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Mori T, Teramoto T, Kakuta Y. Crystal structure of activating sulfotransferase SgdX2 involved in biosynthesis of secondary metabolite sungeidine. Biochem Biophys Res Commun 2024; 711:149891. [PMID: 38621346 DOI: 10.1016/j.bbrc.2024.149891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
Microorganisms synthesize a plethora of complex secondary metabolites, many of which are beneficial to human health, such as anticancer agents and antibiotics. Among these, the Sungeidines are a distinct class of secondary metabolites known for their bulky and intricate structures. They are produced by a specific biosynthetic gene cluster within the genome of the soil-dwelling actinomycete Micromonospora sp. MD118. A notable enzyme in the Sungeidine biosynthetic pathway is the activating sulfotransferase SgdX2. In this pathway, SgdX2 mediates a key sulfation step, after which the product undergoes spontaneous dehydration to yield a Sungeidine compound. To delineate the structural basis for SgdX2's substrate recognition and catalytic action, we have determined the crystal structure of SgdX2 in complex with its sulfate donor product, 3'-phosphoadenosine 5'-phosphate (PAP), at a resolution of 1.6 Å. Although SgdX2 presents a compact overall structure, its core elements are conserved among other activating sulfotransferases. Our structural analysis reveals a unique substrate-binding pocket that accommodates bulky, complex substrates, suggesting a specialized adaptation for Sungeidine synthesis. Moreover, we have constructed a substrate docking model that provides insights into the molecular interactions between SgdX2 and Sungeidine F, enhancing our understanding of the enzyme's specificity and catalytic mechanism. The model supports a general acid-base catalysis mechanism, akin to other sulfotransferases, and underscores the minor role of disordered regions in substrate recognition. This integrative study of crystallography and computational modeling advances our knowledge of microbial secondary metabolite biosynthesis and may facilitate the development of novel biotechnological applications.
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Affiliation(s)
- Takahiro Mori
- Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Takamasa Teramoto
- Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
| | - Yoshimitsu Kakuta
- Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
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2
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Yoshimura M, Teramoto T, Asano H, Iwamoto Y, Kondo M, Nishimoto E, Kakuta Y. Crystal structure of tick tyrosylprotein sulfotransferase reveals the activation mechanism of the tick anticoagulant protein madanin. J Biol Chem 2024; 300:105748. [PMID: 38354785 PMCID: PMC10951654 DOI: 10.1016/j.jbc.2024.105748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/19/2024] [Accepted: 02/07/2024] [Indexed: 02/16/2024] Open
Abstract
Ticks pose a substantial public health risk as they transmit various pathogens. This concern is related to the adept blood-sucking strategy of ticks, underscored by the action of the anticoagulant, madanin, which is known to exhibit an approximately 1000-fold increase in anticoagulant activity following sulfation of its two tyrosine residues, Tyr51 and Tyr54. Despite this knowledge, the molecular mechanism underlying sulfation by tick tyrosylprotein sulfotransferase (TPST) remains unclear. In this study, we successfully prepared tick TPST as a soluble recombinant enzyme. We clarified the method by which this enzyme proficiently sulfates tyrosine residues in madanin. Biochemical analysis using a substrate peptide based on madanin and tick TPST, along with the analysis of the crystal structure of the complex and docking simulations, revealed a sequential sulfation process. Initial sulfation at the Tyr51 site augments binding, thereby facilitating efficient sulfation at Tyr54. Beyond direct biochemical implications, these findings considerably improve our understanding of tick blood-sucking strategies. Furthermore, combined with the utility of modified tick TPST, our findings may lead to the development of novel anticoagulants, promising avenues for thrombotic disease intervention and advancements in the field of public health.
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Affiliation(s)
- Misa Yoshimura
- Faculty of Agriculture, Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Kyushu University, Fukuoka, Japan
| | - Takamasa Teramoto
- Faculty of Agriculture, Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Kyushu University, Fukuoka, Japan.
| | - Hirai Asano
- Faculty of Agriculture, Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Kyushu University, Fukuoka, Japan
| | - Yuka Iwamoto
- Faculty of Agriculture, Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Kyushu University, Fukuoka, Japan
| | - Mariko Kondo
- Faculty of Agriculture, Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Kyushu University, Fukuoka, Japan
| | - Etsuko Nishimoto
- Faculty of Agriculture, Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Kyushu University, Fukuoka, Japan
| | - Yoshimitsu Kakuta
- Faculty of Agriculture, Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Kyushu University, Fukuoka, Japan.
