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Fitzpatrick PF. The aromatic amino acid hydroxylases: Structures, catalysis, and regulation of phenylalanine hydroxylase, tyrosine hydroxylase, and tryptophan hydroxylase. Arch Biochem Biophys 2023; 735:109518. [PMID: 36639008 DOI: 10.1016/j.abb.2023.109518] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/01/2023] [Accepted: 01/06/2023] [Indexed: 01/12/2023]
Abstract
The aromatic amino acid hydroxylases phenylalanine hydroxylase, tyrosine hydroxylase, and tryptophan hydroxylase are non-heme iron enzymes that catalyze key physiological reactions. This review discusses the present understanding of the common catalytic mechanism of these enzymes and recent advances in understanding the relationship between their structures and their regulation.
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Affiliation(s)
- Paul F Fitzpatrick
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, 78229, USA.
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2
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Li L, Du Y, Wang Y, He N, Wang B, Zhang T. Atractylone Alleviates Ethanol-Induced Gastric Ulcer in Rat with Altered Gut Microbiota and Metabolites. J Inflamm Res 2022; 15:4709-4723. [PMID: 35996682 PMCID: PMC9392477 DOI: 10.2147/jir.s372389] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/03/2022] [Indexed: 11/23/2022] Open
Abstract
Background Gastric ulcer (GU) is the most common multifactor gastrointestinal disorder affecting millions of people worldwide. There is evidence that gut microbiota is closely related to the development of GU. Atractylone (ATR) has been reported to possess potential biological activities, but research on ATR alleviating GU injury is unprecedented. Methods Helicobacter pylori (H. pylori)-induced GU model in zebrafish and ethanol-induced acute GU model in rat were established to evaluate the anti-inflammatory and ulcer inhibitory effects of ATR. Then, 16S rRNA sequencing and metabolomics analysis were performed to investigate the effect of ATR on the microbiota and metabolites in rat feces and their correlation. Results Therapeutically, ATR inhibited H. pylori-induced gastric mucosal injury in zebrafish. In the ulceration model of rat, ATR mitigated the gastric lesions damage caused by ethanol, decreased the ulcer area, and reduced the production of inflammatory factors. Additionally, ATR alleviated the gastric oxidative stress injury by increasing the activity of superoxide dismutase (SOD) and decreasing the level of malondialdehyde (MDA). Furthermore, ATR played a positive role in relieving ulcer through reshaping gut microbiota composition including Parabacteroides and Bacteroides and regulating the levels of metabolites including amino acids, short-chain fatty acids (SCFAs), and bile acids. Conclusion Our work sheded light on the mechanism of ATR treating GU from the perspective of the gut microbiota and explored the correlation between gut microbiota, metabolites, and host phenotype.
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Affiliation(s)
- Ling Li
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, People’s Republic of China
| | - Yaoyao Du
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
| | - Yang Wang
- Metabo-Profile Biotechnology (Shanghai) Co. Ltd, Shanghai, People’s Republic of China
| | - Ning He
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, People’s Republic of China
| | - Bing Wang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
- Chinese Academy of Sciences, Shanghai Institute of Materia Medica, Shanghai, People’s Republic of China
| | - Tong Zhang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
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3
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Solomon EI, DeWeese DE, Babicz JT. Mechanisms of O 2 Activation by Mononuclear Non-Heme Iron Enzymes. Biochemistry 2021; 60:3497-3506. [PMID: 34266238 PMCID: PMC8768060 DOI: 10.1021/acs.biochem.1c00370] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Two major subclasses of mononuclear non-heme ferrous enzymes use two electron-donating organic cofactors (α-ketoglutarate or pterin) to activate O2 to form FeIV═O intermediates that further react with their substrates through hydrogen atom abstraction or electrophilic aromatic substitution. New spectroscopic methodologies have been developed, enabling the study of the active sites in these enzymes and their oxygen intermediates. Coupled to electronic structure calculations, the results of these spectroscopies provide fundamental insight into mechanism. This Perspective summarizes the results of these studies in elucidating the mechanism of dioxygen activation to form the FeIV═O intermediate and the geometric and electronic structure of this intermediate that enables its high reactivity and selectivity in product formation.
