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Michielon A, Marchesani F, Faggiano S, Giaccari R, Campanini B, Bettati S, Mozzarelli A, Bruno S. Human serine racemase is inhibited by glyceraldehyde 3-phosphate, but not by glyceraldehyde 3-phosphate dehydrogenase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140544. [PMID: 32971286 DOI: 10.1016/j.bbapap.2020.140544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/14/2020] [Accepted: 09/19/2020] [Indexed: 11/28/2022]
Abstract
Murine serine racemase (SR), the enzyme responsible for the biosynthesis of the neuromodulator d-serine, was reported to form a complex with glyceraldehyde 3-phosphate dehydrogenase (GAPDH), resulting in SR inhibition. In this work, we investigated the interaction between the two human orthologues. We were not able to observe neither the inhibition nor the formation of the SR-GAPDH complex. Rather, hSR is inhibited by the hGAPDH substrate glyceraldehyde 3-phosphate (G3P) in a time- and concentration-dependent fashion, likely through a covalent reaction of the aldehyde functional group. The inhibition was similar for the two G3P enantiomers but it was not observed for structurally similar aldehydes. We ruled out a mechanism of inhibition based on the competition with either pyridoxal phosphate (PLP) - described for other PLP-dependent enzymes when incubated with small aldehydes - or ATP. Nevertheless, the inhibition time course was affected by the presence of hSR allosteric and orthosteric ligands, suggesting a conformation-dependence of the reaction.
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Affiliation(s)
- Annalisa Michielon
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Francesco Marchesani
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Serena Faggiano
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy; Istituto di Biofisica, CNR, Via G. Moruzzi 1, 56124 Pisa, Italy
| | - Roberta Giaccari
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Barbara Campanini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Stefano Bettati
- Dipartimento di Medicina e Chirurgia, Via Volturno 39, 43125 Parma, Italy
| | - Andrea Mozzarelli
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy; Istituto di Biofisica, CNR, Via G. Moruzzi 1, 56124 Pisa, Italy
| | - Stefano Bruno
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy.
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Bruno S, Margiotta M, Pinto A, Cullia G, Conti P, De Micheli C, Mozzarelli A. Selectivity of 3-bromo-isoxazoline inhibitors between human and Plasmodium falciparum glyceraldehyde-3-phosphate dehydrogenases. Bioorg Med Chem 2016; 24:2654-9. [DOI: 10.1016/j.bmc.2016.04.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 04/14/2016] [Accepted: 04/16/2016] [Indexed: 01/09/2023]
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Bruno S, Pinto A, Paredi G, Tamborini L, De Micheli C, La Pietra V, Marinelli L, Novellino E, Conti P, Mozzarelli A. Discovery of Covalent Inhibitors of Glyceraldehyde-3-phosphate Dehydrogenase, A Target for the Treatment of Malaria. J Med Chem 2014; 57:7465-71. [DOI: 10.1021/jm500747h] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Stefano Bruno
- Dipartimento
di Farmacia and Centro Siteia.Parma, Università di Parma, Parco Area
delle Scienze 23/A, 43124 Parma, Italy
- Istituto di Bioscienze e Biorisorse, CNR, 80131 Napoli, Italy
| | - Andrea Pinto
- Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milano, Italy
| | - Gianluca Paredi
- Dipartimento
di Farmacia and Centro Siteia.Parma, Università di Parma, Parco Area
delle Scienze 23/A, 43124 Parma, Italy
| | - Lucia Tamborini
- Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milano, Italy
| | - Carlo De Micheli
- Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milano, Italy
| | - Valeria La Pietra
- Dipartimento
di Farmacia, Università di Napoli Federico II, Via Montesano,
49, 80138 Napoli, Italy
| | - Luciana Marinelli
- Dipartimento
di Farmacia, Università di Napoli Federico II, Via Montesano,
49, 80138 Napoli, Italy
| | - Ettore Novellino
- Dipartimento
di Farmacia, Università di Napoli Federico II, Via Montesano,
49, 80138 Napoli, Italy
| | - Paola Conti
- Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milano, Italy
| | - Andrea Mozzarelli
- Dipartimento
di Farmacia and Centro Siteia.Parma, Università di Parma, Parco Area
delle Scienze 23/A, 43124 Parma, Italy
