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Aimulajiang K, Chu W, Liao S, Wen Z, He R, Lu M, Xu L, Song X, Li X, Yan R. Succinate coenzyme A ligase β-like protein from Trichinella spiralis is a potential therapeutic molecule for allergic asthma. Immun Inflamm Dis 2024; 12:e1321. [PMID: 38888451 PMCID: PMC11184933 DOI: 10.1002/iid3.1321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 06/04/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND For decades, studies have demonstrated the anti-inflammatory potential of proteins secreted by helminths in allergies and asthma. Previous studies have demonstrated the immunomodulatory capabilities of Succinate Coenzyme A ligase beta-like protein (SUCLA-β) derived from Trichinella spiralis, a crucial excretory product of this parasite. OBJECTIVE To explore the therapeutic potential of SUCLA-β in alleviating and controlling ovalbumin (OVA)-induced allergic asthma, as well as its influence on host immune modulation. METHODS In this research, we utilized the rTs-SUCLA-β protein derived from T. spiralis to investigate its potential in mitigating airway inflammation in a murine model of asthma induced by OVA sensitization/stimulation, both pre- and post-challenge. The treatment's efficacy was assessed by quantifying the extent of inflammation in the lungs. RESULTS Treatment with rTs-SUCLA-β demonstrated efficacy in ameliorating OVA-induced airway inflammation, as evidenced by a reduction in eosinophil infiltration, levels of OVA-specific Immunoglobulin E, interferon-γ, interleukin (IL)-9, and IL-17A, along with an elevation in IL-10. The equilibrium between Th17 and Treg cells plays a pivotal role in modulating the abundance of inflammatory cells within the organism, thereby ameliorating inflammation and alleviating symptoms associated with allergic asthma. CONCLUSIONS AND CLINICAL RELEVANCE Our data revealed that T. spiralis-derived Ts-SUCLA-β protein may inhibit the allergic airway inflammation by regulating host immune responses.
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Affiliation(s)
- Kalibixiati Aimulajiang
- Laboratory of Animal Health and Food Safety, MOE Joint International Research, College of Veterinary MedicineNanjing Agricultural UniversityNanjingJiangsuP. R. China
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medicine InstituteThe First Affiliated Hospital of Xinjiang Medical UniversityUrumqiXinjiangP. R. China
| | - Wen Chu
- Laboratory of Animal Health and Food Safety, MOE Joint International Research, College of Veterinary MedicineNanjing Agricultural UniversityNanjingJiangsuP. R. China
| | - Shuyi Liao
- Laboratory of Animal Health and Food Safety, MOE Joint International Research, College of Veterinary MedicineNanjing Agricultural UniversityNanjingJiangsuP. R. China
- Changsha Animal and Plant Disease Control CenterChangshaHunanP. R. China
| | - Zhaohai Wen
- Laboratory of Animal Health and Food Safety, MOE Joint International Research, College of Veterinary MedicineNanjing Agricultural UniversityNanjingJiangsuP. R. China
- Department of Veterinary Medicine, College of Coastal Agricultural SciencesGuangdong Ocean UniversityZhanjiangP. R. China
| | - Rongdong He
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medicine InstituteThe First Affiliated Hospital of Xinjiang Medical UniversityUrumqiXinjiangP. R. China
| | - Mingmin Lu
- Laboratory of Animal Health and Food Safety, MOE Joint International Research, College of Veterinary MedicineNanjing Agricultural UniversityNanjingJiangsuP. R. China
| | - Lixin Xu
- Laboratory of Animal Health and Food Safety, MOE Joint International Research, College of Veterinary MedicineNanjing Agricultural UniversityNanjingJiangsuP. R. China
| | - Xiaokai Song
- Laboratory of Animal Health and Food Safety, MOE Joint International Research, College of Veterinary MedicineNanjing Agricultural UniversityNanjingJiangsuP. R. China
| | - Xiangrui Li
- Laboratory of Animal Health and Food Safety, MOE Joint International Research, College of Veterinary MedicineNanjing Agricultural UniversityNanjingJiangsuP. R. China
| | - Ruofeng Yan
- Laboratory of Animal Health and Food Safety, MOE Joint International Research, College of Veterinary MedicineNanjing Agricultural UniversityNanjingJiangsuP. R. China
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2
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Lee YT, Savini M, Chen T, Yang J, Zhao Q, Ding L, Gao SM, Senturk M, Sowa JN, Wang JD, Wang MC. Mitochondrial GTP metabolism controls reproductive aging in C. elegans. Dev Cell 2023; 58:2718-2731.e7. [PMID: 37708895 PMCID: PMC10842941 DOI: 10.1016/j.devcel.2023.08.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/17/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023]
Abstract
Healthy mitochondria are critical for reproduction. During aging, both reproductive fitness and mitochondrial homeostasis decline. Mitochondrial metabolism and dynamics are key factors in supporting mitochondrial homeostasis. However, how they are coupled to control reproductive health remains unclear. We report that mitochondrial GTP (mtGTP) metabolism acts through mitochondrial dynamics factors to regulate reproductive aging. We discovered that germline-only inactivation of GTP- but not ATP-specific succinyl-CoA synthetase (SCS) promotes reproductive longevity in Caenorhabditis elegans. We further identified an age-associated increase in mitochondrial clustering surrounding oocyte nuclei, which is attenuated by GTP-specific SCS inactivation. Germline-only induction of mitochondrial fission factors sufficiently promotes mitochondrial dispersion and reproductive longevity. Moreover, we discovered that bacterial inputs affect mtGTP levels and dynamics factors to modulate reproductive aging. These results demonstrate the significance of mtGTP metabolism in regulating oocyte mitochondrial homeostasis and reproductive longevity and identify mitochondrial fission induction as an effective strategy to improve reproductive health.
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Affiliation(s)
- Yi-Tang Lee
- Integrative Program of Molecular and Biochemical Sciences, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Marzia Savini
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA; Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tao Chen
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Jin Yang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Qian Zhao
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Lang Ding
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA; Graduate Program in Chemical, Physical & Structural Biology, Graduate School of Biomedical Science, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shihong Max Gao
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Mumine Senturk
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jessica N Sowa
- Department of Biology, West Chester University, West Chester, PA 19383, USA
| | - Jue D Wang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Meng C Wang
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.
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3
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Zhang Y, Fernie AR. The Role of TCA Cycle Enzymes in Plants. Adv Biol (Weinh) 2023; 7:e2200238. [PMID: 37341441 DOI: 10.1002/adbi.202200238] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 04/29/2023] [Indexed: 06/22/2023]
Abstract
As one of the iconic pathways in plant metabolism, the tricarboxylic acid (TCA) cycle is commonly thought to not only be responsible for the oxidization of respiratory substrate to drive ATP synthesis but also provide carbon skeletons to anabolic processes and contribute to carbon-nitrogen interaction and biotic stress responses. The functions of the TCA cycle enzymes are characterized by a saturation transgenesis approach, whereby the constituent expression of proteins is knocked out or reduced in order to investigate their function in vivo. The alteration of TCA cycle enzyme expression results in changed plant growth and photosynthesis under controlled conditions. Moreover, improvements in plant performance and postharvest properties are reported by overexpression of either endogenous forms or heterologous genes of a number of the enzymes. Given the importance of the TCA cycle in plant metabolism regulation, here, the function of each enzyme and its roles in different tissues are discussed. This article additionally highlights the recent finding that the plant TCA cycle, like that of mammals and microbes, dynamically assembles functional substrate channels or metabolons and discusses the implications of this finding to the current understanding of the metabolic regulation of the plant TCA cycle.