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Affiliation(s)
- Edward I. Solomon
- Department of Chemistry, Stanford University, 333 Campus Dr. Stanford, CA, 94305, United States,SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, United States
| | - Dory E. DeWeese
- Department of Chemistry, Stanford University, 333 Campus Dr. Stanford, CA, 94305, United States
| | - Jeffrey T. Babicz
- Department of Chemistry, Stanford University, 333 Campus Dr. Stanford, CA, 94305, United States
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4
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Direct coordination of pterin to Fe II enables neurotransmitter biosynthesis in the pterin-dependent hydroxylases. Proc Natl Acad Sci U S A 2021; 118:2022379118. [PMID: 33876764 PMCID: PMC8053929 DOI: 10.1073/pnas.2022379118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The pterin-dependent nonheme iron enzymes hydroxylate aromatic amino acids to perform the biosynthesis of neurotransmitters to maintain proper brain function. These enzymes activate oxygen using a pterin cofactor and an aromatic amino acid substrate bound to the FeII active site to form a highly reactive FeIV = O species that initiates substrate oxidation. In this study, using tryptophan hydroxylase, we have kinetically generated a pre-FeIV = O intermediate and characterized its structure as a FeII-peroxy-pterin species using absorption, Mössbauer, resonance Raman, and nuclear resonance vibrational spectroscopies. From parallel characterization of the pterin cofactor and tryptophan substrate-bound ternary FeII active site before the O2 reaction (including magnetic circular dichroism spectroscopy), these studies both experimentally define the mechanism of FeIV = O formation and demonstrate that the carbonyl functional group on the pterin is directly coordinated to the FeII site in both the ternary complex and the peroxo intermediate. Reaction coordinate calculations predict a 14 kcal/mol reduction in the oxygen activation barrier due to the direct binding of the pterin carbonyl to the FeII site, as this interaction provides an orbital pathway for efficient electron transfer from the pterin cofactor to the iron center. This direct coordination of the pterin cofactor enables the biological function of the pterin-dependent hydroxylases and demonstrates a unified mechanism for oxygen activation by the cofactor-dependent nonheme iron enzymes.
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Affiliation(s)
- Michael Hellwig
- Professur für LebensmittechemieTechnische Universität Dresden D-01062 Dresden Deutschland
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6
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Enabling HEK293 cells for antibiotic-free media bioprocessing through CRISPR/Cas9 gene editing. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.107299] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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7
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Abstract
Oxidation is one of the deterioration reactions of proteins in food, the importance of which is comparable to others such as Maillard, lipation, or protein-phenol reactions. While research on protein oxidation has led to a precise understanding of the processes and consequences in physiological systems, knowledge about the specific effects of protein oxidation in food or the role of "oxidized" dietary protein for the human body is comparatively scarce. Food protein oxidation can occur during the whole processing axis, from primary production to intestinal digestion. The present review summarizes the current knowledge and mechanisms of food protein oxidation from a chemical, technological, and nutritional-physiological viewpoint and gives a comprehensive classification of the individual reactions. Different analytical approaches are compared, and the relationship between oxidation of food proteins and oxidative stress in vivo is critically evaluated.
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Affiliation(s)
- Michael Hellwig
- Chair of Food Chemistry, Technische Universität Dresden, D-01062, Dresden, Germany
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Grüschow S, Sadler JC, Sharratt PJ, Goss RJM. Phenylalanine meta-Hydroxylase: A Single Residue Mediates Mechanistic Control of Aromatic Amino Acid Hydroxylation. Chembiochem 2019; 21:417-422. [PMID: 31318464 PMCID: PMC7027792 DOI: 10.1002/cbic.201900320] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/15/2019] [Indexed: 01/31/2023]
Abstract
The rare nonproteinogenic amino acid, meta‐l‐tyrosine is biosynthetically intriguing. Whilst the biogenesis of tyrosine from phenylalanine is well characterised, the mechanistic basis for meta‐hydroxylation is unknown. Herein, we report the analysis of 3‐hydroxylase (Phe3H) from Streptomyces coeruleorubidus. Insights from kinetic analyses of the wild‐type enzyme and key mutants as well as of the biocatalytic conversion of synthetic isotopically labelled substrates and fluorinated substrate analogues advance understanding of the process by which meta‐hydroxylation is mediated, revealing T202 to play an important role. In the case of the WT enzyme, a deuterium label at the 3‐position is lost, whereas in in the T202A mutant 75 % retention is observed, with loss of stereospecificity. These data suggest that one of two possible mechanisms is at play; direct, enzyme‐catalysed deprotonation following electrophilic aromatic substitution or stereospecific loss of one proton after a 1,2‐hydride shift. Furthermore, our kinetic parameters for Phe3H show efficient regiospecific generation of meta‐l‐tyrosine from phenylalanine and demonstrate the enzyme's ability to regiospecifically hydroxylate unnatural fluorinated substrates.