- Istituto Nazionale di Biostrutture e Biosistemi, 00136 Roma, Italy
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Moniot S, Bruno S, Vonrhein C, Didierjean C, Boschi-Muller S, Vas M, Bricogne G, Branlant G, Mozzarelli A, Corbier C. Trapping of the thioacylglyceraldehyde-3-phosphate dehydrogenase intermediate from Bacillus stearothermophilus. Direct evidence for a flip-flop mechanism. J Biol Chem 2008; 283:21693-702. [PMID: 18480053 DOI: 10.1074/jbc.m802286200] [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
The crystal structure of the thioacylenzyme intermediate of the phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Bacillus stearothermophilus has been solved at 1.8A resolution. Formation of the intermediate was obtained by diffusion of the natural substrate within the crystal of the holoenzyme in the absence of inorganic phosphate. To define the soaking conditions suitable for the isolation and accumulation of the intermediate, a microspectrophotometric characterization of the reaction of GAPDH in single crystals was carried out, following NADH formation at 340 nm. When compared with the structure of the Michaelis complex (Didierjean, C., Corbier, C., Fatih, M., Favier, F., Boschi-Muller, S., Branlant, G., and Aubry, A. (2003) J. Biol. Chem. 278, 12968-12976) the 206-210 loop is shifted and now forms part of the so-called "new P(i)" site. The locations of both the O1 atom and the C3-phosphate group of the substrate are also changed. Altogether, the results provide evidence for the flipping of the C3-phosphate group occurring concomitantly or after the redox step.
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Affiliation(s)
- Sébastien Moniot
- Laboratoire de Cristallographie et de Modélisation des Matériaux Minéraux et Biologiques, UMR CNRS-Université Henri Poincaré (UHP) 7036
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Mozzarelli A, Bettati S, Rivetti C, Rossi GL, Colotti G, Chiancone E. Cooperative oxygen binding to scapharca inaequivalvis hemoglobin in the crystal. J Biol Chem 1996; 271:3627-32. [PMID: 8631972 DOI: 10.1074/jbc.271.7.3627] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Oxygen binding to homodimeric Scapharca inaequivalvis hemoglobin (HbI) crystals has been investigated by single-crystal polarized absorption microspectrophotometry. The saturation curve, characterized by a Hill coefficient nH = 1.45 and an oxygen pressure at half saturation p50 = 4.8 torr, at 15 degrees C, shows that HbI in the crystalline state retains positive cooperativity in ligand binding. This finding will permit the correlation of the oxygen-linked conformational changes in the crystal with the expression of cooperativity. Polarized absorption spectra of deoxy-HbI, oxy-HbI, and oxidized HbI crystals indicate that oxygenation does not induce heme reorientation, whereas oxidation does. Lattice interactions prevent the dissociation of oxidized dimers that occurs in solution and stabilize an equilibrium distribution of pentacoordinate and hexacoordinate high spin species.
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Affiliation(s)
- A Mozzarelli
- Istituto di Scienze Biochimiche, Università di Parma, 43100 Parma, Italy
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Leonidas DD, Oikonomakos NG, Papageorgiou AC, Sotiroudis TG. Kinetic properties of tetrameric glycogen phosphorylase b in solution and in the crystalline state. Protein Sci 1992; 1:1123-32. [PMID: 1304391 PMCID: PMC2142183 DOI: 10.1002/pro.5560010906] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
R-state monoclinic P2(1) crystals of phosphorylase have been shown to be catalytically active in the presence of an oligosaccharide primer and glucose-1-phosphate in 0.9 M ammonium sulfate, 10 mM beta-glycerophosphate, 0.5 mM EDTA, and 1 mM dithiothreitol, the medium in which the crystals are grown or equilibrated for crystallographic studies (Barford, D. & Johnson, L.N., 1989, Nature 360, 609-616; Barford, D., Hu, S.-H., & Johnson, L.N., 1991, J. Mol. Biol. 218, 233-260). Kinetic data suggest that the activity of crystalline tetrameric phosphorylase is similar to that determined in solution for the enzyme tetramer. However, large differences were found in the maximal velocities for both oligosaccharide or glucose-1-phosphate substrates between the soluble dimeric and crystalline tetrameric enzyme.