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3
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Iwamoto Y, Saito S, Teramoto T, Maruyama-Nakashita A, Kakuta Y. Crystal structure of Arabidopsis thaliana sulfotransferase SOT16 involved in glucosinolate biosynthesis. Biochem Biophys Res Commun 2023; 677:149-154. [PMID: 37586213 DOI: 10.1016/j.bbrc.2023.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023]
Abstract
Glucosinolates (GSLs), a class of secondary metabolites found in Brassicaceae plants, play important roles in plant defense and contribute distinct flavors and aromas when used as food ingredients. Following tissue damage, GSLs undergo enzymatic hydrolysis to release bioactive volatile compounds. Understanding GSL biosynthesis and enzyme involvement is crucial for improving crop quality and advancing agriculture. Plant sulfotransferases (SOTs) play a key role in the final step of GSL biosynthesis by transferring sulfate groups to the precursor molecules. In the present study, we investigated the enzymatic reaction mechanism and broad substrate specificity of Arabidopsis thaliana sulfotransferase AtSOT16, which is involved in GSL biosynthesis, using crystal structure analysis. Our analysis revealed the specific catalytic residues involved in the sulfate transfer reaction and supported the hypothesis of a concerted acid-base catalytic mechanism. Furthermore, the docking models showed a strong correlation between the substrates with high predicted binding affinities and those experimentally reported to exhibit high activity. These findings provide valuable insights into the enzymatic reaction mechanisms and substrate specificity of GSL biosynthesis. The information obtained in this study may contribute to the development of novel strategies for manipulating GSL synthesis pathways in Brassica plants and has potential agricultural applications.
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Affiliation(s)
- Yuka Iwamoto
- Laboratory of Biophysical Chemistry, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan; Kyushu University Future Creators in Science Project (QFC-SP), Japan
| | - Seira Saito
- Kyushu University Future Creators in Science Project (QFC-SP), Japan; Meizen High School, Fukuoka, 830-0022, Japan
| | - Takamasa Teramoto
- Laboratory of Biophysical Chemistry, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan; Kyushu University Future Creators in Science Project (QFC-SP), Japan.
| | - Akiko Maruyama-Nakashita
- Laboratory of Plant Nutrition, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yoshimitsu Kakuta
- Laboratory of Biophysical Chemistry, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan; Kyushu University Future Creators in Science Project (QFC-SP), Japan.
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4
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Kawakami T, Teramoto T, Kakuta Y. Crystal structure of adenosine 5'-phosphosulfate kinase isolated from Archaeoglobus fulgidus. Biochem Biophys Res Commun 2023; 643:105-110. [PMID: 36592583 DOI: 10.1016/j.bbrc.2022.12.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022]
Abstract
The 3'-phosphoadenosine-5'-phosphosulfate (PAPS) molecule is essential during enzyme-catalyzed sulfation reactions as a sulfate donor and is an intermediate in the reduction of sulfate to sulfite in the sulfur assimilation pathway. PAPS is produced through a two-step reaction involving ATP sulfurylase and adenosine 5'-phosphosulfate (APS) kinase enzymes/domains. However, archaeal APS kinases have not yet been characterized and their mechanism of action remains unclear. Here, we first structurally characterized APS kinase from the hyperthermophilic archaeon Archaeoglobus fulgidus, (AfAPSK). We demonstrated the PAPS production activity of AfAPSK at the optimal growth temperature (83 °C). Furthermore, we determined the two crystal structures of AfAPSK: ADP complex and ATP analog adenylyl-imidodiphosphate (AMP-PNP)/Mg2+/APS complex. Structural and complementary mutational analyses revealed the catalytic and substrate recognition mechanisms of AfAPSK. This study also hints at the molecular basis behind the thermal stability of AfAPSK.
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Affiliation(s)
- Tomoya Kawakami
- Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Takamasa Teramoto
- Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan.
| | - Yoshimitsu Kakuta
- Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan.
