, Munich 80337 and
| | - Michael Staudigl
- From the Department of Molecular Pediatrics, Dr. von Hauner Children's Hospital, Munich 80337 and
| | - Marietta S. Truger
- From the Department of Molecular Pediatrics, Dr. von Hauner Children's Hospital, Munich 80337 and
| | - Dunja D. Messing
- From the Department of Molecular Pediatrics, Dr. von Hauner Children's Hospital, Munich 80337 and
| | - Marta K. Danecka
- From the Department of Molecular Pediatrics, Dr. von Hauner Children's Hospital, Munich 80337 and
| | - Christian P. Sommerhoff
- the Department of Clinical Chemistry and Clinical Biochemistry, Surgical Clinic, Ludwig-Maximilians-University, Munich 80336, Germany
| | - Kristina F. Kemter
- From the Department of Molecular Pediatrics, Dr. von Hauner Children's Hospital, Munich 80337 and
| | - Ania C. Muntau
- From the Department of Molecular Pediatrics, Dr. von Hauner Children's Hospital, Munich 80337 and
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21
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Phenylalanine hydroxylase (PAH) from the lower eukaryote Leishmania major. Mol Biochem Parasitol 2010; 175:58-67. [PMID: 20887755 DOI: 10.1016/j.molbiopara.2010.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2010] [Revised: 09/10/2010] [Accepted: 09/19/2010] [Indexed: 11/20/2022]
Abstract
Aromatic amino acid hydroxylases (AAAH) typically use tetrahydrobiopterin (H(4)B) as the cofactor. The protozoan parasite Leishmania major requires biopterin for growth and expresses strong salvage and regeneration systems to maintain H(4)B levels. Here we explored the consequences of genetic manipulation of the sole L. major phenylalanine hydroxylase (PAH) to explore whether it could account for the Leishmania H(4)B requirement. L. major PAH resembles AAAHs of other organisms, bearing eukaryotic-type domain organization, and conservation of key catalytic residues including those implicated in pteridine binding. A pah(-) null mutant and an episomal complemented overexpressing derivative (pah-/+PAH) were readily obtained, and metabolic labeling studies established that PAH was required to hydroxylate Phe to Tyr. Neither WT nor overexpressing lines were able to hydroxylate radiolabeled tyrosine or tryptophan, nor to synthesize catecholamines. WT but not pah(-) parasites showed reactivity with an antibody to melanin when grown with l-3,4-dihydroxyphenylalanine (L-DOPA), although the reactive product is unlikely to be melanin sensu strictu. WT was auxotrophic for Phe, Trp and Tyr, suggesting that PAH activity was insufficient to meet normal Tyr requirements. However, pah(-) showed an increased sensitivity to Tyr deprivation, while the pah(-)/+PAH overexpressor showed increased survival and could be adapted to grow well without added Tyr. pah(-) showed no alterations in H(4)B-dependent differentiation, as established by in vitro metacyclogenesis, or survival in mouse or macrophage infections. Thus Leishmania PAH may mitigate but not alleviate Tyr auxotrophy, but plays no essential role in the steps of the parasite infectious cycle. These findings suggest PAH is unlikely to explain the Leishmania requirement for biopterin.
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22
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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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23
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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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24
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Olsson E, Martinez A, Teigen K, Jensen VR. Water Dissociation and Dioxygen Binding in Phenylalanine Hydroxylase. Eur J Inorg Chem 2010. [DOI: 10.1002/ejic.200900489] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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25