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Affiliation(s)
- Sabine Grüschow
- School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, KY16 9ST, UK
| | - Joanna C Sadler
- School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, KY16 9ST, UK
| | - Peter J Sharratt
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Rebecca J M Goss
- School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, KY16 9ST, UK
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Lacy DC. Applications of the Marcus cross relation to inner sphere reduction of O 2: implications in small-molecule activation. Inorg Chem Front 2019. [DOI: 10.1039/c9qi00828d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The Marcus cross relation is demonstrated to be applicable to inner sphere electron transfer from iron to molecular oxygen by incorporation of the Fe(iii)–O2to Fe(iii) + superoxide BDFE inKeq. A few case-studies are provided as working examples.
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Affiliation(s)
- David C. Lacy
- Department of Chemistry
- University at Buffalo
- State University of New York
- Buffalo
- USA
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10
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Subedi BP, Fitzpatrick PF. Mutagenesis of an Active-Site Loop in Tryptophan Hydroxylase Dramatically Slows the Formation of an Early Intermediate in Catalysis. J Am Chem Soc 2018; 140:5185-5192. [PMID: 29589922 DOI: 10.1021/jacs.8b00936] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Solution studies of the aromatic amino acid hydroxylases are consistent with the FeIVO intermediate not forming until both the amino acid and tetrahydropterin substrates have bound. Structural studies have shown that the positions of active-site loops differs significantly between the free enzyme and the enzyme-amino acid-tetrahydropterin complex. In tryptophan hydroxylase (TrpH) these mobile loops contain residues 124-134 and 365-371, with a key interaction involving Ile366. The I366N mutation in TrpH results in decreases of 1-2 orders of magnitude in the kcat and kcat/ Km values. Single turnover analyses establish that the limiting rate constant for turnover is product release for the wild-type enzyme but is formation of the first detectable intermediate I in catalysis in the mutant enzyme. The mutation does not alter the kinetics of NO binding to the ternary complex nor does it uncouple FeIVO formation from amino acid hydroxylation. The effects on the kcat value of wild-type TrpH of changing viscosity are consistent with rate-limiting product release. While the effect of viscosity on the kcat/ KO2 value is small, consistent with reversible oxygen binding, the effects on the kcat/ Km values for tryptophan and the tetrahydropterin are large, with the latter value exceeding the expected limit and varying with the identity of the viscogen. In contrast, the kinetic parameters of I366N TrpH show small changes with viscosity. The results are consistent with binding of the amino acid and pterin substrate to form the ternary complex being directly coupled to closure of loops over the active site and formation of the reactive complex. The mutation destabilizes this initial event.
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Affiliation(s)
- Bishnu P Subedi
- Department of Biochemistry and Structural Biology , University of Texas Health Science Center at San Antonio , San Antonio , Texas 78229 , United States
| | - Paul F Fitzpatrick
- Department of Biochemistry and Structural Biology , University of Texas Health Science Center at San Antonio , San Antonio , Texas 78229 , United States
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11
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Turcas R, Lakk-Bogáth D, Speier G, Kaizer J. Steric control and the mechanism of benzaldehyde oxidation by polypyridyl oxoiron(iv) complexes: aromatic versus benzylic hydroxylation of aromatic aldehydes. Dalton Trans 2018; 47:3248-3252. [PMID: 29446776 DOI: 10.1039/c7dt03727a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The present study describes the first example of the hydroxylation of benzaldehydes by synthetic nonheme oxoiron(iv) complexes, where the reactivity, chemoselectivity, and mechanism were strongly influenced by the ligand environment of the iron center.
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Affiliation(s)
- Ramona Turcas
- Department of Chemistry, University of Pannonia, H-8201 Veszprém, Hungary.