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Affiliation(s)
- Youjun Zhang
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, Plovdiv, 4000, Bulgaria
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4
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Iverson TM, Singh PK, Cecchini G. An evolving view of Complex II - non-canonical complexes, megacomplexes, respiration, signaling, and beyond. J Biol Chem 2023; 299:104761. [PMID: 37119852 DOI: 10.1016/j.jbc.2023.104761] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/20/2023] [Accepted: 04/22/2023] [Indexed: 05/01/2023] Open
Abstract
Mitochondrial Complex II is traditionally studied for its participation in two key respiratory processes: the electron transport chain and the Krebs cycle. There is now a rich body of literature explaining how Complex II contributes to respiration. However, more recent research shows that not all of the pathologies associated with altered Complex II activity clearly correlate with this respiratory role. Complex II activity has now been shown to be necessary for a range of biological processes peripherally-related to respiration, including metabolic control, inflammation, and cell fate. Integration of findings from multiple types of studies suggests that Complex II both participates in respiration and controls multiple succinate-dependent signal transduction pathways. Thus, the emerging view is that the true biological function of Complex II is well beyond respiration. This review uses a semi-chronological approach to highlight major paradigm shifts that occurred over time. Special emphasis is given to the more recently identified functions of Complex II and its subunits because these findings have infused new directions into an established field.
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Affiliation(s)
- T M Iverson
- Departments of Pharmacology, Vanderbilt University, Nashville, TN 37232; Departments of Biochemistry, Vanderbilt University, Nashville, TN 37232; Departments of Center for Structural Biology, Vanderbilt University, Nashville, TN 37232; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232.
| | - Prashant K Singh
- Departments of Pharmacology, Vanderbilt University, Nashville, TN 37232; Departments of Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
| | - Gary Cecchini
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA 94121; Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158.
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Lee YT, Savini M, Chen T, Yang J, Zhao Q, Ding L, Gao SM, Senturk M, Sowa J, Wang JD, Wang MC. Mitochondrial GTP Metabolism Regulates Reproductive Aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.02.535296. [PMID: 37066227 PMCID: PMC10103970 DOI: 10.1101/2023.04.02.535296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Healthy mitochondria are critical for reproduction. During aging, both reproductive fitness and mitochondrial homeostasis decline. Mitochondrial metabolism and dynamics are key factors in supporting mitochondrial homeostasis. However, how they are coupled to control reproductive health remains unclear. We report that mitochondrial GTP metabolism acts through mitochondrial dynamics factors to regulate reproductive aging. We discovered that germline-only inactivation of GTP- but not ATP-specific succinyl-CoA synthetase (SCS), promotes reproductive longevity in Caenorhabditis elegans. We further revealed an age-associated increase in mitochondrial clustering surrounding oocyte nuclei, which is attenuated by the GTP-specific SCS inactivation. Germline-only induction of mitochondrial fission factors sufficiently promotes mitochondrial dispersion and reproductive longevity. Moreover, we discovered that bacterial inputs affect mitochondrial GTP and dynamics factors to modulate reproductive aging. These results demonstrate the significance of mitochondrial GTP metabolism in regulating oocyte mitochondrial homeostasis and reproductive longevity and reveal mitochondrial fission induction as an effective strategy to improve reproductive health.
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6
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Wang H, Gao R, Liu J, Zhang S, Zhao Y, Yu Z. UPLC-Q-Exactive-based rats serum metabolomics for characterization of traditional Chinese medicine Natures and Flavors. JOURNAL OF ETHNOPHARMACOLOGY 2023; 302:115931. [PMID: 36410573 DOI: 10.1016/j.jep.2022.115931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/17/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
UNLABELLED ETHNOPHARMACOLOGY RELEVANT: "Four Natures and five "Flavors" comes from the high generalization of medicine pharmacological rules from clinical practice by ancients. "Flavor" and "Natures"are both descriptions of the effect properties of traditional Chinese medicine. At present, researchers have realized that the "Flavors" (Pungent, Sour, Sweet, Bitter and Salty) are related to the different pharmacological effects of treatment. The "Natures" (Warm, Hot, Cold and Cool) are closely related to energy and substance metabolism and contribute to the effect of the "Flavors". Since "Four Natures and five Flavors" are the rules derived from clinical practice, how to describe and characterize "Natures" and "Flavors" scientifically is still a problem that needs to be solved. AIM OF THE STUDY the aim is to objectively further understand the scientific connotations of properties ("Flavors"and "Natures") from the perspective of metabolomics and characterize them by metabolites. MATERIALS AND METHOD "Pungent-Neutral", "Sweet-Neutral and "Bitter-Neutral" TCMs were selected to characterize the "Flavors" (Pungent, Sweet and Bitter). "Pungent-Warm" and "Bitter-Cold" were selected to characterize the "Natures" (Warm and Cold). The rat serum metabolomics was performed on UHPLC-Q-Exactive. Metabolites were identified through the metabolites databases and related literature. RESULTS The "Flavors" and "Natures" metabolites were identified, respectively, including four "Pungent", four "Sweet" and thirteen "Bitter" characterized metabolites and thirteen "Cold" and sixteen "Warm"related metabolites. CONCLUSIONS The "Natures" characterized metabolites show the "Natures" are closely related to lipid and energy metabolism. The "Warm" may promote lipid metabolism to produce ATP to generate energy through bile acid metabolism and purine metabolism. The "Cold" may inhibit lipid metabolism to generate ATP to decrease energy through the way of tryptophan metabolism and purine metabolism. The "Flavors" characteristic metabolites can provide a theoretical basis for the rules of the "Flavors". These metabolites can also be used to characterize TCM's "Natures" and "Flavors" in the development of traditional Chinese medicine resources and quality control.
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Affiliation(s)
- Hong Wang
- Department of Pharmaceutical Analysis, College of Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Ruofang Gao
- Department of Pharmaceutical Analysis, College of Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Jing Liu
- Department of Pharmaceutical Analysis, College of Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Shuang Zhang
- Department of Pharmaceutical Analysis, College of Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yunli Zhao
- Department of Pharmaceutical Analysis, College of Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, China.
| | - Zhiguo Yu
- Department of Pharmaceutical Analysis, College of Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, China.