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Miyazaki S, Kojima T, Mayer JM, Fukuzumi S. Proton-coupled electron transfer of ruthenium(III)-pterin complexes: a mechanistic insight. J Am Chem Soc 2009; 131:11615-24. [PMID: 19722655 DOI: 10.1021/ja904386r] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ruthenium(II) complexes having pterins of redox-active heteroaromatic coenzymes as ligands were demonstrated to perform multistep proton transfer (PT), electron transfer (ET), and proton-coupled electron transfer (PCET) processes. Thermodynamic parameters including pK(a) and bond dissociation energy (BDE) of multistep PCET processes in acetonitrile (MeCN) were determined for ruthenium-pterin complexes, [Ru(II)(Hdmp)(TPA)](ClO(4))(2) (1), [Ru(II)(Hdmdmp)(TPA)](ClO(4))(2) (2), [Ru(II)(dmp(-))(TPA)]ClO(4) (3), and [Ru(II)(dmdmp(-))(TPA)]ClO(4) (4) (Hdmp = 6,7-dimethylpterin, Hdmdmp = N,N-dimethyl-6,7-dimethylpterin, TPA = tris(2-pyridylmethyl)amine), all of which had been isolated and characterized before. The BDE difference between 1 and one-electron oxidized species, [Ru(III)(dmp(-))(TPA)](2+), was determined to be 89 kcal mol(-1), which was large enough to achieve hydrogen atom transfer (HAT) from phenol derivatives. In the HAT reactions from phenol derivatives to [Ru(III)(dmp(-))(TPA)](2+), the second-order rate constants (k) were determined to exhibit a linear relationship with BDE values of phenol derivatives with a slope (-0.4), suggesting that this HAT is simultaneous proton and electron transfer. As for HAT reaction from 2,4,6-tri-tert-buthylphenol (TBP; BDE = 79.15 kcal mol(-1)) to [Ru(III)(dmp(-))(TPA)](2+), the activation parameters were determined to be DeltaH(double dagger) = 1.6 +/- 0.2 kcal mol(-1) and DeltaS(double dagger) = -36 +/- 2 cal K(-1) mol(-1). This small activation enthalpy suggests a hydrogen-bonded adduct formation prior to HAT. Actually, in the reaction of 4-nitrophenol with [Ru(III)(dmp(-))(TPA)](2+), the second-order rate constants exhibited saturation behavior at higher concentrations of the substrate, and low-temperature ESI-MS allowed us to detect the hydrogen-bonding adduct. This also lends credence to an associative mechanism of the HAT involving intermolecular hydrogen bonding between the deprotonated dmp ligand and the phenolic O-H to facilitate the reaction. In particular, a two-point hydrogen bonding between the complex and the substrate involving the 2-amino group of the deprotonated pterin ligand effectively facilitates the HAT reaction from the substrate to the Ru(III)-pterin complex.
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Affiliation(s)
- Soushi Miyazaki
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
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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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Chow MS, Eser BE, Wilson SA, Hodgson KO, Hedman B, Fitzpatrick PF, Solomon EI. Spectroscopy and kinetics of wild-type and mutant tyrosine hydroxylase: mechanistic insight into O2 activation. J Am Chem Soc 2009; 131:7685-98. [PMID: 19489646 DOI: 10.1021/ja810080c] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Tyrosine hydroxylase (TH) is a pterin-dependent nonheme iron enzyme that catalyzes the hydroxylation of L-tyr to L-DOPA in the rate-limiting step of catecholamine neurotransmitter biosynthesis. We have previously shown that the Fe(II) site in phenylalanine hydroxylase (PAH) converts from six-coordinate (6C) to five-coordinate (5C) only when both substrate + cofactor are bound. However, steady-state kinetics indicate that TH has a different co-substrate binding sequence (pterin + O(2) + L-tyr) than PAH (L-phe + pterin + O(2)). Using X-ray absorption spectroscopy (XAS), and variable-temperature-variable-field magnetic circular dichroism (VTVH MCD) spectroscopy, we have investigated the geometric and electronic structure of the wild-type (WT) TH and two mutants, S395A and E332A, and their interactions with substrates. All three forms of TH undergo 6C --> 5C conversion with tyr + pterin, consistent with the general mechanistic strategy established for O(2)-activating nonheme iron enzymes. We have also applied single-turnover kinetic experiments with spectroscopic data to evaluate the mechanism of the O(2) and pterin reactions in TH. When the Fe(II) site is 6C, the two-electron reduction of O(2) to peroxide by Fe(II) and pterin is favored over individual one-electron reactions, demonstrating that both a 5C Fe(II) and a redox-active pterin are required for coupled O(2) reaction. When the Fe(II) is 5C, the O(2) reaction is accelerated by at least 2 orders of magnitude. Comparison of the kinetics of WT TH, which produces Fe(IV)=O + 4a-OH-pterin, and E332A TH, which does not, shows that the E332 residue plays an important role in directing the protonation of the bridged Fe(II)-OO-pterin intermediate in WT to productively form Fe(IV)=O, which is responsible for hydroxylating L-tyr to L-DOPA.
