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McCorvie TJ, Adamoski D, Machado RAC, Tang J, Bailey HJ, Ferreira DSM, Strain-Damerell C, Baslé A, Ambrosio ALB, Dias SMG, Yue WW. Architecture and regulation of filamentous human cystathionine beta-synthase. Nat Commun 2024; 15:2931. [PMID: 38575566 PMCID: PMC10995199 DOI: 10.1038/s41467-024-46864-x] [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: 03/31/2023] [Accepted: 03/13/2024] [Indexed: 04/06/2024] Open
Abstract
Cystathionine beta-synthase (CBS) is an essential metabolic enzyme across all domains of life for the production of glutathione, cysteine, and hydrogen sulfide. Appended to the conserved catalytic domain of human CBS is a regulatory domain that modulates activity by S-adenosyl-L-methionine (SAM) and promotes oligomerisation. Here we show using cryo-electron microscopy that full-length human CBS in the basal and SAM-bound activated states polymerises as filaments mediated by a conserved regulatory domain loop. In the basal state, CBS regulatory domains sterically block the catalytic domain active site, resulting in a low-activity filament with three CBS dimers per turn. This steric block is removed when in the activated state, one SAM molecule binds to the regulatory domain, forming a high-activity filament with two CBS dimers per turn. These large conformational changes result in a central filament of SAM-stabilised regulatory domains at the core, decorated with highly flexible catalytic domains. Polymerisation stabilises CBS and reduces thermal denaturation. In PC-3 cells, we observed nutrient-responsive CBS filamentation that disassembles when methionine is depleted and reversed in the presence of SAM. Together our findings extend our understanding of CBS enzyme regulation, and open new avenues for investigating the pathogenic mechanism and therapeutic opportunities for CBS-associated disorders.
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Affiliation(s)
- Thomas J McCorvie
- Nuffield Department of Clinical Medicine, Centre for Medicines Discovery, University of Oxford, Oxford, OX3 7DQ, UK.
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
| | - Douglas Adamoski
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, 13083-970, Campinas, Brazil
| | - Raquel A C Machado
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, 13083-970, Campinas, Brazil
| | - Jiazhi Tang
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Henry J Bailey
- Nuffield Department of Clinical Medicine, Centre for Medicines Discovery, University of Oxford, Oxford, OX3 7DQ, UK
- Faculty of Medicine, Institute of Biochemistry II, Goethe University Frankfurt, Frankfurt, Germany
| | - Douglas S M Ferreira
- Nuffield Department of Clinical Medicine, Centre for Medicines Discovery, University of Oxford, Oxford, OX3 7DQ, UK
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Claire Strain-Damerell
- Nuffield Department of Clinical Medicine, Centre for Medicines Discovery, University of Oxford, Oxford, OX3 7DQ, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Arnaud Baslé
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Andre L B Ambrosio
- Sao Carlos Institute of Physics, University of Sao Paulo, Sao Carlos, SP, Brazil
| | - Sandra M G Dias
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, 13083-970, Campinas, Brazil
| | - Wyatt W Yue
- Nuffield Department of Clinical Medicine, Centre for Medicines Discovery, University of Oxford, Oxford, OX3 7DQ, UK.
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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Al-Sadeq DW, Thanassoulas A, Islam Z, Kolatkar P, Al-Dewik N, Safieh-Garabedian B, Nasrallah GK, Nomikos M. Pyridoxine non-responsive R336C mutation alters the molecular properties of cystathionine beta-synthase leading to severe homocystinuria phenotype. Biochim Biophys Acta Gen Subj 2022; 1866:130148. [DOI: 10.1016/j.bbagen.2022.130148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/07/2022] [Accepted: 04/07/2022] [Indexed: 11/29/2022]
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Yan X, Chu Y, Liu B, Ru G, Di Y, Feng J. Dynamic mechanism of halide salts on the phase transition of protein models, poly(N-isopropylacrylamide) and poly(N,N-diethylacrylamide). Phys Chem Chem Phys 2020; 22:12644-12650. [PMID: 32458929 DOI: 10.1039/d0cp01366h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The effects of salts on protein systems are not yet fully understood. We investigated the ionic dynamics of three halide salts (NaI, NaBr, and NaCl) with two protein models, namely poly(N-isopropylacrylamide) (PNIPAM) and poly(N,N-diethylacrylamide) (PDEA), using multinuclear NMR, dispersion corrected density functional theory (DFT-D) calculations and dynamic light scattering (DLS) methods. The variation in ionic line-widths and chemical shifts induced by the polymers clearly illustrates that anions rather than cations interact directly with the polymers. From the variable temperature measurements of the NMR transverse relaxation rates of anions, which characterize the polymer-anion interaction intensities, the evolution behaviors of Cl-/Br-/I- during phase transitions are similar in each polymer system but differ between the two polymer systems. The NMR transverse relaxation rates of anions change synchronously with the phase transition of PNIPAM upon heating, but they drop rapidly and vanish about 3-4.5 °C before the phase transition of PDEA. By combining the DFT-D and DLS data, the relaxation results imply that anions escape from the interacting sites with PDEA prior to full polymer dehydration or collapse, which can be attributed to the lack of anion-NH interactions. The different dynamic evolutions of the anions in the PNIPAM and PDEA systems give us an important clue for understanding the micro-mechanism of protein folding in a complex salt aqueous solvent.