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12
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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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13
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Kal S, Que L. Dioxygen activation by nonheme iron enzymes with the 2-His-1-carboxylate facial triad that generate high-valent oxoiron oxidants. J Biol Inorg Chem 2017; 22:339-365. [PMID: 28074299 DOI: 10.1007/s00775-016-1431-2] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/13/2016] [Indexed: 11/24/2022]
Abstract
The 2-His-1-carboxylate facial triad is a widely used scaffold to bind the iron center in mononuclear nonheme iron enzymes for activating dioxygen in a variety of oxidative transformations of metabolic significance. Since the 1990s, over a hundred different iron enzymes have been identified to use this platform. This structural motif consists of two histidines and the side chain carboxylate of an aspartate or a glutamate arranged in a facial array that binds iron(II) at the active site. This triad occupies one face of an iron-centered octahedron and makes the opposite face available for the coordination of O2 and, in many cases, substrate, allowing the tailoring of the iron-dioxygen chemistry to carry out a plethora of diverse reactions. Activated dioxygen-derived species involved in the enzyme mechanisms include iron(III)-superoxo, iron(III)-peroxo, and high-valent iron(IV)-oxo intermediates. In this article, we highlight the major crystallographic, spectroscopic, and mechanistic advances of the past 20 years that have significantly enhanced our understanding of the mechanisms of O2 activation and the key roles played by iron-based oxidants.
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Affiliation(s)
- Subhasree Kal
- Department of Chemistry, Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Lawrence Que
- Department of Chemistry, Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN, 55455, USA.
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14
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Metal dependence and branched RNA cocrystal structures of the RNA lariat debranching enzyme Dbr1. Proc Natl Acad Sci U S A 2016; 113:14727-14732. [PMID: 27930312 DOI: 10.1073/pnas.1612729114] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Intron lariats are circular, branched RNAs (bRNAs) produced during pre-mRNA splicing. Their unusual chemical and topological properties arise from branch-point nucleotides harboring vicinal 2',5'- and 3',5'-phosphodiester linkages. The 2',5'-bonds must be hydrolyzed by the RNA debranching enzyme Dbr1 before spliced introns can be degraded or processed into small nucleolar RNA and microRNA derived from intronic RNA. Here, we measure the activity of Dbr1 from Entamoeba histolytica by using a synthetic, dark-quenched bRNA substrate that fluoresces upon hydrolysis. Purified enzyme contains nearly stoichiometric equivalents of Fe and Zn per polypeptide and demonstrates turnover rates of ∼3 s-1 Similar rates are observed when apo-Dbr1 is reconstituted with Fe(II)+Zn(II) under aerobic conditions. Under anaerobic conditions, a rate of ∼4.0 s-1 is observed when apoenzyme is reconstituted with Fe(II). In contrast, apo-Dbr1 reconstituted with Mn(II) or Fe(II) under aerobic conditions is inactive. Diffraction data from crystals of purified enzyme using X-rays tuned to the Fe absorption edge show Fe partitions primarily to the β-pocket and Zn to the α-pocket. Structures of the catalytic mutant H91A in complex with 7-mer and 16-mer synthetic bRNAs reveal bona fide RNA branchpoints in the Dbr1 active site. A bridging hydroxide is in optimal position for nucleophilic attack of the scissile phosphate. The results clarify uncertainties regarding structure/function relationships in Dbr1 enzymes, and the fluorogenic probe permits high-throughput screening for inhibitors that may hold promise as treatments for retroviral infections and neurodegenerative disease.
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15
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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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16
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Meisburger SP, Taylor AB, Khan CA, Zhang S, Fitzpatrick PF, Ando N. Domain Movements upon Activation of Phenylalanine Hydroxylase Characterized by Crystallography and Chromatography-Coupled Small-Angle X-ray Scattering. J Am Chem Soc 2016; 138:6506-16. [PMID: 27145334 PMCID: PMC4896396 DOI: 10.1021/jacs.6b01563] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mammalian phenylalanine hydroxylase (PheH) is an allosteric enzyme that catalyzes the first step in the catabolism of the amino acid phenylalanine. Following allosteric activation by high phenylalanine levels, the enzyme catalyzes the pterin-dependent conversion of phenylalanine to tyrosine. Inability to control elevated phenylalanine levels in the blood leads to increased risk of mental disabilities commonly associated with the inherited metabolic disorder, phenylketonuria. Although extensively studied, structural changes associated with allosteric activation in mammalian PheH have been elusive. Here, we examine the complex allosteric mechanisms of rat PheH using X-ray crystallography, isothermal titration calorimetry (ITC), and small-angle X-ray scattering (SAXS). We describe crystal structures of the preactivated state of the PheH tetramer depicting the regulatory domains docked against the catalytic domains and preventing substrate binding. Using SAXS, we further describe the domain movements involved in allosteric activation of PheH in solution and present the first demonstration of chromatography-coupled SAXS with Evolving Factor Analysis (EFA), a powerful method for separating scattering components in a model-independent way. Together, these results support a model for allostery in PheH in which phenylalanine stabilizes the dimerization of the regulatory domains and exposes the active site for substrate binding and other structural changes needed for activity.