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7
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Huang J, Fraser ME. The structure of succinyl-CoA synthetase bound to the succinyl-phosphate intermediate clarifies the catalytic mechanism of ATP-citrate lyase. Acta Crystallogr F Struct Biol Commun 2022; 78:363-370. [PMID: 36189720 PMCID: PMC9527654 DOI: 10.1107/s2053230x22008810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/04/2022] [Indexed: 11/10/2022] Open
Abstract
Succinyl-CoA synthetase (SCS) catalyzes a three-step reaction in the citric acid cycle with succinyl-phosphate proposed as a catalytic intermediate. However, there are no structural data to show the binding of succinyl-phosphate to SCS. Recently, the catalytic mechanism underlying acetyl-CoA production by ATP-citrate lyase (ACLY) has been debated. The enzyme belongs to the family of acyl-CoA synthetases (nucleoside diphosphate-forming) for which SCS is the prototype. It was postulated that the amino-terminal portion catalyzes the full reaction and the carboxy-terminal portion plays only an allosteric role. This interpretation was based on the partial loss of the catalytic activity of ACLY when Glu599 was mutated to Gln or Ala, and on the interpretation that the phospho-citryl-CoA intermediate was trapped in the 2.85 Å resolution structure from cryogenic electron microscopy (cryo-EM). To better resolve the structure of the intermediate bound to the E599Q mutant, the equivalent mutation, E105αQ, was made in human GTP-specific SCS. The structure of the E105αQ mutant shows succinyl-phosphate bound to the enzyme at 1.58 Å resolution when the mutant, after phosphorylation in solution by Mg2+-ATP, was crystallized in the presence of magnesium ions, succinate and desulfo-CoA. The E105αQ mutant is still active but has a specific activity that is 120-fold less than that of the wild-type enzyme, with apparent Michaelis constants for succinate and CoA that are 50-fold and 11-fold higher, respectively. Based on this high-resolution structure, the cryo-EM maps of the E599Q ACLY complex reported previously should have revealed the binding of citryl-phosphate and CoA and not phospho-citryl-CoA.
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Affiliation(s)
- Ji Huang
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Marie E. Fraser
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
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8
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Xu Y, Shi Z, Bao L. An expanding repertoire of protein acylations. Mol Cell Proteomics 2022; 21:100193. [PMID: 34999219 PMCID: PMC8933697 DOI: 10.1016/j.mcpro.2022.100193] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/22/2021] [Accepted: 01/04/2022] [Indexed: 01/03/2023] Open
Abstract
Protein post-translational modifications play key roles in multiple cellular processes by allowing rapid reprogramming of individual protein functions. Acylation, one of the most important post-translational modifications, is involved in different physiological activities including cell differentiation and energy metabolism. In recent years, the progression in technologies, especially the antibodies against acylation and the highly sensitive and effective mass spectrometry–based proteomics, as well as optimized functional studies, greatly deepen our understanding of protein acylation. In this review, we give a general overview of the 12 main protein acylations (formylation, acetylation, propionylation, butyrylation, malonylation, succinylation, glutarylation, palmitoylation, myristoylation, benzoylation, crotonylation, and 2-hydroxyisobutyrylation), including their substrates (histones and nonhistone proteins), regulatory enzymes (writers, readers, and erasers), biological functions (transcriptional regulation, metabolic regulation, subcellular targeting, protein–membrane interactions, protein stability, and folding), and related diseases (cancer, diabetes, heart disease, neurodegenerative disease, and viral infection), to present a complete picture of protein acylations and highlight their functional significance in future research. Provide a general overview of the 12 main protein acylations. Acylation of viral proteins promotes viral integration and infection. Hyperacylation of histone has antitumous and neuroprotective effects. MS is widely used in the identification of acylation but has its challenges.
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Affiliation(s)
- Yuxuan Xu
- Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research center for Cancer, 300060, Tianjin, China
| | - Zhenyu Shi
- Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research center for Cancer, 300060, Tianjin, China
| | - Li Bao
- Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research center for Cancer, 300060, Tianjin, China.
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9
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Cui J, Tcherkez G. Potassium dependency of enzymes in plant primary metabolism. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:522-530. [PMID: 34174657 DOI: 10.1016/j.plaphy.2021.06.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
Potassium is a macroelement essential to many aspects of plant life, such as photosynthesis, phloem transport or cellular electrochemistry. Many enzymes in animals or microbes are known to be stimulated or activated by potassium (K+ ions). Several plant enzymes are also strictly K+-dependent, and this can be critical when plants are under K deficiency and thus intracellular K+ concentration is low. Although metabolic effects of low K conditions have been documented, there is presently no review focusing on roles of K+ for enzyme catalysis or activation in plants. In this mini-review, we compile the current knowledge on K+-requirement of plant enzymes and take advantage of structural data to present biochemical roles of K+. This information is instrumental to explain direct effects of low K+ content on metabolism and this is illustrated with recent metabolomics data.
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Affiliation(s)
- Jing Cui
- Research School of Biology, ANU Joint College of Sciences, Australian National University, 2601, Canberra, Australia
| | - Guillaume Tcherkez
- Research School of Biology, ANU Joint College of Sciences, Australian National University, 2601, Canberra, Australia; Institut de Recherche en Horticulture et Semences, INRAe Angers, Université d'Angers, 42 rue Georges Morel, 49070, Beaucouzé, France.
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10
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Huang J, Fraser ME. Second distinct conformation of the phosphohistidine loop in succinyl-CoA synthetase. Acta Crystallogr D Struct Biol 2021; 77:357-368. [PMID: 33645539 PMCID: PMC7919408 DOI: 10.1107/s2059798321000334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/11/2021] [Indexed: 11/10/2022] Open
Abstract
Succinyl-CoA synthetase (SCS) catalyzes a reversible reaction that is the only substrate-level phosphorylation in the citric acid cycle. One of the essential steps for the transfer of the phosphoryl group involves the movement of the phosphohistidine loop between active site I, where CoA, succinate and phosphate bind, and active site II, where the nucleotide binds. Here, the first crystal structure of SCS revealing the conformation of the phosphohistidine loop in site II of the porcine GTP-specific enzyme is presented. The phosphoryl transfer bridges a distance of 29 Å between the binding sites for phosphohistidine in site I and site II, so these crystal structures support the proposed mechanism of catalysis by SCS. In addition, a second succinate-binding site was discovered at the interface between the α- and β-subunits of SCS, and another magnesium ion was found that interacts with the side chains of Glu141β and Glu204β via water-mediated interactions. These glutamate residues interact with the active-site histidine residue when it is bound in site II.
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Affiliation(s)
- Ji Huang
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Marie E. Fraser
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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11
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Huang J, Fraser ME. Tartryl-CoA inhibits succinyl-CoA synthetase. Acta Crystallogr F Struct Biol Commun 2020; 76:302-308. [PMID: 32627745 PMCID: PMC7336359 DOI: 10.1107/s2053230x20008201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 06/20/2020] [Indexed: 11/10/2022] Open
Abstract
Succinyl-CoA synthetase (SCS) catalyzes the only substrate-level phosphorylation step in the tricarboxylic acid cycle. Human GTP-specific SCS (GTPSCS), an αβ-heterodimer, was produced in Escherichia coli. The purified protein crystallized from a solution containing tartrate, CoA and magnesium chloride, and a crystal diffracted to 1.52 Å resolution. Tartryl-CoA was discovered to be bound to GTPSCS. The CoA portion lies in the amino-terminal domain of the α-subunit and the tartryl end extends towards the catalytic histidine residue. The terminal carboxylate binds to the phosphate-binding site of GTPSCS.