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5
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Teramoto T, Nishio T, Kurogi K, Sakakibara Y, Kakuta Y. The crystal structure of mouse SULT2A8 reveals the mechanism of 7α-hydroxyl, bile acid sulfation. Biochem Biophys Res Commun 2021; 562:15-20. [PMID: 34030040 DOI: 10.1016/j.bbrc.2021.04.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 04/26/2021] [Indexed: 10/21/2022]
Abstract
Bile acids play essential roles in facilitating the intestinal absorption of lipophilic nutrients as well as regulation of glucose, lipid, and energy homeostasis via activation of some receptors. Bile acids are cytotoxic, and consequently their concentrations are tightly controlled. A critical pathway for bile acid elimination and detoxification is sulfation. The pattern of bile acid sulfation differs by species. Sulfation preferentially occurs at the 3α-OH of bile acids in humans, but at the 7α-OH in mice. A recent study identified mouse cytosolic sulfotransferase 2A8 (mSULT2A8) as the major hepatic 7α-hydroxyl bile acid-sulfating enzyme. To elucidate the 7α-OH specific sulfation mechanism of mSULT2A8, instead of 3α-OH specific sulfation in humans, we determined a crystal structure of mSULT2A8 in complex with cholic acid, a major bile acid, and 3'-phosphoadenosine-5'-phosphate, the sulfate donor product. Our study shows that bile acid-binding mode of mSULT2A8 and how the enzyme holds the 7α-OH group of bile acids at the catalytic center, revealing that the mechanism underlying 7α-OH specific sulfation. The structure shows the substrate binds to mSULT2A8 in an orientation perpendicular to that of human 3α-hydroxyl bile acid-sulfotransferase (hSULT2A1). The structure of the complex provides new insight into species different bile acid metabolism.
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Affiliation(s)
- Takamasa Teramoto
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan
| | - Takeaki Nishio
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan
| | - Katsuhisa Kurogi
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Yoichi Sakakibara
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Yoshimitsu Kakuta
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan.
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Taylor AB, Roberts KM, Cao X, Clark NE, Holloway SP, Donati E, Polcaro CM, Pica-Mattoccia L, Tarpley RS, McHardy SF, Cioli D, LoVerde PT, Fitzpatrick PF, Hart PJ. Structural and enzymatic insights into species-specific resistance to schistosome parasite drug therapy. J Biol Chem 2017; 292:11154-11164. [PMID: 28536265 PMCID: PMC5500785 DOI: 10.1074/jbc.m116.766527] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 05/17/2017] [Indexed: 02/05/2023] Open
Abstract
The antischistosomal prodrug oxamniquine is activated by a sulfotransferase (SULT) in the parasitic flatworm Schistosoma mansoni. Of the three main human schistosome species, only S. mansoni is sensitive to oxamniquine therapy despite the presence of SULT orthologs in Schistosoma hematobium and Schistosoma japonicum The reason for this species-specific drug action has remained a mystery for decades. Here we present the crystal structures of S. hematobium and S. japonicum SULTs, including S. hematobium SULT in complex with oxamniquine. We also examined the activity of the three enzymes in vitro; surprisingly, all three are active toward oxamniquine, yet we observed differences in catalytic efficiency that implicate kinetics as the determinant for species-specific toxicity. These results provide guidance for designing oxamniquine derivatives to treat infection caused by all species of schistosome to combat emerging resistance to current therapy.