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Affiliation(s)
- Marina S Chow
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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Miyazaki S, Ohkubo K, Kojima T, Fukuzumi S. Proton Shift upon One-Electron Reduction in Ruthenium(II)-Coordinated Pterins. Angew Chem Int Ed Engl 2008; 47:9669-72. [DOI: 10.1002/anie.200802835] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Miyazaki S, Ohkubo K, Kojima T, Fukuzumi S. Proton Shift upon One-Electron Reduction in Ruthenium(II)-Coordinated Pterins. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200802835] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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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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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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Martinez A, Calvo AC, Teigen K, Pey AL. Rescuing Proteins of Low Kinetic Stability by Chaperones and Natural Ligands: Phenylketonuria, a Case Study. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2008; 83:89-134. [DOI: 10.1016/s0079-6603(08)00603-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Miyazaki S, Kojima T, Sakamoto T, Matsumoto T, Ohkubo K, Fukuzumi S. Proton-Coupled Electron Transfer in Ruthenium(II)−Pterin Complexes: Formation of Ruthenium-Coordinated Pterin Radicals and Their Electronic Structures. Inorg Chem 2007; 47:333-43. [DOI: 10.1021/ic701759c] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Soushi Miyazaki
- Department of Material and Life Science, Graduate School of Engineering, Osaka University and SORST (JST), Suita, Osaka 565-0871 and Department of Chemistry, Faculty of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-Ku, Fukuoka 812-8581, Japan
| | - Takahiko Kojima
- Department of Material and Life Science, Graduate School of Engineering, Osaka University and SORST (JST), Suita, Osaka 565-0871 and Department of Chemistry, Faculty of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-Ku, Fukuoka 812-8581, Japan
| | - Taisuke Sakamoto
- Department of Material and Life Science, Graduate School of Engineering, Osaka University and SORST (JST), Suita, Osaka 565-0871 and Department of Chemistry, Faculty of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-Ku, Fukuoka 812-8581, Japan
| | - Tetsuya Matsumoto
- Department of Material and Life Science, Graduate School of Engineering, Osaka University and SORST (JST), Suita, Osaka 565-0871 and Department of Chemistry, Faculty of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-Ku, Fukuoka 812-8581, Japan
| | - Kei Ohkubo
- Department of Material and Life Science, Graduate School of Engineering, Osaka University and SORST (JST), Suita, Osaka 565-0871 and Department of Chemistry, Faculty of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-Ku, Fukuoka 812-8581, Japan
| | - Shunichi Fukuzumi
- Department of Material and Life Science, Graduate School of Engineering, Osaka University and SORST (JST), Suita, Osaka 565-0871 and Department of Chemistry, Faculty of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-Ku, Fukuoka 812-8581, Japan
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Pey AL, Stricher F, Serrano L, Martinez A. Predicted effects of missense mutations on native-state stability account for phenotypic outcome in phenylketonuria, a paradigm of misfolding diseases. Am J Hum Genet 2007; 81:1006-24. [PMID: 17924342 PMCID: PMC2265664 DOI: 10.1086/521879] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Accepted: 07/25/2007] [Indexed: 12/15/2022] Open
Abstract
Phenylketonuria (PKU) is a genetic disease caused by mutations in human phenylalanine hydroxylase (PAH). Most missense mutations result in misfolding of PAH, increased protein turnover, and a loss of enzymatic function. We studied the prediction of the energetic impact on PAH native-state stability of 318 PKU-associated missense mutations, using the protein-design algorithm FoldX. For the 80 mutations for which expression analyses have been performed in eukaryote systems, in most cases we found substantial overall correlations between the mutational energetic impact and both in vitro residual activities and patient metabolic phenotype. This finding confirmed that the decrease in protein stability is the main molecular pathogenic mechanism in PKU and the determinant for phenotypic outcome. Metabolic phenotypes have been shown to be better predicted than in vitro residual activities, probably because of greater stringency in the phenotyping process. Finally, all the remaining 238 PKU missense mutations compiled at the PAH locus knowledgebase (PAHdb) were analyzed, and their phenotypic outcomes were predicted on the basis of the energetic impact provided by FoldX. Residues in exons 7-9 and in interdomain regions within the subunit appear to play an important structural role and constitute hotspots for destabilization. FoldX analysis will be useful for predicting the phenotype associated with rare or new mutations detected in patients with PKU. However, additional factors must be considered that may contribute to the patient phenotype, such as possible effects on catalysis and interindividual differences in physiological and metabolic processes.
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Affiliation(s)
- Angel L Pey
- Department of Biomedicine, University of Bergen, Bergen, Norway
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Fang TY, Tseng WC, Pan CH, Chun YT, Wang MY. Protein engineering of Sulfolobus solfataricus maltooligosyltrehalose synthase to alter its selectivity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2007; 55:5588-94. [PMID: 17567140 DOI: 10.1021/jf0701279] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Maltooligosyltrehalose synthase (MTSase) is one of the key enzymes involved in trehalose production from starch and catalyzes an intramolecular transglycosylation reaction by converting the alpha-1,4- to alpha,alpha-1,1-glucosidic linkage. Mutations at residues F206, F207, and F405 were constructed to change the selectivity of the enzyme because the changes in selectivity could reduce the side hydrolysis reaction of releasing glucose and thus increase trehalose production from starch. As compared with wild-type MTSase, F405Y and F405M MTSases had decreased ratios of the initial rate of glucose formation to that of trehalose formation in starch digestion at 75 degrees C when wild-type and mutant MTSases were, respectively, used with isoamylase and maltooligosyltrehalose trehalohydrolase (MTHase). The highest trehalose yield from starch digestion was by the mutant MTSase having the lowest initial rate of glucose formation to trehalose formation, and this predicted high trehalose yield better than the ratio of catalytic efficiency for hydrolysis to that for transglycosylation.