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Affiliation(s)
- Ji Huang
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Marie E. Fraser
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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12
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Sun X, Li Y, Naqvi MAUH, Naqvi SZ, Chu W, Xu L, Song X, Li X, Yan R. Succinate Coenzyme A Ligase Beta-Like Protein from Trichinella spiralis Suppresses the Immune Functions of Rat PBMCs in Vitro and Inhibits the Secretions of Interleukin-17 in Vivo. Vaccines (Basel) 2019; 7:vaccines7040167. [PMID: 31684056 PMCID: PMC6963543 DOI: 10.3390/vaccines7040167] [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: 10/16/2019] [Accepted: 10/29/2019] [Indexed: 12/16/2022] Open
Abstract
Succinate Coenzyme A ligase beta-like protein (SUCLA-β) is a subunit of Succinyl-coenzyme A synthetase, which is involved in substrate synergism, unusual kinetic reaction in which the presence of SUCLA-β for one partial reaction stimulates another partial reaction. Trichinella spiralis is a parasitic nematode, which may hinder the development of autoimmune diseases. Immunomodulatory effects of SUCLA-β from Trichinella spiralis in the parasite-host interaction are unidentified. In this study the gene encoding T. spiralis SUCLA-β was cloned and expressed. Binding activities of recombinant T. spiralis SUCLA-β (rTs-SUCLA-β) to rat peripheral blood mononuclear cells (PBMCs) were checked by immunofluorescence assay (IFA) and the immuno-regulatory effects of rTs-SUCLA-β on cell migration, cell proliferation, nitric oxide (NO) production and apoptosis were observed by co-incubation of rTs-SUCLA-β with rat PBMCs in vitro, while cytokine secretions in rTs-SUCLA-β treated rats were evaluated in vivo. Furthermore, phagocytosis of monocytes was detected by flow cytometry and effects of rTs-SUCLA-β-induced protective immunity on T. spiralis adult worms and muscle larva were evaluated in rats. The IFA results revealed that rTs-SUCLA-β could bind to rat PBMCs. Treatment of PBMCs with rTs-SUCLA-β significantly decreased the monocyte phagocytosis, cell migration and cell proliferation, while NO production and apoptosis of PBMCs were unaffected. Results of the in vivo study showed that the IL-17 secretion decreased significantly after rTs-SUCLA-β administration in rats, while no significant effects were observed on the secretions of IFN-γ, IL-9, TGF-β and IL-4. Moreover, significant reduction of T. spiralis muscle larvae burden and significant increase in anti-rTs-SUCLA-β immunoglobulin level of IgG, IgG1 and IgG2a was observed in rTs-SUCLA-β-administered rats. The results indicated that rTs-SUCLA-β may be a potential target for controlling T. spiralis infection by suppressing the immune functions of the rat PBMCs and by reducing the parasite burden. Additionally it may also contribute to the treatment of autoimmune diseases and graft rejection by suppressing IL-17 immune response in the host.
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Affiliation(s)
- Xiaoke Sun
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yin Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
| | - Muhammad Ali-Ul-Husnain Naqvi
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
| | - Sana Zahra Naqvi
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
| | - Wen Chu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
| | - Lixin Xu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xiaokai Song
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xiangrui Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
| | - Ruofeng Yan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
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13
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Huang J, Nguyen VH, Hamblin KA, Maytum R, van der Giezen M, Fraser ME. ATP-specificity of succinyl-CoA synthetase from Blastocystis hominis. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:647-659. [PMID: 31282474 DOI: 10.1107/s2059798319007976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/03/2019] [Indexed: 11/10/2022]
Abstract
Succinyl-CoA synthetase (SCS) catalyzes the only step of the tricarboxylic acid cycle that leads to substrate-level phosphorylation. Some forms of SCS are specific for ADP/ATP or for GDP/GTP, while others can bind all of these nucleotides, generally with different affinities. The theory of `gatekeeper' residues has been proposed to explain the nucleotide-specificity. Gatekeeper residues lie outside the binding site and create specific electrostatic interactions with incoming nucleotides to determine whether the nucleotides can enter the binding site. To test this theory, the crystal structure of the nucleotide-binding domain in complex with Mg2+-ADP was determined, as well as the structures of four proteins with single mutations, K46βE, K114βD, V113βL and L227βF, and one with two mutations, K46βE/K114βD. The crystal structures show that the enzyme is specific for ADP/ATP because of interactions between the nucleotide and the binding site. Nucleotide-specificity is provided by hydrogen-bonding interactions between the adenine base and Gln20β, Gly111β and Val113β. The O atom of the side chain of Gln20β interacts with N6 of ADP, while the side-chain N atom interacts with the carbonyl O atom of Gly111β. It is the different conformations of the backbone at Gln20β, of the side chain of Gln20β and of the linker that make the enzyme ATP-specific. This linker connects the two subdomains of the ATP-grasp fold and interacts differently with adenine and guanine bases. The mutant proteins have similar conformations, although the L227βF mutant shows structural changes that disrupt the binding site for the magnesium ion. Although the K46βE/K114βD double mutant of Blastocystis hominis SCS binds GTP better than ATP according to kinetic assays, only the complex with Mg2+-ADP was obtained.
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Affiliation(s)
- Ji Huang
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Vinh H Nguyen
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Karleigh A Hamblin
- Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Robin Maytum
- School of Life Sciences, University of Bedfordshire, University Square, Luton LU1 3JU, England
| | | | - Marie E Fraser
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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14
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Brasil S, Leal F, Vega A, Navarrete R, Ecay MJ, Desviat LR, Riera C, Padilla N, de la Cruz X, Couce ML, Martin-Hernández E, Morais A, Pedrón C, Peña-Quintana L, Rigoldi M, Specola N, de Almeida IT, Vives I, Yahyaoui R, Rodríguez-Pombo P, Ugarte M, Pérez-Cerda C, Merinero B, Pérez B. Improving the diagnosis of cobalamin and related defects by genomic analysis, plus functional and structural assessment of novel variants. Orphanet J Rare Dis 2018; 13:125. [PMID: 30041674 PMCID: PMC6057060 DOI: 10.1186/s13023-018-0862-y] [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: 01/18/2018] [Accepted: 06/29/2018] [Indexed: 12/04/2022] Open
Abstract
Background Cellular cobalamin defects are a locus and allelic heterogeneous disorder. The gold standard for coming to genetic diagnoses of cobalamin defects has for some time been gene-by-gene Sanger sequencing of individual DNA fragments. Enzymatic and cellular methods are employed before such sequencing to help in the selection of the gene defects to be sought, but this is time-consuming and laborious. Furthermore some cases remain undiagnosed because no biochemical methods have been available to test for cobalamin absorption and transport defects. Results This paper reports the use of massive parallel sequencing of DNA (exome analysis) for the accurate and rapid genetic diagnosis of cobalamin-related defects in a cohort of affected patients. The method was first validated in an initial cohort with different cobalamin defects. Mendelian segregation, the frequency of mutations, and the comprehensive structural and functional analysis of gene variants, identified disease-causing mutations in 12 genes involved in the absorption and synthesis of active cofactors of vitamin B12 (22 cases), and in the non-cobalamin metabolism-related genes ACSF3 (in four biochemically misdiagnosed patients) and SUCLA2 (in one patient with an unusual presentation). We have identified thirteen new variants all classified as pathogenic according to the ACGM recommendation but four were classified as variant likely pathogenic in MUT and SUCLA2. Functional and structural analysis provided evidences to classify them as pathogenic variants. Conclusions The present findings suggest that the technology used is sufficiently sensitive and specific, and the results it provides sufficiently reproducible, to recommend its use as a second-tier test after the biochemical detection of cobalamin disorder markers in the first days of life. However, for accurate diagnoses to be made, biochemical and functional tests that allow comprehensive clinical phenotyping are also needed. Electronic supplementary material The online version of this article (10.1186/s13023-018-0862-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sandra Brasil
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Fátima Leal
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Ana Vega
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Rosa Navarrete
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - María Jesús Ecay
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Lourdes R Desviat
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Casandra Riera
- Grupo de Bioinformática Translacional Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Natàlia Padilla
- Grupo de Bioinformática Translacional Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Xavier de la Cruz
- Grupo de Bioinformática Translacional Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Mari Luz Couce
- Hospital Clínico Universitario de Santiago, Santiago de Compostela, CIBERER, Santiago de Compostela, Spain
| | | | - Ana Morais
- Hospital Universitario La Paz, Madrid, Spain
| | | | - Luis Peña-Quintana
- Hospital Universitario Materno Infantil, CIBEROBN, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Miriam Rigoldi
- Center for Rare Disorders, ASST- Monza, Ospedale San Gerardo, Monza, Italy
| | - Norma Specola
- Unidad de Metabolismo Hospital de Niños de La Plata, La Plata, Argentina
| | | | | | - Raquel Yahyaoui
- Hospital Universitario Regional de Málaga, Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain
| | - Pilar Rodríguez-Pombo
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Magdalena Ugarte
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Celia Pérez-Cerda
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Begoña Merinero
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Belén Pérez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain.