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Affiliation(s)
- Alexander B Taylor
- From the Departments of Biochemistry and Structural Biology and
- the X-ray Crystallography Core Laboratory, University of Texas Health Science Center, San Antonio, Texas 78229
| | - Kenneth M Roberts
- Department of Chemistry and Physics, University of South Carolina, Aiken, South Carolina 29801
| | - Xiaohang Cao
- From the Departments of Biochemistry and Structural Biology and
| | | | | | - Enrica Donati
- Institute of Chemical Methodologies, Consiglio Nazionale delle Ricerche, Via Salaria Km 29.500, 00015 Monterotondo, Rome, Italy
| | - Chiara M Polcaro
- Institute of Chemical Methodologies, Consiglio Nazionale delle Ricerche, Via Salaria Km 29.500, 00015 Monterotondo, Rome, Italy
| | - Livia Pica-Mattoccia
- Institute of Cell Biology and Neurobiology, Consiglio Nazionale delle Ricerche, Via E. Ramarini 32, 00015 Monterotondo, Rome, Italy
| | - Reid S Tarpley
- Center for Innovative Drug Discovery, Department of Chemistry, University of Texas, San Antonio, Texas 78249, and
| | - Stanton F McHardy
- Center for Innovative Drug Discovery, Department of Chemistry, University of Texas, San Antonio, Texas 78249, and
| | - Donato Cioli
- Institute of Chemical Methodologies, Consiglio Nazionale delle Ricerche, Via Salaria Km 29.500, 00015 Monterotondo, Rome, Italy
| | - Philip T LoVerde
- From the Departments of Biochemistry and Structural Biology and
- Pathology and
| | | | - P John Hart
- From the Departments of Biochemistry and Structural Biology and
- the X-ray Crystallography Core Laboratory, University of Texas Health Science Center, San Antonio, Texas 78229
- Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, Texas 78229
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7
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Structural and biochemical studies of sulphotransferase 18 from Arabidopsis thaliana explain its substrate specificity and reaction mechanism. Sci Rep 2017. [PMID: 28646214 PMCID: PMC5482895 DOI: 10.1038/s41598-017-04539-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Sulphotransferases are a diverse group of enzymes catalysing the transfer of a sulfuryl group from 3'-phosphoadenosine 5'-phosphosulphate (PAPS) to a broad range of secondary metabolites. They exist in all kingdoms of life. In Arabidopsis thaliana (L.) Heynh. twenty-two sulphotransferase (SOT) isoforms were identified. Three of those are involved in glucosinolate (Gl) biosynthesis, glycosylated sulphur-containing aldoximes containing chemically different side chains, whose break-down products are involved in stress response against herbivores, pathogens, and abiotic stress. To explain the differences in substrate specificity of desulpho (ds)-Gl SOTs and to understand the reaction mechanism of plant SOTs, we determined the first high-resolution crystal structure of the plant ds-Gl SOT AtSOT18 in complex with 3'-phosphoadenosine 5'-phosphate (PAP) alone and together with the Gl sinigrin. These new structural insights into the determination of substrate specificity were complemented by mutagenesis studies. The structure of AtSOT18 invigorates the similarity between plant and mammalian sulphotransferases, which illustrates the evolutionary conservation of this multifunctional enzyme family. We identified the essential residues for substrate binding and catalysis and demonstrated that the catalytic mechanism is conserved between human and plant enzymes. Our study indicates that the loop-gating mechanism is likely to be a source of the substrate specificity in plants.
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8
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Tibbs ZE, Rohn-Glowacki KJ, Crittenden F, Guidry AL, Falany CN. Structural plasticity in the human cytosolic sulfotransferase dimer and its role in substrate selectivity and catalysis. Drug Metab Pharmacokinet 2015; 30:3-20. [DOI: 10.1016/j.dmpk.2014.10.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/02/2014] [Accepted: 10/08/2014] [Indexed: 10/24/2022]
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9
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Ayuso-Fernández I, Galmés MA, Bastida A, García-Junceda E. Aryl Sulfotransferase from Haliangium ochraceum
: A Versatile Tool for the Sulfation of Small Molecules. ChemCatChem 2014. [DOI: 10.1002/cctc.201300853] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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10
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Malojčić G, Owen RL, Glockshuber R. Structural and Mechanistic Insights into the PAPS-Independent Sulfotransfer Catalyzed by Bacterial Aryl Sulfotransferase and the Role of the DsbL/DsbI System in Its Folding. Biochemistry 2014; 53:1870-7. [DOI: 10.1021/bi401725j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Goran Malojčić
- Institute
of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Robin L. Owen
- Diamond
Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, U.K
| | - Rudi Glockshuber
- Institute
of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
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11
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Teramoto T, Fujikawa Y, Kawaguchi Y, Kurogi K, Soejima M, Adachi R, Nakanishi Y, Mishiro-Sato E, Liu MC, Sakakibara Y, Suiko M, Kimura M, Kakuta Y. Crystal structure of human tyrosylprotein sulfotransferase-2 reveals the mechanism of protein tyrosine sulfation reaction. Nat Commun 2013; 4:1572. [PMID: 23481380 PMCID: PMC3601584 DOI: 10.1038/ncomms2593] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 02/08/2013] [Indexed: 11/30/2022] Open
Abstract
Post-translational protein modification by tyrosine-sulfation plays an important role in extracellular protein-protein interactions. The protein tyrosine sulfation reaction is catalyzed by the Golgi-enzyme called the tyrosylprotein sulfotransferase (TPST). To date, no crystal structure is available for TPST. Detailed mechanism of protein tyrosine sulfation reaction has thus remained unclear. Here we present the first crystal structure of the human TPST isoform 2 (TPST2) complexed with a substrate peptide (C4P5Y3) derived from complement C4 and 3’-phosphoadenosine-5’-phosphate (PAP) at 1.9Å resolution. Structural and complementary mutational analyses revealed the molecular basis for catalysis being an SN2-like in-line displacement mechanism. TPST2 appeared to recognize the C4 peptide in a deep cleft by using a short parallel β-sheet type interaction, and the bound C4P5Y3 forms an L-shaped structure. Surprisingly, the mode of substrate peptide recognition observed in the TPST2 structure resembles that observed for the receptor type tyrosine kinases.