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Affiliation(s)
- D D Leonidas
- Institute of Biological Research and Biotechnology, National Hellenic Research Foundation, Athens, Greece
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Hajdu J, Johnson LN. Progress with Laue diffraction studies on protein and virus crystals. Biochemistry 1990; 29:1669-78. [PMID: 2184884 DOI: 10.1021/bi00459a001] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- J Hajdu
- Laboratory of Molecular Biophysics, University of Oxford, U.K
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Vas M, Berni R, Batke J, Keleti T, Rossi GL. Kinetic evidence for a reversible isomerization of pig muscle glyceraldehyde-3-phosphate dehydrogenase in its crystallization medium. Arch Biochem Biophys 1988; 263:121-9. [PMID: 3369857 DOI: 10.1016/0003-9861(88)90620-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Ammonium sulfate, a typical component of crystallization media of proteins, stabilizes an inactive conformation of pig muscle glyceraldehyde-3-phosphate dehydrogenase. In fact, in the presence of ammonium sulfate the reconstitution of the catalytically active holoenzyme from the apoenzyme and NAD is not instantaneous, as in the case of enzymes from Bacillus stearothermophilus and the Mediterranean lobster Palinurus vulgaris. With pig muscle enzyme, at pH 6.0, the time course of formation of the characteristic Racker band can be monitored by a rapid mixing stopped flow technique. Activation follows a single exponential curve with a rate constant independent of the concentration of both NAD and protein and, therefore, appears to be limited by a slow protein isomerization (k = 7 +/- 2 s-1). Accordingly, when the apoenzyme is simultaneously exposed to NAD and either glyceraldehyde 3-phosphate or 1,3-bisphosphoglycerate, the ensuing reactions (the redox and the acylation steps, respectively) are kinetically limited by the same protein isomerization. At pH 7.0 and 8.0, however, two among the four active sites react with NAD at an unmeasurably high rate, while the other two sites behave as they do at pH 6.0. When the pig muscle apoenzyme is preincubated and allowed to react with either glyceraldehyde 3-phosphate or 1,3-bisphosphoglycerate before the rapid mixing with NAD, both the redox reaction and the NAD-dependent activation of apo-acyl-enzyme toward arsenolysis become unmeasurably fast. Similarly, when the sulfate in the medium is replaced by ions such as phosphate and citrate, the reconstitution of the active holoenzyme is practically instantaneous. Thus, the slow protein isomerization observed in the presence of sulfate and abolished by competing substrates and anions is diagnostic of a structural state of the pig muscle apoenzyme, which is induced by sulfate ions bound within the enzyme active site.
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Affiliation(s)
- M Vas
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest
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Keleti T, Ovádi J. Control of metabolism by dynamic macromolecular interactions. CURRENT TOPICS IN CELLULAR REGULATION 1988; 29:1-33. [PMID: 3293924 DOI: 10.1016/b978-0-12-152829-4.50003-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- T Keleti
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest
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Vértessy B, Vas M, Keleti T. Microenvironment of the enzyme-bound NADH is different in lobster and pig muscle glyceraldehyde-3-phosphate dehydrogenase microcrystals. Arch Biochem Biophys 1986; 251:299-305. [PMID: 3789735 DOI: 10.1016/0003-9861(86)90077-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Two possible consequences of crystal lattice formation were studied with glyceraldehyde-3-phosphate dehydrogenases isolated from lobster (Palinurus vulgaris) and pig muscle: changes in the microenvironment of the NADH-binding site as detected by fluorescence polarization, and differences in the maximal activities of the microcrystalline enzymes as compared to those in solution. In solution practically no difference was found between the polarization values of the enzyme-NADH and the catalytic intermediate 3-phosphoglyceroyl-enzyme-NADH complexes whether with lobster or with pig enzyme. In microcrystalline state a similar effect was found with the lobster enzyme. However, fluorescence polarization of NADH bound to the pig enzyme was significantly different in the presence and in the absence of the 3-phosphoglyceroyl group. This indicates some change in the microenvironment of the pig enzyme-bound NADH which occurs upon decomposition of the catalytic intermediate. The difference between the microcrystalline lobster and pig muscle glyceraldehyde-3-phosphate dehydrogenases pertains also to their functional properties. Packing of soluble pig muscle enzyme into a crystal lattice stabilizes a unique protein conformation of extremely low activity (about 3% of that measured in solution). The maximal molar activity of the lobster enzyme is identical in crystalline state and in solution, which is an exceptional phenomenon.
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Tegoni M, Mozzarelli A, Rossi GL, Labeyrie F. Complex formation and intermolecular electron transfer between flavocytochrome b2 in the crystal and cytochrome c. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(20)81907-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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