1
|
Abo Qoura L, Balakin KV, Hoffman RM, Pokrovsky VS. The potential of methioninase for cancer treatment. Biochim Biophys Acta Rev Cancer 2024; 1879:189122. [PMID: 38796027 DOI: 10.1016/j.bbcan.2024.189122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 05/07/2024] [Accepted: 05/21/2024] [Indexed: 05/28/2024]
Abstract
Cancer cells are addicted to L-methionine (L-Met) and have a much greater requirement for L-Met than normal cells due to excess transmethylation, termed the Hoffman effect. By targeting this vulnerability through dietary restriction of L-Met, researchers have been able to achieve promising results in inhibiting tumor growth and eradicating cancer cells. Methioninase (EC 4.4.1.11; METase) catalyzes the transformation of L-Met into α-ketobutyrate, ammonia, and methanethiol. The use of METase was initially limited due to its poor stability in vivo, high immunogenicity, and enzyme-induced inactivating antibodies. These issues could be partially resolved by PEGylation, encapsulation in erythrocytes, and various site-directed mutagenesis. The big breakthrough came when it was discovered that METase is effectively administered orally. The enzyme L-asparaginase is approved by the FDA for treatment of acute lymphoblastic leukemia. METase has more potential as a therapeutic since addiction to L-Met is a general and fundamental hallmark of cancer.
Collapse
Affiliation(s)
- Louay Abo Qoura
- Research Institute of Molecular and Cellular Medicine, People's Friendship University of Russia (RUDN University), 117198 Moscow, Russia; N.N. Blokhin National Medical Research Center of Oncology of Ministry of Health of Russian Federation, 115478 Moscow, Russia
| | | | - Robert M Hoffman
- AntiCancer Inc., San Diego, CA 92111, USA; Department of Surgery, University of California, San Diego, La Jolla, CA 92037-7400, USA
| | - Vadim S Pokrovsky
- Research Institute of Molecular and Cellular Medicine, People's Friendship University of Russia (RUDN University), 117198 Moscow, Russia; N.N. Blokhin National Medical Research Center of Oncology of Ministry of Health of Russian Federation, 115478 Moscow, Russia.
| |
Collapse
|
2
|
Raboni S, Faggiano S, Bettati S, Mozzarelli A. Methionine gamma lyase: Structure-activity relationships and therapeutic applications. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140991. [PMID: 38147934 DOI: 10.1016/j.bbapap.2023.140991] [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: 11/28/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 12/28/2023]
Abstract
Methionine gamma lyase (MGL) is a bacterial and plant enzyme that catalyzes the conversion of methionine in methanthiol, 2-oxobutanoate and ammonia. The enzyme belongs to fold type I of the pyridoxal 5'-dependent family. The catalytic mechanism and the structure of wild type MGL and variants were determined in the presence of the natural substrate as well as of many sulfur-containing derivatives. Structure-function relationship studies were pivotal for MGL exploitation in the treatment of cancer, bacterial infections, and other diseases. MGL administration to cancer cells leads to methionine starvation, thus decreasing cells viability and increasing their vulnerability towards other drugs. In antibiotic therapy, MGL acts by transforming prodrugs in powerful drugs. Numerous strategies have been pursued for the delivering of MGL in vivo to prolong its bioavailability and decrease its immunogenicity. These include conjugation with polyethylene glycol and encapsulation in synthetic or natural vesicles, eventually decorated with tumor targeting molecules, such as the natural phytoestrogens daidzein and genistein. The scientific achievements in studying MGL structure, function and perspective therapeutic applications came from the efforts of many talented scientists, among which late Tatyana Demidkina to whom we dedicate this review.