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Affiliation(s)
- Takamasa Teramoto
- Laboratory of Structural Biology, Graduate School of Systems Life Sciences, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
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12
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Cook I, Wang T, Almo SC, Kim J, Falany CN, Leyh TS. The gate that governs sulfotransferase selectivity. Biochemistry 2012; 52:415-24. [PMID: 23256751 DOI: 10.1021/bi301492j] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Human cytosolic sulfotransferases (SULTs) transfer the sulfuryl moiety (-SO(3)) from activated sulfate [3'-phosphoadenosine 5'-phosphosulfate (PAPS)] to the hydroxyls and primary amines of numerous metabolites, drugs, and xenobiotics. Receipt of the sulfuryl group often radically alters acceptor-target interactions. How these enzymes select particular substrates from the hundreds of candidates in a complex cytosol remains an important question. Recent work reveals PAPS binding causes SULT2A1 to undergo an isomerization that controls selectivity by constricting the opening through which acceptors must pass to enter the active site. The enzyme maintains an affinity for large substrates by isomerizing between the open and closed states with nucleotide bound. Here, the molecular basis of the nucleotide-induced closure is explored in equilibrium and nonequilibrium molecular dynamics simulations. The simulations predict that the active-site "cap," which covers both the nucleotide and acceptor binding sites, opens and closes in response to nucleotide. The cap subdivides into nucleotide and acceptor halves whose motions, while coupled, exhibit an independence that can explain the isomerization. In silico weakening of electrostatic interactions between the cap and base of the active site causes the acceptor half of the cap to open and close while the nucleotide lid remains shut. Simulations predict that SULT1A1, the most abundant SULT in human liver, will utilize a similar selection mechanism. This prediction is tested using fulvestrant, an anti-estrogen too large to pass through the closed pore, and estradiol, which is not restricted by closure. Equilibrium and pre-steady-state binding studies confirm that SULT1A1 undergoes a nucleotide-induced isomerzation that controls substrate selection.
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Affiliation(s)
- Ian Cook
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461-1926, USA
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McCarthy JG, Eisman EB, Kulkarni S, Gerwick L, Gerwick WH, Wipf P, Sherman DH, Smith JL. Structural basis of functional group activation by sulfotransferases in complex metabolic pathways. ACS Chem Biol 2012; 7:1994-2003. [PMID: 22991895 PMCID: PMC3528841 DOI: 10.1021/cb300385m] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Sulfated molecules with diverse functions are common in biology, but sulfonation as a method to activate a metabolite for chemical catalysis is rare. Catalytic activity was characterized and crystal structures were determined for two such "activating" sulfotransferases (STs) that sulfonate β-hydroxyacyl thioester substrates. The CurM polyketide synthase (PKS) ST domain from the curacin A biosynthetic pathway of Moorea producens and the olefin synthase (OLS) ST from a hydrocarbon-producing system of Synechococcus PCC 7002 both occur as a unique acyl carrier protein (ACP), ST, and thioesterase (TE) tridomain within a larger polypeptide. During pathway termination, these cyanobacterial systems introduce a terminal double bond into the β-hydroxyacyl-ACP-linked substrate by the combined action of the ST and TE. Under in vitro conditions, CurM PKS ST and OLS ST acted on β-hydroxy fatty acyl-ACP substrates; however, OLS ST was not reactive toward analogues of the natural PKS ST substrate bearing a C5-methoxy substituent. The crystal structures of CurM ST and OLS ST revealed that they are members of a distinct protein family relative to other prokaryotic and eukaryotic sulfotransferases. A common binding site for the sulfonate donor 3'-phosphoadenosine-5'-phosphosulfate was visualized in complexes with the product 3'-phosphoadenosine-5'-phosphate. Critical functions for several conserved amino acids in the active site were confirmed by site-directed mutagenesis, including a proposed glutamate catalytic base. A dynamic active-site flap unique to the "activating" ST family affects substrate selectivity and product formation, based on the activities of chimeras of the PKS and OLS STs with exchanged active-site flaps.