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Affiliation(s)
- Xiaoshuang Yan
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China.
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Anion-specific interaction with human NQO1 inhibits flavin binding. Int J Biol Macromol 2019; 126:1223-1233. [PMID: 30615965 DOI: 10.1016/j.ijbiomac.2019.01.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/03/2019] [Accepted: 01/03/2019] [Indexed: 12/11/2022]
Abstract
Ion binding to biomacromolecules can modulate their activity and stability in vivo. It is of particular interest to understand the structural and energetic basis of anion binding to functional sites of biomacromolecules. In this work, binding of anions to the FAD binding pocket of human NAD(P)H:quinone oxidoreductase 1 (NQO1), a flavoprotein associated with cancer due to a common polymorphism causing a P187S amino acid substitution, was investigated. It is known that NQO1 stability in vivo is strongly modulated by binding of its flavin cofactor. Herein, binding and protein stability analyses were carried out to show that anion binding to the apo-state of NQO1 P187S inhibits FAD binding with increasing strength following the chaotropic behavior of anions. These inhibitory effects were significant for some anions even at low millimolar concentrations. Additional pH dependent analyses suggested that protonation of histidine residues in the FAD binding pocket was not critical for anion or flavin binding. Overall, this detailed biophysical analysis helps to understanding how anions modulate NQO1 functionality in vitro, thus allowing hypothesize that NQO1 stability in vivo could be modulated by differential anion binding and subsequent inhibition of FAD binding.
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Kapusta DP, Firsov DA, Khrenova MG, Grigorenko BL, Nemukhin AV. Effect of solvation water shells on enzyme active sites in zinc-dependent hydrolases. Struct Chem 2018. [DOI: 10.1007/s11224-018-1206-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Tajwar R, Shahid S, Zafar R, Akhtar MW. Impact of orientation of carbohydrate binding modules family 22 and 6 on the catalytic activity of Thermotoga maritima xylanase XynB. Enzyme Microb Technol 2017; 106:75-82. [DOI: 10.1016/j.enzmictec.2017.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 06/09/2017] [Accepted: 07/07/2017] [Indexed: 10/19/2022]
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Pey AL, Martínez-Cruz LA, Kraus JP, Majtan T. Oligomeric status of human cystathionine beta-synthase modulates AdoMet binding. FEBS Lett 2016; 590:4461-4471. [DOI: 10.1002/1873-3468.12488] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 10/26/2016] [Accepted: 11/06/2016] [Indexed: 01/26/2023]
Affiliation(s)
- Angel L. Pey
- Department of Physical Chemistry; Faculty of Sciences; University of Granada; Spain
| | | | - Jan P. Kraus
- Department of Pediatrics; University of Colorado Denver; Aurora CO USA
| | - Tomas Majtan
- Department of Pediatrics; University of Colorado Denver; Aurora CO USA
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Kinetic stability of cystathionine beta-synthase can be modulated by structural analogs of S-adenosylmethionine: Potential approach to pharmacological chaperone therapy for homocystinuria. Biochimie 2016; 126:6-13. [DOI: 10.1016/j.biochi.2016.01.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 01/15/2016] [Indexed: 11/19/2022]
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Dziegelewska M, Holtze S, Vole C, Wachter U, Menzel U, Morhart M, Groth M, Szafranski K, Sahm A, Sponholz C, Dammann P, Huse K, Hildebrandt T, Platzer M. Low sulfide levels and a high degree of cystathionine β-synthase (CBS) activation by S-adenosylmethionine (SAM) in the long-lived naked mole-rat. Redox Biol 2016; 8:192-8. [PMID: 26803480 PMCID: PMC4732021 DOI: 10.1016/j.redox.2016.01.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 01/12/2016] [Accepted: 01/12/2016] [Indexed: 12/13/2022] Open
Abstract
Hydrogen sulfide (H2S) is a gaseous signalling molecule involved in many physiological and pathological processes. There is increasing evidence that H2S is implicated in aging and lifespan control in the diet-induced longevity models. However, blood sulfide concentration of naturally long-lived species is not known. Here we measured blood sulfide in the long-lived naked mole-rat and five other mammalian species considerably differing in lifespan and found a negative correlation between blood sulfide and maximum longevity residual. In addition, we show that the naked mole-rat cystathionine β-synthase (CBS), an enzyme whose activity in the liver significantly contributes to systemic sulfide levels, has lower activity in the liver and is activated to a higher degree by S-adenosylmethionine compared to other species. These results add complexity to the understanding of the role of H2S in aging and call for detailed research on naked mole-rat transsulfuration. Blood sulfide levels are low in long-lived species. Naked mole-rat CBS harbours a mutation at an evolutionarily conserved cysteine C412L. Naked mole-rat CBS is activated to an unusually high degree by SAM. C431L, in contrast to C431S, in human CBS does not confer constitutive activation.