Collapse
Affiliation(s)
- 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
| | - Stefano Bettati
- Institute of Biophysics, National Research Council, Pisa, Italy; National Institute of Biostructures and Biosystems (INBB), Rome, Italy; Department of Medicine, University of Parma, Parma, Italy
| | - Andrea Mozzarelli
- Department of Food and Drug, University of Parma, Parma, Italy; Institute of Biophysics, National Research Council, Pisa, Italy
| |
Collapse
|
3
|
Kulikova VV, Revtovich SV, Lyfenko AD, Morozova EA, Koval VS, Bazhulina NP, Demidkina TV. O-Acetylhomoserine Sulfhydrylase from Clostridioides difficile: Role of Tyrosine Residues in the Active Site. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:600-609. [PMID: 37331706 DOI: 10.1134/s0006297923050036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/10/2023] [Accepted: 02/10/2023] [Indexed: 06/20/2023]
Abstract
O-acetylhomoserine sulfhydrylase is one of the key enzymes in biosynthesis of methionine in Clostridioides difficile. The mechanism of γ-substitution reaction of O-acetyl-L-homoserine catalyzed by this enzyme is the least studied among the pyridoxal-5'-phosphate-dependent enzymes involved in metabolism of cysteine and methionine. To clarify the role of active site residues Tyr52 and Tyr107, four mutant forms of the enzyme with replacements of these residues with phenylalanine and alanine were generated. Catalytic and spectral properties of the mutant forms were investigated. The rate of γ-substitution reaction catalyzed by the mutant forms with replaced Tyr52 residue decreased by more than three orders of magnitude compared to the wild-type enzyme. The Tyr107Phe and Tyr107Ala mutant forms practically did not catalyze this reaction. Replacements of the Tyr52 and Tyr107 residues led to the decrease in affinity of apoenzyme to coenzyme by three orders of magnitude and changes in the ionic state of the internal aldimine of the enzyme. The obtained results allowed us to assume that Tyr52 is involved in ensuring optimal position of the catalytic coenzyme-binding lysine residue at the stages of C-α-proton elimination and elimination of the side group of the substrate. Tyr107 could act as a general acid catalyst at the stage of acetate elimination.
Collapse
Affiliation(s)
- Vitalia V Kulikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
| | - Svetlana V Revtovich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Anna D Lyfenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Elena A Morozova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Vasiliy S Koval
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Natalya P Bazhulina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Tatyana V Demidkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| |
Collapse
|
4
|
Structural Basis of the Inhibition of L-Methionine γ-Lyase from Fusobacterium nucleatum. Int J Mol Sci 2023; 24:ijms24021651. [PMID: 36675166 PMCID: PMC9865163 DOI: 10.3390/ijms24021651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Fusobacterium nucleatum is a lesion-associated obligate anaerobic pathogen of destructive periodontal disease; it is also implicated in the progression and severity of colorectal cancer. Four genes (FN0625, FN1055, FN1220, and FN1419) of F. nucleatum are involved in producing hydrogen sulfide (H2S), which plays an essential role against oxidative stress. The molecular functions of Fn1419 are known, but their mechanisms remain unclear. We determined the crystal structure of Fn1419 at 2.5 Å, showing the unique conformation of the PLP-binding site when compared with L-methionine γ-lyase (MGL) proteins. Inhibitor screening for Fn1419 with L-cysteine showed that two natural compounds, gallic acid and dihydromyricetin, selectively inhibit the H2S production of Fn1419. The chemicals of gallic acid, dihydromyricetin, and its analogs containing trihydroxybenzene, were potentially responsible for the enzyme-inhibiting activity on Fn1419. Molecular docking and mutational analyses suggested that Gly112, Pro159, Val337, and Arg373 are involved in gallic acid binding and positioned close to the substrate and pyridoxal-5'-phosphate-binding site. Gallic acid has little effect on the other H2S-producing enzymes (Fn1220 and Fn1055). Overall, we proposed a molecular mechanism underlying the action of Fn1419 from F. nucleatum and found a new lead compound for inhibitor development.
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Raboni S, Revtovich S, Demitri N, Giabbai B, Storici P, Cocconcelli C, Faggiano S, Rosini E, Pollegioni L, Galati S, Buschini A, Morozova E, Kulikova V, Nikulin A, Gabellieri E, Cioni P, Demidkina T, Mozzarelli A. Engineering methionine γ-lyase from Citrobacter freundii for anticancer activity. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:1260-1270. [PMID: 30268810 DOI: 10.1016/j.bbapap.2018.09.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/27/2018] [Accepted: 09/25/2018] [Indexed: 12/16/2022]
Abstract
Methionine deprivation of cancer cells, which are deficient in methionine biosynthesis, has been envisioned as a therapeutic strategy to reduce cancer cell viability. Methionine γ-lyase (MGL), an enzyme that degrades methionine, has been exploited to selectively remove the amino acid from cancer cell environment. In order to increase MGL catalytic activity, we performed sequence and structure conservation analysis of MGLs from various microorganisms. Whereas most of the residues in the active site and at the dimer interface were found to be conserved, residues located in the C-terminal flexible loop, forming a wall of the active site entry channel, were found to be variable. Therefore, we carried out site-saturation mutagenesis at four independent positions of the C-terminal flexible loop, P357, V358, P360 and A366 of MGL from Citrobacter freundii, generating libraries that were screened for activity. Among the active variants, V358Y exhibits a 1.9-fold increase in the catalytic rate and a 3-fold increase in KM, resulting in a catalytic efficiency similar to wild type MGL. V358Y cytotoxic activity was assessed towards a panel of cancer and nonmalignant cell lines and found to exhibit IC50 lower than the wild type. The comparison of the 3D-structure of V358Y MGL with other MGL available structures indicates that the C-terminal loop is either in an open or closed conformation that does not depend on the amino acid at position 358. Nevertheless, mutations at this position allosterically affects catalysis.