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Affiliation(s)
- Jennifer Gehret McCarthy
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Eli B. Eisman
- Life Sciences Institute and Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, MI 48109
| | - Sarang Kulkarni
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260
| | - David H. Sherman
- Life Sciences Institute and Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology University of Michigan, Ann Arbor, MI 48109
| | - Janet L. Smith
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109
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14
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Gulcan HO, Duffel MW. Substrate inhibition in human hydroxysteroid sulfotransferase SULT2A1: studies on the formation of catalytically non-productive enzyme complexes. Arch Biochem Biophys 2011; 507:232-40. [PMID: 21187059 PMCID: PMC3058861 DOI: 10.1016/j.abb.2010.12.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 12/20/2010] [Accepted: 12/21/2010] [Indexed: 12/14/2022]
Abstract
The cytosolic sulfotransferase hSULT2A1 is the major hydroxysteroid (alcohol) sulfotransferase in human liver, and it catalyzes the 3'-phosphoadenosine-5'-phosphosulfate (PAPS)-dependent sulfation of various endogenous hydroxysteroids as well as many xenobiotics that contain alcohol and phenol functional groups. The hSULT2A1 often displays substrate inhibition, and we have hypothesized that a key element in this response to increasing substrate concentration is the formation of non-productive ternary dead-end enzyme complexes involving the nucleotide product, adenosine 3',5'-diphosphate (PAP). One of these substrates for hSULT2A1 is dehydroepiandrosterone (DHEA), a major circulating steroid hormone in humans that serves as precursor to both androgens and estrogens. We have utilized DHEA in both initial velocity studies and equilibrium binding experiments in order to evaluate the potential role of ternary complexes in substrate inhibition of the enzyme. Our results indicate that hSULT2A1 forms non-productive ternary complexes that involve either DHEA or dehydroepiandrosterone sulfate, and the formation of these ternary complexes displays negative cooperativity in the binding of DHEA.
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Affiliation(s)
- Hayrettin Ozan Gulcan
- Division of Medicinal and Natural Products Chemistry, College of Pharmacy, The University of Iowa, Iowa City, IA 52242, USA
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Hossain MM, Moriizumi Y, Tanaka S, Kimura M, Kakuta Y. Molecular cloning, expression, and functional analysis of a predicted sulfotransferase STF9 from Mycobacterium avium. Mol Cell Biochem 2010; 350:155-62. [DOI: 10.1007/s11010-010-0693-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 12/10/2010] [Indexed: 11/24/2022]
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16
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Malojcić G, Glockshuber R. The PAPS-independent aryl sulfotransferase and the alternative disulfide bond formation system in pathogenic bacteria. Antioxid Redox Signal 2010; 13:1247-59. [PMID: 20136513 DOI: 10.1089/ars.2010.3119] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Sulfurylation of biomolecules (often termed sulfonation or sulfation) has been described in many organisms in all kingdoms of life. To date, most studies on sulfotransferases, the enzymes catalyzing sulfurylation, have focused on 3'-phosphate-5'-phosphosulfate (PAPS)-dependent enzymes, which transfer the sulfuryl group from this activated anhydride to hydroxyl groups of acceptor molecules. By contrast, the PAPS-independent aryl sulfotransferases (ASSTs) from bacteria, which catalyze sulfotransfer from phenolic sulfate esters to another phenol in the bacterial periplasm, were not well characterized until recently, although they were first described in 1986 in a search for nonhepatic sulfurylation processes. Recent studies revealed that this unusual class of sulfotransferases differs profoundly in both molecular structure and catalytic mechanism from PAPS-dependent sulfotransferases, and that ASSTs from certain bacterial pathogens are upregulated during infection. In this review, we summarize the literature on the roles of sulfurylation in prokaryotes and analyze the occurrence of ASSTs and their dependence on Dsb proteins catalyzing oxidative folding in the periplasm. Furthermore, we discuss structural differences and similarities between aryl sulfotransferases and PAPS-dependent sulfotransferases.