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15
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Olp MD, Zhu N, Smith BC. Metabolically Derived Lysine Acylations and Neighboring Modifications Tune the Binding of the BET Bromodomains to Histone H4. Biochemistry 2017; 56:5485-5495. [PMID: 28945351 DOI: 10.1021/acs.biochem.7b00595] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Recent proteomic studies discovered histone lysines are modified by acylations beyond acetylation. These acylations derive from acyl-CoA metabolites, potentially linking metabolism to transcription. Bromodomains bind lysine acylation on histones and other nuclear proteins to influence transcription. However, the extent bromodomains bind non-acetyl acylations is largely unknown. Also unclear are the effects of neighboring post-translational modifications, especially within heavily modified histone tails. Using peptide arrays, binding assays, sucrose gradients, and computational methods, we quantified 10 distinct acylations for binding to the bromodomain and extraterminal domain (BET) family. Four of these acylations (hydroxyisobutyrylation, malonylation, glutarylation, and homocitrullination) had never been tested for bromodomain binding. We found N-terminal BET bromodomains bound acetylated and propionylated peptides, consistent with previous studies. Interestingly, all other acylations inhibited binding of the BET bromodomains to peptides and nucleosomes. To understand how context tunes bromodomain binding, effects of neighboring methylation, phosphorylation, and acylation within histone H4 tails were determined. Serine 1 phosphorylation inhibited binding of the BRD4 N-terminal bromodomain to polyacetylated H4 tails by >5-fold, whereas methylation had no effect. Furthermore, binding of BRDT and BRD4 N-terminal bromodomains to H4K5acetyl was enhanced 1.4-9.5-fold by any neighboring acylation of lysine 8, indicating a secondary H4K8acyl binding site that is more permissive of non-acetyl acylations than previously appreciated. In contrast, C-terminal BET bromodomains exhibited 9.9-13.5-fold weaker binding for polyacylated than for monoacylated H4 tails, indicating the C-terminal bromodomains do not cooperatively bind multiple acylations. These results suggest acyl-CoA levels tune or block recruitment of the BET bromodomains to histones, linking metabolism to bromodomain-mediated transcription.
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Affiliation(s)
- Michael D Olp
- Department of Biochemistry, Medical College of Wisconsin , Milwaukee, Wisconsin 53226, United States
| | - Nan Zhu
- Stem Cell Biology and Hematopoiesis Program, Blood Research Institute, Blood Center of Wisconsin , Milwaukee, Wisconsin 53226, United States
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin , Milwaukee, Wisconsin 53226, United States
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16
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Vashisht K, Verma S, Gupta S, Lynn AM, Dixit R, Mishra N, Valecha N, Hamblin KA, Maytum R, Pandey KC, van der Giezen M. Engineering Nucleotide Specificity of Succinyl-CoA Synthetase in Blastocystis: The Emerging Role of Gatekeeper Residues. Biochemistry 2017; 56:534-542. [PMID: 27478903 PMCID: PMC5404824 DOI: 10.1021/acs.biochem.6b00098] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Charged,
solvent-exposed residues at the entrance to the substrate
binding site (gatekeeper residues) produce electrostatic dipole interactions
with approaching substrates, and control their access by a novel mechanism
called “electrostatic gatekeeper effect”. This proof-of-concept
study demonstrates that the nucleotide specificity can be engineered
by altering the electrostatic properties of the gatekeeper residues
outside the binding site. Using Blastocystis succinyl-CoA
synthetase (SCS, EC 6.2.1.5), we demonstrated that the gatekeeper
mutant (ED) resulted in ATP-specific SCS to show high GTP specificity.
Moreover, nucleotide binding site mutant (LF) had no effect on GTP
specificity and remained ATP-specific. However, via combination of
the gatekeeper mutant with the nucleotide binding site mutant (ED+LF),
a complete reversal of nucleotide specificity was obtained with GTP,
but no detectable activity was obtained with ATP. This striking result
of the combined mutant (ED+LF) was due to two changes; negatively
charged gatekeeper residues (ED) favored GTP access, and nucleotide
binding site residues (LF) altered ATP binding, which was consistent
with the hypothesis of the “electrostatic gatekeeper effect”.
These results were further supported by molecular modeling and simulation
studies. Hence, it is imperative to extend the strategy of the gatekeeper
effect in a different range of crucial enzymes (synthetases, kinases,
and transferases) to engineer substrate specificity for various industrial
applications and substrate-based drug design.
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Affiliation(s)
- Kapil Vashisht
- Host-parasite Interaction Biology Group, National Institute of Malaria Research, ICMR , New Delhi 110077, India
| | - Sonia Verma
- Host-parasite Interaction Biology Group, National Institute of Malaria Research, ICMR , New Delhi 110077, India
| | - Sunita Gupta
- School of Computational and Integrative Sciences, Jawaharlal Nehru University , New Delhi 110067, India
| | - Andrew M Lynn
- School of Computational and Integrative Sciences, Jawaharlal Nehru University , New Delhi 110067, India
| | - Rajnikant Dixit
- Host-parasite Interaction Biology Group, National Institute of Malaria Research, ICMR , New Delhi 110077, India
| | - Neelima Mishra
- Host-parasite Interaction Biology Group, National Institute of Malaria Research, ICMR , New Delhi 110077, India
| | - Neena Valecha
- Host-parasite Interaction Biology Group, National Institute of Malaria Research, ICMR , New Delhi 110077, India
| | | | - Robin Maytum
- School of Life Sciences, University of Bedfordshire , University Square, Luton LU1 3JU, U.K
| | - Kailash C Pandey
- Host-parasite Interaction Biology Group, National Institute of Malaria Research, ICMR , New Delhi 110077, India
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17
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Huang J, Fraser ME. Structural basis for the binding of succinate to succinyl-CoA synthetase. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:912-21. [PMID: 27487822 DOI: 10.1107/s2059798316010044] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/20/2016] [Indexed: 01/19/2023]
Abstract
Succinyl-CoA synthetase catalyzes the only step in the citric acid cycle that provides substrate-level phosphorylation. Although the binding sites for the substrates CoA, phosphate, and the nucleotides ADP and ATP or GDP and GTP have been identified, the binding site for succinate has not. To determine this binding site, pig GTP-specific succinyl-CoA synthetase was crystallized in the presence of succinate, magnesium ions and CoA, and the structure of the complex was determined by X-ray crystallography to 2.2 Å resolution. Succinate binds in the carboxy-terminal domain of the β-subunit. The succinate-binding site is near both the active-site histidine residue that is phosphorylated in the reaction and the free thiol of CoA. The carboxy-terminal domain rearranges when succinate binds, burying this active site. However, succinate is not in position for transfer of the phosphoryl group from phosphohistidine. Here, it is proposed that when the active-site histidine residue has been phosphorylated by GTP, the phosphohistidine displaces phosphate and triggers the movement of the carboxylate of succinate into position to be phosphorylated. The structure shows why succinyl-CoA synthetase is specific for succinate and does not react appreciably with citrate nor with the other C4-dicarboxylic acids of the citric acid cycle, fumarate and oxaloacetate, but shows some activity with L-malate.
