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Anufrieva NV, Morozova EA, Revtovich SV, Bazhulina NP, Timofeev V, Tkachev YV, Faleev N, Nikulin AD, Demidkina TV. Serine 339 in the Catalysis of γ- and β-Elimination Reactions. Acta Naturae 2022; 14:50-61. [PMID: 35923564 PMCID: PMC9307983 DOI: 10.32607/actanaturae.11242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 07/21/2021] [Indexed: 11/20/2022] Open
Abstract
Serine 339 of the active site of Citrobacter freundii
methionine γ-lyase (MGL) is a conserved amino acid in most
pyridoxal 5’-phosphate-dependent enzymes of the cystathionine
β-lyase subclass, to which MGL belongs. The reaction mechanism of the
MGL-catalyzed γ-elimination reaction is poorly explored. We replaced
serine 339 with alanine using site-directed mutagenesis. The replacement of
serine 339 with alanine led to a significant (by two orders of magnitude)
decrease in efficiency in the catalysis of the γ- and β-elimination
reactions by the mutant form of the enzyme. The exchange rates of the C-α-
and C-β-protons in the amino acids in complexes consisting of the enzyme
and competitive inhibitors decreased by one-two orders of magnitude. The
spectral characteristics of the mutant form indicated that the replacement did
not lead to significant changes in the conformation and tautomerism of MGL
internal aldimine. We crystallized the holoenzyme and determined its spatial
structure at 1.7 E resolution. The replacement of serine 339 with alanine did
not affect the overall course of the polypeptide chain of the MGL subunit and
the tetrameric enzyme structure. An analysis of the obtained kinetic and
spectral data, as well as the known spatial structures of C. freundii
MGL, indicates that serine 339 is necessary for efficient catalysis of
γ- and β-elimination reactions at the stage of C-α-proton
abstraction from the external aldimine, the γ-elimination reaction at the
stages of coenzyme C4’-atom protonation, and C-β-proton abstraction
from a ketimine intermediate.
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Affiliation(s)
- N. V. Anufrieva
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, 119991 Russia
| | - E. A. Morozova
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, 119991 Russia
| | - S. V. Revtovich
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, 119991 Russia
| | - N. P. Bazhulina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, 119991 Russia
| | - V.P. Timofeev
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, 119991 Russia
| | - Ya. V. Tkachev
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, 119991 Russia
| | - N.G. Faleev
- Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences, Moscow, 119991 Russia
| | - A. D. Nikulin
- Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia
| | - T. V. Demidkina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, 119991 Russia
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2
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Kulikova VV, Anufrieva NV, Kotlov MI, Morozova EA, Koval VS, Belyi YF, Revtovich SV, Demidkina TV. O-acetylhomoserine sulfhydrylase from Clostridium novyi. Cloning, expression of the gene and characterization of the enzyme. Protein Expr Purif 2020; 180:105810. [PMID: 33338587 DOI: 10.1016/j.pep.2020.105810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/08/2020] [Accepted: 12/13/2020] [Indexed: 11/19/2022]
Abstract
The gene NT01CX_1210 of pathogenic bacterium Clostridium novyi annotated as encoding O-acetylhomoserine sulfhydrylase was cloned and expressed in Escherichia coli. The gene product having O-acetylhomoserine sulfhydrylase activity was purified to homogeneity. The protein showed molecular mass of approximately 184 kDa for the native form and 46 kDa for the subunit. The enzyme catalyzes the γ-substitution reaction of O-acetylhomoserine with maximum activity at pH 7.5. Analysis of C. novyi genome allowed us to suggest that there is only one way for the synthesis of l-methionine in the bacterium. The data obtained may provide the basis for further study of the role of OAHS in Clostridium bacteria and an ascertainment of its mechanism.
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Affiliation(s)
- Vitalia V Kulikova
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia.
| | - Natalya V Anufrieva
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia
| | - Mikhail I Kotlov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia
| | - Elena A Morozova
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia
| | - Vasiliy S Koval
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia
| | - Yury F Belyi
- Gamaleya National Research Centre of Epidemiology and Microbiology, Ministry of Health of Russian Federation, Gamaleya Street, 18, Moscow, 123098, Russia
| | - Svetlana V Revtovich
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia
| | - Tatyana V Demidkina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia
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3
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Revtovich S, Morozova E, Kulikova V, Koval V, Anufrieva N, Nikulin A, Demidkina T. Sulfoxides of sulfur-containing amino acids are suicide substrates of Citrobacter freundii methionine γ-lyase. Structural bases of the enzyme inactivation. Biochimie 2019; 168:190-197. [PMID: 31711941 DOI: 10.1016/j.biochi.2019.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 11/05/2019] [Indexed: 11/18/2022]
Abstract
Interactions of Citrobacter freundii methionine γ-lyase (MGL) with sulfoxides of typical substrates were investigated. It was found that sulfoxides are suicide substrates of the enzyme. The products of the β- and γ-elimination reactions of sulfoxides, thiosulfinates, oxidize three cysteine residues of the enzyme. Three-dimensional structures of MGL inactivated by dimethyl thiosulfinate and diethyl thiosulfinate were determined at 1.46 Å and 1.59 Å resolution. Analysis of the structures identified SH groups oxidized by thiosulfinates and revealed the structural bases of MGL inactivation. The extent of inactivation of MGL in the catalysis of the β-elimination reaction depends on the length of the «tail» at oxidized Cys115. Oxidation of Cys115 results in MGL incapable to catalyze the stage of methyl mercaptan elimination of the physiological reaction.