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Affiliation(s)
- Steve P. Meisburger
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Alexander B. Taylor
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229, USA
| | - Crystal A. Khan
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229, USA
| | - Shengnan Zhang
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229, USA
| | - Paul F. Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229, USA
| | - Nozomi Ando
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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First structure of full-length mammalian phenylalanine hydroxylase reveals the architecture of an autoinhibited tetramer. Proc Natl Acad Sci U S A 2016; 113:2394-9. [PMID: 26884182 DOI: 10.1073/pnas.1516967113] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Improved understanding of the relationship among structure, dynamics, and function for the enzyme phenylalanine hydroxylase (PAH) can lead to needed new therapies for phenylketonuria, the most common inborn error of amino acid metabolism. PAH is a multidomain homo-multimeric protein whose conformation and multimerization properties respond to allosteric activation by the substrate phenylalanine (Phe); the allosteric regulation is necessary to maintain Phe below neurotoxic levels. A recently introduced model for allosteric regulation of PAH involves major domain motions and architecturally distinct PAH tetramers [Jaffe EK, Stith L, Lawrence SH, Andrake M, Dunbrack RL, Jr (2013) Arch Biochem Biophys 530(2):73-82]. Herein, we present, to our knowledge, the first X-ray crystal structure for a full-length mammalian (rat) PAH in an autoinhibited conformation. Chromatographic isolation of a monodisperse tetrameric PAH, in the absence of Phe, facilitated determination of the 2.9 Å crystal structure. The structure of full-length PAH supersedes a composite homology model that had been used extensively to rationalize phenylketonuria genotype-phenotype relationships. Small-angle X-ray scattering (SAXS) confirms that this tetramer, which dominates in the absence of Phe, is different from a Phe-stabilized allosterically activated PAH tetramer. The lack of structural detail for activated PAH remains a barrier to complete understanding of phenylketonuria genotype-phenotype relationships. Nevertheless, the use of SAXS and X-ray crystallography together to inspect PAH structure provides, to our knowledge, the first complete view of the enzyme in a tetrameric form that was not possible with prior partial crystal structures, and facilitates interpretation of a wealth of biochemical and structural data that was hitherto impossible to evaluate.
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18
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Fitzpatrick PF. Structural insights into the regulation of aromatic amino acid hydroxylation. Curr Opin Struct Biol 2015; 35:1-6. [PMID: 26241318 DOI: 10.1016/j.sbi.2015.07.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 06/30/2015] [Accepted: 07/15/2015] [Indexed: 11/30/2022]
Abstract
The aromatic amino acid hydroxylases phenylalanine hydroxylase, tyrosine hydroxylase, and tryptophan hydroxylase are homotetramers, with each subunit containing a homologous catalytic domain and a divergent regulatory domain. The solution structure of the regulatory domain of tyrosine hydroxylase establishes that it contains a core ACT domain similar to that in phenylalanine hydroxylase. The isolated regulatory domain of tyrosine hydroxylase forms a stable dimer, while that of phenylalanine hydroxylase undergoes a monomer-dimer equilibrium, with phenylalanine stabilizing the dimer. These solution properties are consistent with the regulatory mechanisms of the two enzymes, in that phenylalanine hydroxylase is activated by phenylalanine binding to an allosteric site, while tyrosine hydroxylase is regulated by binding of catecholamines in the active site.
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Affiliation(s)
- Paul F Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, United States.
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Yin L, Maben ZJ, Becerra A, Stern LJ. Evaluating the Role of HLA-DM in MHC Class II-Peptide Association Reactions. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2015; 195:706-16. [PMID: 26062997 PMCID: PMC4490944 DOI: 10.4049/jimmunol.1403190] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 05/15/2015] [Indexed: 01/07/2023]
Abstract
Ag presentation by MHC class II (MHC II) molecules to CD4(+) T cells plays a key role in the regulation of the adaptive immune response. Loading of antigenic peptides onto MHC II is catalyzed by HLA-DM (DM), a nonclassical MHC II molecule. The mechanism of DM-facilitated peptide loading is an outstanding problem in the field of Ag presentation. In this study, we systemically explored possible kinetic mechanisms for DM-catalyzed peptide association by measuring real-time peptide association kinetics using fluorescence polarization assays and comparing the experimental data with numerically modeled peptide association reactions. We found that DM does not facilitate peptide association by stabilizing peptide-free MHC II against aggregation. Moreover, DM does not promote transition of an inactive peptide-averse conformation of MHC II to an active peptide-receptive conformation. Instead, DM forms an intermediate with MHC II that binds peptide with faster kinetics than MHC II in the absence of DM. In the absence of peptides, interaction of MHC II with DM leads to inactivation and formation of a peptide-averse form. This study provides novel insights into how DM efficiently catalyzes peptide loading during Ag presentation.