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Affiliation(s)
- Ji Huang
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Marie E Fraser
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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18
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Structure of NDP-forming Acetyl-CoA synthetase ACD1 reveals a large rearrangement for phosphoryl transfer. Proc Natl Acad Sci U S A 2016; 113:E519-28. [PMID: 26787904 DOI: 10.1073/pnas.1518614113] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The NDP-forming acyl-CoA synthetases (ACDs) catalyze the conversion of various CoA thioesters to the corresponding acids, conserving their chemical energy in form of ATP. The ACDs are the major energy-conserving enzymes in sugar and peptide fermentation of hyperthermophilic archaea. They are considered to be primordial enzymes of ATP synthesis in the early evolution of life. We present the first crystal structures, to our knowledge, of an ACD from the hyperthermophilic archaeon Candidatus Korachaeum cryptofilum. These structures reveal a unique arrangement of the ACD subunits alpha and beta within an α2β2-heterotetrameric complex. This arrangement significantly differs from other members of the superfamily. To transmit an activated phosphoryl moiety from the Ac-CoA binding site (within the alpha subunit) to the NDP-binding site (within the beta subunit), a distance of 51 Å has to be bridged. This transmission requires a larger rearrangement within the protein complex involving a 21-aa-long phosphohistidine-containing segment of the alpha subunit. Spatial restraints of the interaction of this segment with the beta subunit explain the necessity for a second highly conserved His residue within the beta subunit. The data support the proposed four-step reaction mechanism of ACDs, coupling acyl-CoA thioesters with ATP synthesis. Furthermore, the determined crystal structure of the complex with bound Ac-CoA allows first insight, to our knowledge, into the determinants for acyl-CoA substrate specificity. The composition and size of loops protruding into the binding pocket of acyl-CoA are determined by the individual arrangement of the characteristic subdomains.
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19
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Huang J, Malhi M, Deneke J, Fraser ME. Structure of GTP-specific succinyl-CoA synthetase in complex with CoA. Acta Crystallogr F Struct Biol Commun 2015; 71:1067-71. [PMID: 26249701 PMCID: PMC4528943 DOI: 10.1107/s2053230x15011188] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 06/09/2015] [Indexed: 11/10/2022] Open
Abstract
Pig GTP-specific succinyl-CoA synthetase is an αβ-heterodimer. The crystal structure of the complex with the substrate CoA was determined at 2.1 Å resolution. The structure shows CoA bound to the amino-terminal domain of the α-subunit, with the free thiol extending from the adenine portion into the site where the catalytic histidine residue resides.
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Affiliation(s)
- Ji Huang
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Manpreet Malhi
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Jan Deneke
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Marie Elizabeth Fraser
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
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20
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Hirschey MD, Zhao Y. Metabolic Regulation by Lysine Malonylation, Succinylation, and Glutarylation. Mol Cell Proteomics 2015; 14:2308-15. [PMID: 25717114 DOI: 10.1074/mcp.r114.046664] [Citation(s) in RCA: 302] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Indexed: 12/14/2022] Open
Abstract
Protein acetylation is a well-studied regulatory mechanism for several cellular processes, ranging from gene expression to metabolism. Recent discoveries of new post-translational modifications, including malonylation, succinylation, and glutarylation, have expanded our understanding of the types of modifications found on proteins. These three acidic lysine modifications are structurally similar but have the potential to regulate different proteins in different pathways. The deacylase sirtuin 5 (SIRT5) catalyzes the removal of these modifications from a wide range of proteins in different subcellular compartments. Here, we review these new modifications, their regulation by SIRT5, and their emerging role in cellular regulation and diseases.
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Affiliation(s)
- Matthew D Hirschey
- From the ‡Duke Molecular Physiology Institute, Sarah W. Stedman Metabolism and Nutrition Center, §Departments of Medicine & Pharmacology and Cancer Biology, Duke University, Medical Center, Durham, NC 27710;
| | - Yingming Zhao
- ¶Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637
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21
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Joyce MA, Hayakawa K, Wolodko WT, Fraser ME. Biochemical and structural characterization of the GTP-preferring succinyl-CoA synthetase from Thermus aquaticus. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:751-62. [PMID: 22751660 PMCID: PMC3388811 DOI: 10.1107/s0907444912010852] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 03/12/2012] [Indexed: 11/11/2022]
Abstract
Succinyl-CoA synthetase (SCS) from Thermus aquaticus was characterized biochemically via measurements of the activity of the enzyme and determination of its quaternary structure as well as its stability and refolding properties. The enzyme is most active between pH 8.0 and 8.4 and its activity increases with temperature to about 339 K. Gel-filtration chromatography and sedimentation equilibrium under native conditions demonstrated that the enzyme is a heterotetramer of two α-subunits and two β-subunits. The activity assays showed that the enzyme uses either ADP/ATP or GDP/GTP, but prefers GDP/GTP. This contrasts with Escherichia coli SCS, which uses GDP/GTP but prefers ADP/ATP. To understand the nucleotide preference, T. aquaticus SCS was crystallized in the presence of GDP, leading to the determination of the structure in complex with GDP-Mn(2+). A water molecule and Pro20β in T. aquaticus take the place of Gln20β in pig GTP-specific SCS, interacting well with the guanine base and other residues of the nucleotide-binding site. This leads to the preference for GDP/GTP, but does not hinder the binding of ADP/ATP.
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Affiliation(s)
- Michael A. Joyce
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Koto Hayakawa
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - William T. Wolodko
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Marie E. Fraser
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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22
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Araújo WL, Nunes-Nesi A, Nikoloski Z, Sweetlove LJ, Fernie AR. Metabolic control and regulation of the tricarboxylic acid cycle in photosynthetic and heterotrophic plant tissues. PLANT, CELL & ENVIRONMENT 2012; 35:1-21. [PMID: 21477125 DOI: 10.1111/j.1365-3040.2011.02332.x] [Citation(s) in RCA: 183] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The tricarboxylic acid (TCA) cycle is a crucial component of respiratory metabolism in both photosynthetic and heterotrophic plant organs. All of the major genes of the tomato TCA cycle have been cloned recently, allowing the generation of a suite of transgenic plants in which the majority of the enzymes in the pathway are progressively decreased. Investigations of these plants have provided an almost complete view of the distribution of control in this important pathway. Our studies suggest that citrate synthase, aconitase, isocitrate dehydrogenase, succinyl CoA ligase, succinate dehydrogenase, fumarase and malate dehydrogenase have control coefficients flux for respiration of -0.4, 0.964, -0.123, 0.0008, 0.289, 0.601 and 1.76, respectively; while 2-oxoglutarate dehydrogenase is estimated to have a control coefficient of 0.786 in potato tubers. These results thus indicate that the control of this pathway is distributed among malate dehydrogenase, aconitase, fumarase, succinate dehydrogenase and 2-oxoglutarate dehydrogenase. The unusual distribution of control estimated here is consistent with specific non-cyclic flux mode and cytosolic bypasses that operate in illuminated leaves. These observations are discussed in the context of known regulatory properties of the enzymes and some illustrative examples of how the pathway responds to environmental change are given.