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Affiliation(s)
- Svetlana Revtovich
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia.
| | - Elena Morozova
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Vitalia Kulikova
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Vasiliy Koval
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Natalya Anufrieva
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Alexei Nikulin
- Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Tatyana Demidkina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
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4
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Kulikova VV, Revtovich SV, Bazhulina NP, Anufrieva NV, Kotlov MI, Koval VS, Morozova EA, Hayashi H, Belyi YF, Demidkina TV. Identification of O-acetylhomoserine sulfhydrylase, a putative enzyme responsible for methionine biosynthesis in Clostridioides difficile: Gene cloning and biochemical characterizations. IUBMB Life 2019; 71:1815-1823. [PMID: 31359602 DOI: 10.1002/iub.2139] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/16/2019] [Indexed: 11/09/2022]
Abstract
O-acetylhomoserine sulfhydrylase (OAHS) is a pyridoxal 5'-phosphate-dependent enzyme involved in microbial methionine biosynthesis. In this study, we report gene cloning, protein purification, and some biochemical characteristics of OAHS from Clostridioides difficile. The enzyme is a tetramer with molecular weight of 185 kDa. It possesses a high activity in the reaction of L-homocysteine synthesis, comparable to reported activities of OAHSes from other sources. OAHS activity is inhibited by metabolic end product L-methionine. L-Propargylglycine was found to be a suicide inhibitor of the enzyme. Substrate analogue Nγ -acetyl-L-2,4-diaminobutyric acid is a competitive inhibitor of OAHS with Ki = 0.04 mM. Analysis of C. difficile genome allows to suggest that the bacterium uses the way of direct sulfhydrylation for the synthesis of L-methionine. The data obtained may provide the basis for further study of the role of OAHS in the pathogenic bacterium and the development of potential inhibitors.
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Affiliation(s)
- Vitalia V Kulikova
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Svetlana V Revtovich
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Natalia P Bazhulina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Natalya V Anufrieva
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Mikhail I Kotlov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Vasiliy S Koval
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Elena A Morozova
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
| | | | - Yury F Belyi
- Gamaleya Research Center for Epidemiology and Microbiology, Russian Ministry of Public Health, Moscow, Russia
| | - Tatyana V Demidkina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
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5
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Kulikova VV, Morozova EA, Revtovich SV, Kotlov MI, Anufrieva NV, Bazhulina NP, Raboni S, Faggiano S, Gabellieri E, Cioni P, Belyi YF, Mozzarelli A, Demidkina TV. Gene cloning, characterization, and cytotoxic activity of methionine γ-lyase fromClostridium novyi. IUBMB Life 2017; 69:668-676. [DOI: 10.1002/iub.1649] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/07/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Vitalia V. Kulikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences; Moscow Russia
| | - Elena A. Morozova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences; Moscow Russia
| | - Svetlana V. Revtovich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences; Moscow Russia
| | - Mikhail I. Kotlov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences; Moscow Russia
| | - Natalya V. Anufrieva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences; Moscow Russia
| | - Natalya P. Bazhulina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences; Moscow Russia
| | - Samanta Raboni
- Department of Food and Drug; University of Parma; Parma Italy
- Institute of Biophysics, National Research Council; Pisa Italy
| | - Serena Faggiano
- Department of Food and Drug; University of Parma; Parma Italy
- Institute of Biophysics, National Research Council; Pisa Italy
| | - Edi Gabellieri
- Institute of Biophysics, National Research Council; Pisa Italy
| | - Patrizia Cioni
- Institute of Biophysics, National Research Council; Pisa Italy
| | - Yury F. Belyi
- Gamaleya Research Institute of Epidemiology and Microbiology, Ministry of Public Health; Moscow Russia
| | - Andrea Mozzarelli
- Department of Food and Drug; University of Parma; Parma Italy
- Institute of Biophysics, National Research Council; Pisa Italy
- National Institute of Biostructures and Biosystems; Rome Italy
| | - Tatyana V. Demidkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences; Moscow Russia
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6
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Plasma methionine depletion and pharmacokinetic properties in mice of methionine γ-lyase from Citrobacter freundii, Clostridium tetani and Clostridium sporogenes. Biomed Pharmacother 2017; 88:978-984. [PMID: 28178629 DOI: 10.1016/j.biopha.2017.01.127] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 01/21/2017] [Accepted: 01/21/2017] [Indexed: 11/21/2022] Open
Abstract
PK studies were carried out after a single i.v. administration of 500 and 1000 U/kg by measuring of MGL activity in plasma samples. L-methionine concentration was measured by mass spectrometry. After single i.v. injection of 500U/kg the circulating T1/2 of enzymes in mice varies from 73 to 123min. The AUC0-tinf values determined for MGL 500U/kg from C. freundii, C. tetani and C. sporogenes are 8.21±0.28, 9.04±0.33 and 13.88±0.39U/(ml×h), respectively. Comparison of PK parameters of three MGL sources in the dose of 500U/kg indicated the MGL C. sporogenes to have better PK parameters: clearance 0.83(95%CI: 0.779-0.871) - was lower than C. tetanii 1.27(95%CI: 1.18-1.36) and C. freundii 1.39(95%CI: 1.30-1.49). Mice plasma methionine decreased to undetectable level 10min after MGL 1000 U/kg injection. After MGL C. sporogenes 500U/kg injection plasma methionine level completely omitted after 10min till 6h, assuming the sustainability of negligible levels of methionine (<5μM) in plasma of mice for about 6h. The recovery of methionine concentration showed the advantageous efficiency of MGL from C. sporogenes: 95% 0.010-0.022 vs 0.023-0.061 for MGL C. freundii and 0.036-0.056 for MGL C. tetani. There are no significant differences between methionine cleavage after MGL C. tetani and MGL C. sporogenes i.v. injection at all doses. MGL from C. sporogenes may be considered as promising enzyme for further investigation as potential anticancer agent.