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Affiliation(s)
- Tsuei-Yun Fang
- Department of Food Science, National Taiwan Ocean University, Keelung, Taiwan.
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Fang TY, Tseng WC, Chung YT, Pan CH. Mutations on aromatic residues of the active site to alter selectivity of the Sulfolobus solfataricus maltooligosyltrehalose synthase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2006; 54:3585-3590. [PMID: 19127729 DOI: 10.1021/jf060152z] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Mutations Y290F, Y367F, F405Y, and Y409F located near subsite +1 were constructed in maltooligosyltrehalose synthase (MTSase) to alter the selectivity of the enzyme. These mutations were designed to evaluate the effects of hydrophobic interactions and/or hydrogen bondings on transglycosylation and side hydrolysis reactions. The catalytic efficiencies of Y290F MTSase for hydrolysis and transglycosylation reactions were only 6.6 and 5.6%, respectively, of those of wildtype MTSase, whereas the catalytic efficiencies of Y367F MTSase were decreased by about half. F405Y MTSase had similar catalytic efficiencies for transglycosylation and a somewhat lower catalytic efficiency for hydrolysis. Y409F MTSase had somewhat lower catalytic efficiencies for the transglycosylation and a similar catalytic efficiency for hydrolysis. Y290F and Y367F MTSases had large changes in delta(deltaG), suggesting that there are hydrogen bonds between the substrate and residues Y290 and Y367 of wild-type MTSase. Compared with wild-type MTSase, F405Y MTSase had decreased ratios of hydrolysis to transglycosylation, whereas Y290F, Y367F, and Y409F MTSases had increased ratios. These results suggest that use of F405Y MTSase might result in a higher yield of trehalose production from starch when it replaces wild-type MTSase.
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Affiliation(s)
- Tsuei-Yun Fang
- Department of Food Science, National Taiwan Ocean University, Keelung, Taiwan.
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Leandro J, Nascimento C, de Almeida IT, Leandro P. Co-expression of different subunits of human phenylalanine hydroxylase: evidence of negative interallelic complementation. Biochim Biophys Acta Mol Basis Dis 2006; 1762:544-50. [PMID: 16545551 DOI: 10.1016/j.bbadis.2006.02.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2005] [Revised: 02/01/2006] [Accepted: 02/03/2006] [Indexed: 11/30/2022]
Abstract
To study the interaction between two different subunits of the heteromeric human phenylalanine hydroxylase (hPAH), present in hyperphenylalaninemic (HPA) compound heterozygous patients, heteroallelic hPAH enzymes were produced. A dual vector expression system was used (PRO Bacterial Expression System) in which each mutant subunit was expressed from a separate compatible vector, with different epitope tags, in a single bacterial host. Experimental conditions were selected in order that each plasmid produced equivalent levels of mutant subunits. In this study, we demonstrated that both subunits were expressed and that the purified heteroallelic enzymes, were catalytically active. As expected, the produced proteins displayed enzymatic activities levels lower than the predicted catalytic activity, calculated by averaging in vitro PAH activities from both alleles, and were strongly dependent on the proteins subunit composition. The obtained data suggest that interactions between the studied hPAH subunits, namely the I65T, R261Q, R270K and V388M, and the wild-type protein occurred. As postulated, this phenomenon could be a source of phenotypic variation in genetic diseases involving multimeric proteins.
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Affiliation(s)
- João Leandro
- Unidade de Biologia Molecular e Biopatologia Experimental, Centro de Patogénese Molecular, Faculdade de Farmácia da Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
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Farquhar ER, Koehntop KD, Emerson JP, Que L. Post-translational self-hydroxylation: A probe for oxygen activation mechanisms in non-heme iron enzymes. Biochem Biophys Res Commun 2005; 338:230-9. [PMID: 16165090 DOI: 10.1016/j.bbrc.2005.08.191] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2005] [Accepted: 08/25/2005] [Indexed: 10/25/2022]
Abstract
Recent years have seen considerable evolution in our understanding of the mechanisms of oxygen activation by non-heme iron enzymes, with high-valent iron-oxo intermediates coming to the forefront as formidably potent oxidants. In the absence of substrate, the generation of vividly colored chromophores deriving from the self-hydroxylation of a nearby aromatic amino acid for a number of these enzymes has afforded an opportunity to discern the conditions under which O2 activation occurs to generate a high-valent iron intermediate, and has provided a basis for a rigorous mechanistic examination of the oxygenation process. Here, we summarize the current evidence for self-hydroxylation processes in both mononuclear non-heme iron enzymes and in mutant forms of ribonucleotide reductase, and place it within the context of our developing understanding of the oxidative transformations accomplished by non-heme iron centers.