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Affiliation(s)
- Wagner L Araújo
- Max-Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, Germany
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23
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Sun T, Hayakawa K, Fraser ME. ADP-Mg2+ bound to the ATP-grasp domain of ATP-citrate lyase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1168-72. [PMID: 22102020 PMCID: PMC3212355 DOI: 10.1107/s1744309111028363] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 07/15/2011] [Indexed: 04/10/2023]
Abstract
Human ATP-citrate lyase (EC 2.3.3.8) is the cytoplasmic enzyme that catalyzes the production of acetyl-CoA from citrate, CoA and ATP. The amino-terminal portion of the enzyme, containing residues 1-817, was crystallized in the presence of tartrate, ATP and magnesium ions. The crystals diffracted to 2.3 Å resolution. The structure shows ADP-Mg(2+) bound to the domain that possesses the ATP-grasp fold. The structure demonstrates that this crystal form could be used to investigate the structures of complexes with inhibitors of ATP-citrate lyase that bind at either the citrate- or ATP-binding site.
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Affiliation(s)
- Tianjun Sun
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Koto Hayakawa
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Marie E. Fraser
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
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24
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Sun T, Hayakawa K, Bateman KS, Fraser ME. Identification of the citrate-binding site of human ATP-citrate lyase using X-ray crystallography. J Biol Chem 2010; 285:27418-27428. [PMID: 20558738 PMCID: PMC2930740 DOI: 10.1074/jbc.m109.078667] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Revised: 05/10/2010] [Indexed: 11/06/2022] Open
Abstract
ATP-citrate lyase (ACLY) catalyzes the conversion of citrate and CoA into acetyl-CoA and oxaloacetate, coupled with the hydrolysis of ATP. In humans, ACLY is the cytoplasmic enzyme linking energy metabolism from carbohydrates to the production of fatty acids. In situ proteolysis of full-length human ACLY gave crystals of a truncated form, revealing the conformations of residues 2-425, 487-750, and 767-820 of the 1101-amino acid protein. Residues 2-425 form three domains homologous to the beta-subunit of succinyl-CoA synthetase (SCS), while residues 487-820 form two domains homologous to the alpha-subunit of SCS. The crystals were grown in the presence of tartrate or the substrate, citrate, and the structure revealed the citrate-binding site. A loop formed by residues 343-348 interacts via specific hydrogen bonds with the hydroxyl and carboxyl groups on the prochiral center of citrate. Arg-379 forms a salt bridge with the pro-R carboxylate of citrate. The pro-S carboxylate is free to react, providing insight into the stereospecificity of ACLY. Because this is the first structure of any member of the acyl-CoA synthetase (NDP-forming) superfamily in complex with its organic acid substrate, locating the citrate-binding site is significant for understanding the catalytic mechanism of each member, including the prototype SCS. Comparison of the CoA-binding site of SCSs with the similar structure in ACLY showed that ACLY possesses a different CoA-binding site. Comparisons of the nucleotide-binding site of SCSs with the similar structure in ACLY indicates that this is the ATP-binding site of ACLY.
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Affiliation(s)
- Tianjun Sun
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Koto Hayakawa
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Katherine S Bateman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Marie E Fraser
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
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25
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Valayannopoulos V, Haudry C, Serre V, Barth M, Boddaert N, Arnoux JB, Cormier-Daire V, Rio M, Rabier D, Vassault A, Munnich A, Bonnefont JP, de Lonlay P, Rötig A, Lebre AS. New SUCLG1 patients expanding the phenotypic spectrum of this rare cause of mild methylmalonic aciduria. Mitochondrion 2010; 10:335-41. [PMID: 20197121 DOI: 10.1016/j.mito.2010.02.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 01/20/2010] [Accepted: 02/22/2010] [Indexed: 10/19/2022]
Abstract
Deficiencies in two subunits of the succinyl-coenzyme A synthetase (SCS) have been involved in patients with encephalomyopathy and mild methylmalonic aciduria (MMA). In this study, we described three new SUCLG1 patients and performed a meta-analysis of the literature. Our report enlarges the phenotypic spectrum of SUCLG1 mutations and confirms that a characteristic metabolic profile (presence of MMA and C4-DC carnitine in urines) and basal ganglia MRI lesions are the hallmarks of SCS defects. As mitochondrial DNA depletion in muscle is not a constant finding in SUCLG1 patients, this may suggest that diagnosis should not be based on it, but also that alternative physiopathological mechanisms may be considered to explain the combined respiratory chain deficiency observed in SCS patients.
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Affiliation(s)
- Vassili Valayannopoulos
- Université Paris Descartes, Hôpital Necker-Enfants Malades et Inserm U781 et U797, Départements de Génétique, de Radiologie pédiatrique, des Maladies Métaboliques et de Biochimie B, Paris F-75015, France
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26
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Singh R, Lemire J, Mailloux RJ, Chénier D, Hamel R, Appanna VD. An ATP and oxalate generating variant tricarboxylic acid cycle counters aluminum toxicity in Pseudomonas fluorescens. PLoS One 2009; 4:e7344. [PMID: 19809498 PMCID: PMC2752808 DOI: 10.1371/journal.pone.0007344] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Accepted: 09/11/2009] [Indexed: 01/05/2023] Open
Abstract
Although the tricarboxylic acid (TCA) cycle is essential in almost all aerobic organisms, its precise modulation and integration in global cellular metabolism is not fully understood. Here, we report on an alternative TCA cycle uniquely aimed at generating ATP and oxalate, two metabolites critical for the survival of Pseudomonas fluorescens. The upregulation of isocitrate lyase (ICL) and acylating glyoxylate dehydrogenase (AGODH) led to the enhanced synthesis of oxalate, a dicarboxylic acid involved in the immobilization of aluminum (Al). The increased activity of succinyl-CoA synthetase (SCS) and oxalate CoA-transferase (OCT) in the Al-stressed cells afforded an effective route to ATP synthesis from oxalyl-CoA via substrate level phosphorylation. This modified TCA cycle with diminished efficacy in NADH production and decreased CO(2)-evolving capacity, orchestrates the synthesis of oxalate, NADPH, and ATP, ingredients pivotal to the survival of P. fluorescens in an Al environment. The channeling of succinyl-CoA towards ATP formation may be an important function of the TCA cycle during anaerobiosis, Fe starvation and O(2)-limited conditions.