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Affiliation(s)
- Maja Dziegelewska
- Genome Analysis, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany.
| | - Susanne Holtze
- Reproduction Management, Leibniz Institute for Zoo & Wildlife Research, Alfred-Kowalke-Straße 17, 10315 Berlin, Germany.
| | - Christiane Vole
- Department of General Zoology, University of Duisburg-Essen, Universitätsstraße 2, 45141 Essen, Germany.
| | - Ulrich Wachter
- Klinik für Anästhesiologie, Universitätsklinikum, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Uwe Menzel
- Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Beutenbergstraße 11a, 07745 Jena, Germany.
| | - Michaela Morhart
- Reproduction Management, Leibniz Institute for Zoo & Wildlife Research, Alfred-Kowalke-Straße 17, 10315 Berlin, Germany.
| | - Marco Groth
- Genome Analysis, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany.
| | - Karol Szafranski
- Genome Analysis, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany.
| | - Arne Sahm
- Genome Analysis, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany.
| | - Christoph Sponholz
- Genome Analysis, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany; Department of Anaesthesiology and Intensive Care Therapy, Jena University Hospital, Erlanger Allee 101, 07747 Jena, Germany.
| | - Philip Dammann
- Department of General Zoology, University of Duisburg-Essen, Universitätsstraße 2, 45141 Essen, Germany; Central Animal Laboratory, University Hospital, University of Duisburg-Essen, Hufelandstraße 55, 45122 Essen, Germany.
| | - Klaus Huse
- Genome Analysis, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany.
| | - Thomas Hildebrandt
- Reproduction Management, Leibniz Institute for Zoo & Wildlife Research, Alfred-Kowalke-Straße 17, 10315 Berlin, Germany.
| | - Matthias Platzer
- Genome Analysis, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany.
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McCorvie TJ, Kopec J, Hyung SJ, Fitzpatrick F, Feng X, Termine D, Strain-Damerell C, Vollmar M, Fleming J, Janz JM, Bulawa C, Yue WW. Inter-domain communication of human cystathionine β-synthase: structural basis of S-adenosyl-L-methionine activation. J Biol Chem 2014; 289:36018-30. [PMID: 25336647 PMCID: PMC4276868 DOI: 10.1074/jbc.m114.610782] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Cystathionine β-synthase (CBS) is a key enzyme in sulfur metabolism, and its inherited deficiency causes homocystinuria. Mammalian CBS is modulated by the binding of S-adenosyl-l-methionine (AdoMet) to its regulatory domain, which activates its catalytic domain. To investigate the underlying mechanism, we performed x-ray crystallography, mutagenesis, and mass spectrometry (MS) on human CBS. The 1.7 Å structure of a AdoMet-bound CBS regulatory domain shows one AdoMet molecule per monomer, at the interface between two constituent modules (CBS-1, CBS-2). AdoMet binding is accompanied by a reorientation between the two modules, relative to the AdoMet-free basal state, to form interactions with AdoMet via residues verified by mutagenesis to be important for AdoMet binding (Phe443, Asp444, Gln445, and Asp538) and for AdoMet-driven inter-domain communication (Phe443, Asp538). The observed structural change is further supported by ion mobility MS, showing that as-purified CBS exists in two conformational populations, which converged to one in the presence of AdoMet. We therefore propose that AdoMet-induced conformational change alters the interface and arrangement between the catalytic and regulatory domains within the CBS oligomer, thereby increasing the accessibility of the enzyme active site for catalysis.
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Affiliation(s)
- Thomas J McCorvie
- From the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Jolanta Kopec
- From the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Suk-Joon Hyung
- Worldwide Research and Development, Pfizer Inc., Groton, Connecticut 06340, and
| | - Fiona Fitzpatrick
- From the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Xidong Feng
- Worldwide Research and Development, Pfizer Inc., Groton, Connecticut 06340, and
| | - Daniel Termine
- the Pfizer Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., Cambridge, Massachusetts 02140
| | - Claire Strain-Damerell
- From the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Melanie Vollmar
- From the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - James Fleming
- the Pfizer Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., Cambridge, Massachusetts 02140
| | - Jay M Janz
- the Pfizer Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., Cambridge, Massachusetts 02140
| | - Christine Bulawa
- the Pfizer Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., Cambridge, Massachusetts 02140
| | - Wyatt W Yue
- From the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom,
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