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Affiliation(s)
- Erik R Farquhar
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
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Sarkissian CN, Gámez A. Phenylalanine ammonia lyase, enzyme substitution therapy for phenylketonuria, where are we now? Mol Genet Metab 2005; 86 Suppl 1:S22-6. [PMID: 16165390 DOI: 10.1016/j.ymgme.2005.06.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2005] [Revised: 06/20/2005] [Accepted: 06/24/2005] [Indexed: 11/16/2022]
Abstract
Phenylketonuria (PKU) is an autosomal recessive genetic disorder in which mutations in the phenylalanine-4-hydroxylase (PAH) gene result in an inactive enzyme (PAH, EC 1.14.16.1). The effect is an inability to metabolize phenylalanine (Phe), translating into elevated levels of Phe in the bloodstream (hyperphenylalaninemia). If therapy is not implemented at birth, mental retardation can occur. PKU patients respond to treatment with a low-phenylalanine diet, but compliance with the diet is difficult, therefore the development of alternative treatments is desirable. Enzyme substitution therapy with a recombinant phenylalanine ammonia lyase (PAL) is currently being explored. This enzyme converts Phe to the harmless metabolites, trans-cinnamic acid and trace ammonia. Taken orally and when non-absorbable and protected, PAL lowers plasma Phe in mutant hyperphenylalaninemic mouse models. Subcutaneous administration of PAL results in more substantial lowering of plasma and significant reduction in brain Phe levels, however the metabolic effect is not sustained following repeated injections due to an immune response. We have chemically modified PAL by pegylation to produce a protected form of PAL that possesses better specific activity, prolonged half-life, and reduced immunogenicity in vivo. Subcutaneous administration of pegylated molecules to PKU mice has the desired metabolic response (prolonged reduction in blood Phe levels) with greatly attenuated immunogenicity.
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Affiliation(s)
- Christineh N Sarkissian
- Department of Biology, Human Genetics, and Pediatrics, McGill University, Debelle Laboratory, Montreal Children's Hospital Research Institute, 2300 Tupper Street, A-717, Montreal, QC, Canada H3H 1P3.
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Abu-Omar MM, Loaiza A, Hontzeas N. Reaction mechanisms of mononuclear non-heme iron oxygenases. Chem Rev 2005; 105:2227-52. [PMID: 15941213 DOI: 10.1021/cr040653o] [Citation(s) in RCA: 457] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mahdi M Abu-Omar
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
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Maita N, Hatakeyama K, Okada K, Hakoshima T. Structural basis of biopterin-induced inhibition of GTP cyclohydrolase I by GFRP, its feedback regulatory protein. J Biol Chem 2004; 279:51534-40. [PMID: 15448133 DOI: 10.1074/jbc.m409440200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
GTP cyclohydrolase I (GTPCHI) is the rate-limiting enzyme involved in the biosynthesis of tetrahydrobiopterin, a key cofactor necessary for nitric oxide synthase and for the hydroxylases that are involved in the production of catecholamines and serotonin. In animals, the GTPCHI feedback regulatory protein (GFRP) binds GTPCHI to mediate feed-forward activation of GTPCHI activity in the presence of phenylalanine, whereas it induces feedback inhibition of enzyme activity in the presence of biopterin. Here, we have reported the crystal structure of the biopterin-induced inhibitory complex of GTPCHI and GFRP and compared it with the previously reported phenylalanine-induced stimulatory complex. The structure reveals five biopterin molecules located at each interface between GTPCHI and GFRP. Induced fitting structural changes by the biopterin binding expand large conformational changes in GTPCHI peptide segments forming the active site, resulting in inhibition of the activity. By locating 3,4-dihydroxy-phenylalanine-responsive dystonia mutations in the complex structure, we found mutations that may possibly disturb the GFRP-mediated regulation of GTPCHI.