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Affiliation(s)
- Ranji Singh
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Joseph Lemire
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Ryan J. Mailloux
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Daniel Chénier
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Robert Hamel
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Vasu D. Appanna
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
- * E-mail:
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27
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Qiu J, Gao HQ, Liang Y, Yu H, Zhou RH. Comparative proteomics analysis reveals role of heat shock protein 60 in digoxin-induced toxicity in human endothelial cells. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1857-64. [DOI: 10.1016/j.bbapap.2008.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 06/18/2008] [Accepted: 07/08/2008] [Indexed: 11/25/2022]
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28
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Hamblin K, Standley DM, Rogers MB, Stechmann A, Roger AJ, Maytum R, van der Giezen M. Localization and nucleotide specificity of Blastocystis succinyl-CoA synthetase. Mol Microbiol 2008; 68:1395-405. [PMID: 18452512 PMCID: PMC2440562 DOI: 10.1111/j.1365-2958.2008.06228.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The anaerobic lifestyle of the intestinal parasite Blastocystis raises questions about the biochemistry and function of its mitochondria-like organelles. We have characterized the Blastocystis succinyl-CoA synthetase (SCS), a tricarboxylic acid cycle enzyme that conserves energy by substrate-level phosphorylation. We show that SCS localizes to the enigmatic Blastocystis organelles, indicating that these organelles might play a similar role in energy metabolism as classic mitochondria. Although analysis of residues inside the nucleotide-binding site suggests that Blastocystis SCS is GTP-specific, we demonstrate that it is ATP-specific. Homology modelling, followed by flexible docking and molecular dynamics simulations, indicates that while both ATP and GTP fit into the Blastocystis SCS active site, GTP is destabilized by electrostatic dipole interactions with Lys 42 and Lys 110, the side-chains of which lie outside the nucleotide-binding cavity. It has been proposed that residues in direct contact with the substrate determine nucleotide specificity in SCS. However, our results indicate that, in Blastocystis, an electrostatic gatekeeper controls which ligands can enter the binding site.
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Affiliation(s)
- Karleigh Hamblin
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
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29
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Bräsen C, Schmidt M, Grötzinger J, Schönheit P. Reaction mechanism and structural model of ADP-forming Acetyl-CoA synthetase from the hyperthermophilic archaeon Pyrococcus furiosus: evidence for a second active site histidine residue. J Biol Chem 2008; 283:15409-18. [PMID: 18372246 DOI: 10.1074/jbc.m710218200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In Archaea, acetate formation and ATP synthesis from acetyl-CoA is catalyzed by an unusual ADP-forming acetyl-CoA synthetase (ACD) (acetyl-CoA + ADP + P(i) acetate + ATP + HS-CoA) catalyzing the formation of acetate from acetyl-CoA and concomitant ATP synthesis by the mechanism of substrate level phosphorylation. ACD belongs to the protein superfamily of nucleoside diphosphate-forming acyl-CoA synthetases, which also include succinyl-CoA synthetases (SCSs). ACD differs from SCS in domain organization of subunits and in the presence of a second highly conserved histidine residue in the beta-subunit, which is absent in SCS. The influence of these differences on structure and reaction mechanism of ACD was studied with heterotetrameric ACD (alpha(2)beta(2)) from the hyperthermophilic archaeon Pyrococcus furiosus in comparison with heterotetrameric SCS. A structural model of P. furiosus ACD was constructed suggesting a novel spatial arrangement of the subunits different from SCS, however, maintaining a similar catalytic site. Furthermore, kinetic and molecular properties and enzyme phosphorylation as well as the ability to catalyze arsenolysis of acetyl-CoA were studied in wild type ACD and several mutant enzymes. The data indicate that the formation of enzyme-bound acetyl phosphate and enzyme phosphorylation at His-257alpha, respectively, proceed in analogy to SCS. In contrast to SCS, in ACD the phosphoryl group is transferred from the His-257alpha to ADP via transient phosphorylation of a second conserved histidine residue in the beta-subunit, His-71beta. It is proposed that ACD reaction follows a novel four-step mechanism including transient phosphorylation of two active site histidine residues:
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Affiliation(s)
- Christopher Bräsen
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts Universität Kiel, Am Botanischen Garten 1-9, Kiel, Germany
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30
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Shikata K, Fukui T, Atomi H, Imanaka T. A Novel ADP-forming Succinyl-CoA Synthetase in Thermococcus kodakaraensis Structurally Related to the Archaeal Nucleoside Diphosphate-forming Acetyl-CoA Synthetases. J Biol Chem 2007; 282:26963-26970. [PMID: 17640871 DOI: 10.1074/jbc.m702694200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have identified and characterized a structurally novel succinyl-CoA synthetase (SCS) from the hyperthermophilic Archaea Thermococcus kodakaraensis. The presence of an SCS completes the metabolic pathway from glutamate to succinate in Thermococcales, which had not been clarified because of the absence of classical SCS homologs on their genomes. The SCS from T. kodakaraensis (SCS(Tk)) is a heteromeric enzyme (alpha(2)beta(2)) encoded by TK1880 (alpha-subunit) and TK0943 (beta-subunit). Although both SCS(Tk) and classical SCSs harbor the five domains present in enzymes of the acyl-CoA synthetase (nucleoside diphosphate-forming) superfamily, the domain order and distribution among subunits in SCS(Tk) (alpha-subunit, domains 1-2-5; beta-subunit, domains 3-4) are distinct from those of classical SCSs (alpha-subunit, domains 1-2; beta-subunit, domains 3-4-5) and instead resemble the acetyl-CoA synthetases from Pyrococcus furiosus (ACSs I(Pf) and II(Pf)). Comparison of the four Thermococcales genomes revealed that each strain harbors five alpha- and two beta-subunit homologs. Sequence similarity suggests that the beta-subunit of SCS(Tk) is also a component of the presumed ACS II from T. kodakaraensis (ACS II(Tk)). We coexpressed the alpha/beta-genes of SCS(Tk) (TK1880/TK0943) and of ACS II(Tk) (TK0139/TK0943). ACS II(Tk) recognizes a broad range of hydrophobic/aromatic acid compounds, as is the case with ACS II(Pf), whereas SCS(Tk) displays a distinct and relatively strict substrate specificity for several acids, including succinate. This indicates that the alpha-subunits are responsible for the distinct substrate specificities of SCS(Tk) and ACS II(Tk).
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Affiliation(s)
- Kenichi Shikata
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Toshiaki Fukui
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tadayuki Imanaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
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31
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Joyce MA, Brownie ER, Hayakawa K, Fraser ME. Cloning, expression, purification, crystallization and preliminary X-ray analysis of Thermus aquaticus succinyl-CoA synthetase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:399-402. [PMID: 17565180 PMCID: PMC2335007 DOI: 10.1107/s1744309107017113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Accepted: 04/05/2007] [Indexed: 11/11/2022]
Abstract
Succinyl-CoA synthetase (SCS) is an enzyme of the citric acid cycle and is thus found in most species. To date, there are no structures available of SCS from a thermophilic organism. To investigate how the enzyme adapts to higher temperatures, SCS from Thermus aquaticus was cloned, overexpressed, purified and crystallized. Attempts to crystallize the enzyme were thwarted by proteolysis of the beta-subunit and preferential crystallization of the truncated form. Crystals of full-length SCS were grown after the purification protocol was modified to include frequent additions of protease inhibitors. The resulting crystals, which diffract to 2.35 A resolution, are of the protein in complex with Mn2+-GDP.
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Affiliation(s)
- Michael A. Joyce
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Edward R. Brownie
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Koto Hayakawa
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Marie E. Fraser
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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