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Affiliation(s)
- Liusong Yin
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605; and
| | - Zachary J Maben
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605; and
| | - Aniuska Becerra
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605; and
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605; and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
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20
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Roberts KM, Khan CA, Hinck CS, Fitzpatrick PF. Activation of phenylalanine hydroxylase by phenylalanine does not require binding in the active site. Biochemistry 2014; 53:7846-53. [PMID: 25453233 PMCID: PMC4270383 DOI: 10.1021/bi501183x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
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Phenylalanine
hydroxylase (PheH), a liver enzyme that catalyzes
the hydroxylation of excess phenylalanine in the diet to tyrosine,
is activated by phenylalanine. The lack of activity at low levels
of phenylalanine has been attributed to the N-terminus of the protein’s
regulatory domain acting as an inhibitory peptide by blocking substrate
access to the active site. The location of the site at which phenylalanine
binds to activate the enzyme is unknown, and both the active site
in the catalytic domain and a separate site in the N-terminal regulatory
domain have been proposed. Binding of catecholamines to the active-site
iron was used to probe the accessibility of the active site. Removal
of the regulatory domain increases the rate constants for association
of several catecholamines with the wild-type enzyme by ∼2-fold.
Binding of phenylalanine in the active site is effectively abolished
by mutating the active-site residue Arg270 to lysine. The kcat/Kphe value is
down 104 for the mutant enzyme, and the Km value for phenylalanine for the mutant enzyme is >0.5
M. Incubation of the R270K enzyme with phenylalanine also results
in a 2-fold increase in the rate constants for catecholamine binding.
The change in the tryptophan fluorescence emission spectrum seen in
the wild-type enzyme upon activation by phenylalanine is also seen
with the R270K mutant enzyme in the presence of phenylalanine. Both
results establish that activation of PheH by phenylalanine does not
require binding of the amino acid in the active site. This is consistent
with a separate allosteric site, likely in the regulatory domain.
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Affiliation(s)
- Kenneth M Roberts
- Department of Biochemistry, University of Texas Health Science Center , San Antonio, Texas 78229, United States
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21
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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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22
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Roberts KM, Tormos JR, Fitzpatrick PF. Characterization of unstable products of flavin- and pterin-dependent enzymes by continuous-flow mass spectrometry. Biochemistry 2014; 53:2672-9. [PMID: 24713088 PMCID: PMC4010283 DOI: 10.1021/bi500267c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
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Continuous-flow mass spectrometry
(CFMS) was used to monitor the
products formed during the initial 0.25–20 s of the reactions
catalyzed by the flavoprotein N-acetylpolyamine oxidase
(PAO) and the pterin-dependent enzymes phenylalanine hydroxylase (PheH)
and tyrosine hydroxylase (TyrH). N,N′-Dibenzyl-1,4-diaminobutane (DBDB) is a substrate for PAO
for which amine oxidation is rate-limiting. CFMS of the reaction showed
formation of an initial imine due to oxidation of an exo-carbon–nitrogen bond. Nonenzymatic hydrolysis of the imine
formed benzaldehyde and N-benzyl-1,4-diaminobutane;
the subsequent oxidation by PAO of the latter to an additional imine
could also be followed. Measurement of the deuterium kinetic isotope
effect on DBDB oxidation by CFMS yielded a value of 7.6 ± 0.3,
in good agreement with a value of 6.7 ± 0.6 from steady-state
kinetic analyses. In the PheH reaction, the transient formation of
the 4a-hydroxypterin product was readily detected; tandem mass spectrometry
confirmed attachment of the oxygen to C(4a). With wild-type TyrH,
the 4a-hydroxypterin was also the product. In contrast, no product
other than a dihydropterin could be detected in the reaction of the
mutant protein E332A TyrH.
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Affiliation(s)
- Kenneth M Roberts
- Department of Biochemistry, University of Texas Health Science Center , San Antonio, Texas 78229, United States
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23
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Gelalcha FG. Biomimetic Iron-Catalyzed Asymmetric Epoxidations: Fundamental Concepts, Challenges and Opportunities. Adv Synth Catal 2014. [DOI: 10.1002/adsc.201300716] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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