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Affiliation(s)
- Nobuo Maita
- Structural Biology Laboratory, Nara Institute of Science and Technology, CREST, Japan Science and Technology Agency, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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Erlandsen H, Pey AL, Gámez A, Pérez B, Desviat LR, Aguado C, Koch R, Surendran S, Tyring S, Matalon R, Scriver CR, Ugarte M, Martínez A, Stevens RC. Correction of kinetic and stability defects by tetrahydrobiopterin in phenylketonuria patients with certain phenylalanine hydroxylase mutations. Proc Natl Acad Sci U S A 2004; 101:16903-8. [PMID: 15557004 PMCID: PMC534739 DOI: 10.1073/pnas.0407256101] [Citation(s) in RCA: 135] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2004] [Indexed: 11/18/2022] Open
Abstract
Phenylketonuria patients harboring a subset of phenylalanine hydroxylase (PAH) mutations have recently shown normalization of blood phenylalanine levels upon oral administration of the PAH cofactor tetrahydrobiopterin [(6R)-L-erythro-5,6,7,8-tetrahydrobiopterin (BH4)]. Several hypotheses have been put forward to explain BH4 responsiveness, but the molecular basis for the corrective effect(s) of BH4 has not been understood. We have investigated the biochemical, kinetic, and structural changes associated with BH4-responsive mutations (F39L, I65T, R68S, H170D, E178G, V190A, R261Q, A300S, L308F, A313T, A373T, V388M, E390G, P407S, and Y414C). The biochemical and kinetic characterization of the 15 mutants studied points toward a multifactorial basis for the BH4 responsiveness; the mutants show residual activity (>30% of WT) and display various kinetic defects, including increased Km (BH4) and reduced cooperativity of substrate binding, but no decoupling of cofactor (BH4) oxidation. For some, BH4 seems to function through stabilization and protection of the enzyme from inactivation and proteolytic degradation. In the crystal structures of a phenylketonuria mutant, A313T, minor changes were seen when compared with the WT PAH structures, consistent with the mild effects the mutant has upon activity of the enzyme both in vitro and in vivo. Truncations made in the A313T mutant PAH form revealed that the N and C termini of the enzyme influence active site binding. Of fundamental importance is the observation that BH4 appears to increase Phe catabolism if at least one of the two heterozygous mutations has any residual activity remaining.
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Affiliation(s)
- Heidi Erlandsen
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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43
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Teigen K, Dao KK, McKinney JA, Gorren ACF, Mayer B, Frøystein NA, Haavik J, Martínez A. Tetrahydrobiopterin binding to aromatic amino acid hydroxylases. Ligand recognition and specificity. J Med Chem 2004; 47:5962-71. [PMID: 15537351 DOI: 10.1021/jm0497646] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The three aromatic amino acid hydroxylases (phenylalanine, tyrosine, and tryptophan hydroxylase) and nitric oxide synthase (NOS) all utilize (6R)-l-erythro-5,6,7,8-tetrahydrobiopterin (BH(4)) as cofactor. The pterin binding site in the three hydroxylases is well conserved and different from the binding site in NOS. The structures of phenylalanine hydroxylase (PAH) and of NOS in complex with BH(4) are still the only crystal structures available for the reduced cofactor-enzyme complexes. We have studied the enzyme-bound and free conformations of BH(4) by NMR spectroscopy and molecular docking into the active site of the three hydroxylases, using endothelial NOS as a comparative probe. We have found that the dihydroxypropyl side chain of BH(4) adopts different conformations depending on which hydroxylase it interacts with. All the bound conformations are different from that of BH(4) free in solution at neutral pH. The different bound conformations appear to result from specific interactions with nonconserved amino acids at the BH(4) binding sites of the hydroxylases, notably the stretch 248-251 (numeration in PAH) and the residue corresponding to Ala322 in PAH, i.e., Ser in TH and Ala in TPH. On the basis of analysis of molecular interaction fields, we discuss the selectivity determinants for each hydroxylase and explain the high-affinity inhibitory effect of 7-tetrahydrobiopterin specifically for PAH.
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Affiliation(s)
- Knut Teigen
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009-Bergen, Norway
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44
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Shiota Y, Yoshizawa K. QM/MM Study of the Mononuclear Non-Heme Iron Active Site of Phenylalanine Hydroxylase. J Phys Chem B 2004. [DOI: 10.1021/jp048001r] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Yoshihito Shiota
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 812-8581, Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 812-8581, Japan
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Stokka AJ, Carvalho RN, Barroso JF, Flatmark T. Probing the role of crystallographically defined/predicted hinge-bending regions in the substrate-induced global conformational transition and catalytic activation of human phenylalanine hydroxylase by single-site mutagenesis. J Biol Chem 2004; 279:26571-80. [PMID: 15060071 DOI: 10.1074/jbc.m400879200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phenylalanine hydroxylase (PAH) is generally considered to undergo a large and reversible conformational transition upon l-Phe binding, which is closely linked to the substrate-induced catalytic activation of this hysteretic enzyme. Recently, several crystallographically solvent-exposed hinge-bending regions including residues 31-34, 111-117, 218-226, and 425-429 have been defined/predicted to be involved in the intra-protomer propagation of the substrate-triggered molecular motions generated at the active site. On this basis, single-site mutagenesis of key residues in these regions of the human PAH tetramer was performed in the present study, and their functional impact was measured by steady-state kinetics and the global conformational transition as assessed by surface plasmon resonance and intrinsic tryptophan fluorescence spectroscopy. A strong correlation (r(2) = 0.93-0.96) was observed between the l-Phe-induced global conformational transition and V(max) values for wild-type human PAH and the mutant forms K113P, N223D, N426D, and N32D, in contrast to the substitution T427P, which resulted in a tetrameric form with no kinetic cooperativity. Furthermore, the flexible intra-domain linker region (residues 31-34) seems to be involved in a more local conformational change, and the biochemical/biophysical properties of the G33A/G33V mutant forms support a key function of this residue in the positioning of the autoregulatory sequence (residues 1-30) and thus in the regulation of the solvent and substrate access to the active site. The mutant forms revealed a variably reduced global conformational stability compared with wild-type human PAH, as measured by thermal denaturation and limited proteolysis.