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Engineered Citrobacter freundii methionine γ-lyase effectively produces antimicrobial thiosulfinates. Biochimie 2016; 128-129:92-8. [DOI: 10.1016/j.biochi.2016.07.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 07/13/2016] [Indexed: 11/20/2022]
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8
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Foo TC, Terentis AC, Venkatachalam KV. A continuous spectrophotometric assay and nonlinear kinetic analysis of methionine γ-lyase catalysis. Anal Biochem 2016; 507:21-6. [DOI: 10.1016/j.ab.2016.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 04/08/2016] [Accepted: 05/13/2016] [Indexed: 10/21/2022]
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Revtovich S, Anufrieva N, Morozova E, Kulikova V, Nikulin A, Demidkina T. Structure of methionine γ-lyase from Clostridium sporogenes. Acta Crystallogr F Struct Biol Commun 2016; 72:65-71. [PMID: 26750487 PMCID: PMC4708053 DOI: 10.1107/s2053230x15023869] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 12/11/2015] [Indexed: 11/10/2022] Open
Abstract
Methionine γ-lyase (MGL) is a pyridoxal 5'-phosphate-dependent enzyme that catalyzes the γ-elimination reaction of L-methionine. The enzyme is a promising target for therapeutic intervention in some anaerobic pathogens and has attracted interest as a potential cancer treatment. The crystal structure of MGL from Clostridium sporogenes has been determined at 2.37 Å resolution. The fold of the protein is similar to those of homologous enzymes from Citrobacter freundii, Entamoeba histolytica, Pseudomonas putida and Trichomonas vaginalis. A comparison of these structures revealed differences in the conformation of two flexible regions of the N- and C-terminal domains involved in the active-site architecture.
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Affiliation(s)
- Svetlana Revtovich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow 119991, Russian Federation
| | - Natalya Anufrieva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow 119991, Russian Federation
| | - Elena Morozova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow 119991, Russian Federation
| | - Vitalia Kulikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow 119991, Russian Federation
| | - Alexey Nikulin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow 119991, Russian Federation
| | - Tatyana Demidkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow 119991, Russian Federation
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Morozova EA, Revtovich SV, Anufrieva NV, Kulikova VV, Nikulin AD, Demidkina TV. Alliin is a suicide substrate ofCitrobacter freundiimethionine γ-lyase: structural bases of inactivation of the enzyme. ACTA ACUST UNITED AC 2014; 70:3034-42. [DOI: 10.1107/s1399004714020938] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 09/19/2014] [Indexed: 11/10/2022]
Abstract
The interaction ofCitrobacter freundiimethionine γ-lyase (MGL) and the mutant form in which Cys115 is replaced by Ala (MGL C115A) with the nonprotein amino acid (2R)-2-amino-3-[(S)-prop-2-enylsulfinyl]propanoic acid (alliin) was investigated. It was found that MGL catalyzes the β-elimination reaction of alliin to form 2-propenethiosulfinate (allicin), pyruvate and ammonia. The β-elimination reaction of alliin is followed by the inactivation and modification of SH groups of the wild-type and mutant enzymes. Three-dimensional structures of inactivated wild-type MGL (iMGL wild type) and a C115A mutant form (iMGL C115A) were determined at 1.85 and 1.45 Å resolution and allowed the identification of the SH groups that were oxidized by allicin. On this basis, the mechanism of the inactivation of MGL by alliin, a new suicide substrate of MGL, is proposed.
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Crystal structure of the external aldimine of Citrobacter freundii methionine γ-lyase with glycine provides insight in mechanisms of two stages of physiological reaction and isotope exchange of α- and β-protons of competitive inhibitors. Biochimie 2014; 101:161-7. [DOI: 10.1016/j.biochi.2014.01.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 01/09/2014] [Indexed: 11/17/2022]
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