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Affiliation(s)
- Goran Malojcić
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
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17
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Danan LM, Yu Z, Ludden PJ, Jia W, Moore KL, Leary JA. Catalytic mechanism of Golgi-resident human tyrosylprotein sulfotransferase-2: a mass spectrometry approach. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1633-42. [PMID: 20462768 PMCID: PMC3088362 DOI: 10.1016/j.jasms.2010.03.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Revised: 03/08/2010] [Accepted: 03/12/2010] [Indexed: 05/10/2023]
Abstract
Human tyrosylprotein sulfotransferases catalyze the transfer of a sulfuryl moiety from the universal sulfate donor PAPS to the hydroxyl substituent of tyrosine residues in proteins and peptides to yield tyrosine sulfated products and PAP. Tyrosine sulfation occurs in the trans-Golgi network, affecting an estimated 1% of the tyrosine residues in all secreted and membrane-bound proteins in higher order eukaryotes. In this study, an effective LC-MS-based TPST kinetics assay was developed and utilized to measure the kinetic properties of human TPST-2 and investigate its catalytic mechanism when G protein-coupled CC-chemokine receptor 8 (CCR8) peptides were used as acceptor substrates. Through initial rate kinetics, product inhibition studies, and radioactive-labeling experiments, our data strongly suggest a two-site ping-pong model for TPST-2 action. In this mechanistic model, the enzyme allows independent binding of substrates to two distinct sites, and involves the formation of a sulfated enzyme covalent intermediate. Some insights on the important amino acid residues at the catalytic site of TPST-2 and its covalent intermediate are also presented. To our knowledge, this is the first detailed study of the reaction kinetics and mechanism reported for human TPST-2 or any other Golgi-resident sulfotransferase.
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Affiliation(s)
- Lieza M. Danan
- Department of Chemistry, University of California, Davis, CA, 95616
| | - Zhihao Yu
- Department of Molecular and Cellular Biology, University of California, Davis, CA, 95616
| | - Peter J. Ludden
- Department of Molecular and Cellular Biology, University of California, Davis, CA, 95616
| | - Weitao Jia
- Department of Molecular and Cellular Biology, University of California, Davis, CA, 95616
| | - Kevin L. Moore
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
- Departments of Cell Biology and Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
- Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Julie A. Leary
- Department of Chemistry, University of California, Davis, CA, 95616
- Department of Molecular and Cellular Biology, University of California, Davis, CA, 95616
- To whom correspondence should be addressed, Department of Molecular and Cellular Biology, University of California, Davis, One Shields Ave., Davis, CA 95616, Tel: (530) 754-4987, Fax: (530) 754-9658,
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18
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Teramoto T, Adachi R, Sakakibara Y, Liu MC, Suiko M, Kimura M, Kakuta Y. On the similar spatial arrangement of active site residues in PAPS-dependent and phenolic sulfate-utilizing sulfotransferases. FEBS Lett 2009; 583:3091-4. [PMID: 19695253 DOI: 10.1016/j.febslet.2009.08.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Revised: 08/11/2009] [Accepted: 08/11/2009] [Indexed: 10/20/2022]
Abstract
Mammalian sulfotransferases (STs) utilize exclusively the sulfuryl group donor 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to catalyze the sulfurylation reactions based on a sequential transfer mechanism. In contrast, the commensal intestinal bacterial arylsulfate sulfotransferases (ASSTs) do not use PAPS as the sulfuryl group donor, but instead catalyze sulfuryl transfer from phenolic sulfate to a phenol via a Ping-Pong mechanism. Interestingly, structural comparison revealed a similar spatial arrangement of the active site residues as well as the cognate substrates in mouse ST (mSULT1D1) and Escherichia coli CFT073 ASST, despite that their overall structures bear no discernible relationship. These observations suggest that the active sites of PAPS-dependent SULT1D1 and phenolic sulfate-utilizing ASST represent an example of convergent evolution.
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Affiliation(s)
- Takamasa Teramoto
- Laboratory of Structural Biology, Department of Systems Life Sciences, Graduate School, Faculty of Agriculture, Kyushu University, Hakozaki 6-10-1, Higashi-ku, Fukuoka 812-8581, Japan
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