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Affiliation(s)
- Anne Jorunn Stokka
- Section of Biochemistry and Molecular Biology, Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway
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46
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Zoidakis J, Sam M, Volner A, Han A, Vu K, Abu-Omar MM. Role of the second coordination sphere residue tyrosine 179 in substrate affinity and catalytic activity of phenylalanine hydroxylase. J Biol Inorg Chem 2004; 9:289-96. [PMID: 14999516 DOI: 10.1007/s00775-004-0527-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2003] [Accepted: 01/29/2004] [Indexed: 10/26/2022]
Abstract
Phenylalanine hydroxylase converts phenylalanine to tyrosine utilizing molecular oxygen and tetrahydropterin as a cofactor, and belongs to the aromatic amino acid hydroxylases family. The catalytic domains of these enzymes are structurally similar. According to recent crystallographic studies, residue Tyr179 in Chromobacterium violaceum phenylalanine hydroxylase is located in the active site and its hydroxyl oxygen is 5.1 A from the iron, where it has been suggested to play a role in positioning the pterin cofactor. To determine the catalytic role of this residue, the point mutants Y179F and Y179A of phenylalanine hydroxylase were prepared and characterized. Both mutants displayed comparable stability and metal binding to the native enzyme, as determined by their melting temperatures in the presence and absence of iron. The catalytic activity ( k(cat)) of the Y179F and Y179A proteins was lower than wild-type phenylalanine hydroxylase by an order of magnitude, suggesting that the hydroxyl group of Tyr179 plays a role in the rate-determining step in catalysis. The K(M) values for different tetrahydropterin cofactors and phenylalanine were decreased by a factor of 3-4 in the Y179F mutant. However, the K(M) values for different pterin cofactors were slightly higher in the Y179A mutant than those measured for the wild-type enzyme, and, more significantly, the K(M) value for phenylalanine was increased by 10-fold in the Y179A mutant. By the criterion of k(cat)/ K(Phe), the Y179F and Y179A mutants display 10% and 1%, respectively, of the activity of wild-type phenylalanine hydroxylase. These results are consistent with Tyr179 having a pronounced role in binding phenylalanine but a secondary effect in the formation of the hydroxylating species. In conjunction with recent crystallographic analyses of a ternary complex of phenylalanine hydroxylase, the reported findings establish that Tyr179 is essential in maintaining the catalytic integrity and phenylalanine binding of the enzyme via indirect interactions with the substrate, phenylalanine. A model that accounts for the role of Tyr179 in binding phenylalanine is proposed.
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Affiliation(s)
- Jérôme Zoidakis
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
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47
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Andersen OA, Stokka AJ, Flatmark T, Hough E. 2.0A resolution crystal structures of the ternary complexes of human phenylalanine hydroxylase catalytic domain with tetrahydrobiopterin and 3-(2-thienyl)-L-alanine or L-norleucine: substrate specificity and molecular motions related to substrate binding. J Mol Biol 2003; 333:747-57. [PMID: 14568534 DOI: 10.1016/j.jmb.2003.09.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The crystal structures of the catalytic domain of human phenylalanine hydroxylase (hPheOH) in complex with the physiological cofactor 6(R)-L-erythro-5,6,7,8-tetrahydrobiopterin (BH(4)) and the substrate analogues 3-(2-thienyl)-L-alanine (THA) or L-norleucine (NLE) have been determined at 2.0A resolution. The ternary THA complex confirms a previous 2.5A structure, and the ternary NLE complex shows that similar large conformational changes occur on binding of NLE as those observed for THA. Both structures demonstrate that substrate binding triggers structural changes throughout the entire protomer, including the displacement of Tyr138 from a surface position to a buried position at the active site, with a maximum displacement of 20.7A for its hydroxyl group. Two hinge-bending regions, centred at Leu197 and Asn223, act in consort upon substrate binding to create further large structural changes for parts of the C terminus. Thus, THA/L-Phe binding to the active site is likely to represent the epicentre of the global conformational changes observed in the full-length tetrameric enzyme. The carboxyl and amino groups of THA and NLE are positioned identically in the two structures, supporting the conclusion that these groups are of key importance in substrate binding, thus explaining the broad non-physiological substrate specificity observed for artificially activated forms of the enzyme. However, the specific activity with NLE as the substrate was only about 5% of that with THA, which is explained by the different affinities of binding and different catalytic turnover.
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Affiliation(s)
- Ole Andreas Andersen
- Department of Chemistry, Faculty of Science, University of Tromsø, N-9037, Tromsø, Norway
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48
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Affiliation(s)
- Chin-Chuan Wei
- Department of Immunology, The Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
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49
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Teigen K, Martinez A. Probing cofactor specificity in phenylalanine hydroxylase by molecular dynamics simulations. J Biomol Struct Dyn 2003; 20:733-40. [PMID: 12744702 DOI: 10.1080/07391102.2003.10506889] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Phenylalanine hydroxylase (PAH) is a tetrahydrobiopterin-dependent enzyme that catalyzes the hydroxylation of L-phenylalanine (L-Phe) to L-tyrosine using dioxygen as an additional substrate. The requirement of PAH for a cofactor is absolute, but several cofactor analogs are able to substitute the natural cofactor in catalysis. However, it is only the natural cofactor 6R-tetrahydrobiopterin (6R-BH(4)) that induces a negative regulatory effect on the enzyme. In order to get further insights on the molecular basis for this specificity, we studied the structure of the cofactor-enzyme complex and the conformational changes induced by cofactor binding by molecular dynamics simulations. Simulations were carried out on the enzyme alone and complexed with 6R-BH(4) and with two cofactor analogs, 6S-BH(4) and 6-methyl-tetrahydropterin (6M-PH(4)). In the resting unbound enzyme Tyr377 in the catalytic domain is hydrogen bonded to both Ser23 and Glu21 of the autoregulatory N-terminal sequence. This hydrogen bonding network is disturbed by the binding of BH(4), which interacts with Ser23. By doing so, 6R-BH(4) facilitates an interaction between Glu21 and the active site iron, further pulling the N-terminal into the active site of PAH and blocking the L-Phe binding site. Thus, in the 6R-BH(4) complexed enzyme, the N-terminal functions as an intrinsic amino acid regulatory sequence (IARS). Neither 6M-PH(4) nor 6S-BH(4) can interact favorably with Ser23, and do not induce an inhibitory effect on PAH. These simulations thus explain the previous findings that the two hydroxyl groups in the side chain of the 6R epimer of BH(4) are essential for the inhibitory regulatory effect on PAH.
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Affiliation(s)
- Knut Teigen
- Department of Biochemistry and Molecular Biology, University of Bergen, Jonas Liesvei 91, 5009 Bergen, Norway
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Kemsley JN, Wasinger EC, Datta S, Mitić N, Acharya T, Hedman B, Caradonna JP, Hodgson KO, Solomon EI. Spectroscopic and kinetic studies of PKU-inducing mutants of phenylalanine hydroxylase: Arg158Gln and Glu280Lys. J Am Chem Soc 2003; 125:5677-86. [PMID: 12733906 DOI: 10.1021/ja029106f] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phenylalanine hydroxylase (PAH) is a tetrahydrobiopterin-dependent, nonheme iron enzyme that catalyzes the hydroxylation of L-Phe to L-Tyr in the rate-limiting step of phenylalanine catabolism. This reaction is tightly coupled in the wild-type enzyme to oxidation of the tetrahydropterin cofactor. Dysfunction of PAH activity in humans leads to the disease phenylketonuria (PKU). We have investigated two PKU-inducing mutants, Arg158Gln and Glu280Lys, using kinetic methods, magnetic circular dichrosim (MCD) spectroscopy, and X-ray absorption spectroscopy (XAS). Analysis of the products produced by the mutant enzymes shows that although both oxidize pterin at more than twice the rate of wild-type enzyme, these reactions are only approximately 20% coupled to production of L-Tyr. Previous MCD and XAS studies had demonstrated that the resting Fe(II) site is six-coordinate in the wild-type enzyme and converts to a five-coordinate site when both L-Phe and reduced pterin are present in the active site. Although the Arg158Gln mutant forms the five-coordinate site when both cosubstrates are bound, the Fe(II) site of the Glu280Lys mutant remains six-coordinate. These results provide insight into the PAH reaction and disease mechanism at a molecular level, indicating that the first step of the mechanism is formation of a peroxy-pterin species, which subsequently reacts with the Fe(II) site if the pterin is properly oriented for formation of an Fe-OO-pterin bridge and an open coordination position is available on the Fe(II).
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Affiliation(s)
- Jyllian N Kemsley
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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