Collapse
Affiliation(s)
- Samanta Raboni
- Department of Food and Drug, University of Parma, Parma, Italy; Institute of Biophysics, National Research Council, Pisa, Italy
| | - Svetlana Revtovich
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
| | | | | | | | | | - Serena Faggiano
- Department of Food and Drug, University of Parma, Parma, Italy; Institute of Biophysics, National Research Council, Pisa, Italy
| | - Elena Rosini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Serena Galati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Annamaria Buschini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - 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
| | - Alexey Nikulin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - Edi Gabellieri
- Institute of Biophysics, National Research Council, Pisa, Italy
| | - Patrizia Cioni
- Institute of Biophysics, National Research Council, Pisa, Italy
| | - Tatyana Demidkina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 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.
| |
Collapse
|
8
|
Lin B, Tian G, Liu Y. Mechanistic insights into the γ-elimination reaction of l-methionine catalyzed by methionine γ-lyase (MGL). Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2140-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
9
|
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
| |
Collapse
|
10
|
Revtovich SV, Morozova EA, Kulikova VV, Anufrieva NV, Osipova TI, Koval VS, Nikulin AD, Demidkina TV. Crystal structure of mutant form Cys115His of Citrobacter freundii methionine γ-lyase complexed with l-norleucine. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1123-1128. [PMID: 28602917 DOI: 10.1016/j.bbapap.2017.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 06/02/2017] [Accepted: 06/05/2017] [Indexed: 11/30/2022]
Abstract
The mutant form of Citrobacter freundii methionine γ-lyase with the replacement of active site Cys115 for His has been found to be inactive in the γ-elimination reaction of methionine while fully active in the γ-elimination reaction of O-acetyl-l-homoserine and in the β-elimination reaction of S-alk(en)yl-substituted cysteines. In this work, the crystal structure of the mutant enzyme complexed with competitive inhibitor, l-norleucine was determined at 1.45Å resolution. At the enzyme active site the inhibitor proved to be bound both noncovalently and covalently, which corresponds to the two intermediates of the γ- and β-elimination reactions, Michaelis complex and the external aldimine. Analysis of the structure allowed us to suggest the possible reason for the inability of the mutant enzyme to catalyze the physiological reaction.
Collapse
Affiliation(s)
- Svetlana V Revtovich
- 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
| | - Vitalia V Kulikova
- 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
| | - Tatyana I Osipova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vasiliy S Koval
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey D Nikulin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Tatyana V Demidkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
| |
Collapse
|
11
|
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.
Collapse
|
12
|
Molecular and Spectroscopic Characterization of Aspergillus flavipes and Pseudomonas putida L-Methionine γ-Lyase in Vitro. Appl Biochem Biotechnol 2016; 181:1513-1532. [PMID: 27796875 DOI: 10.1007/s12010-016-2299-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/20/2016] [Indexed: 01/11/2023]
Abstract
Pseudomonas putida L-methionine γ-lyase (PpMGL) has been recognized as an efficient anticancer agent, however, its antigenicity and stability remain as critical challenges for its clinical use. From our studies, Aspergillus flavipes L-methionine γ-lyase (AfMGL) displayed more affordable biochemical properties than PpMGL. Thus, the objective of this work was to comparatively assess the functional properties of AfMGL and PpMGL via stability of their internal aldimine linkage, tautomerism of pyridoxal 5'-phosphate (PLP) and structural stability responsive to physicochemical factors. The internal Schiff base of AfMGL and PpMGL have the same stability to hydroxylamine and human serum albumin. Acidic pHs resulted in strong cleavage of the internal Schiff base, inducing the unfolding of MGLs, compared to neutral-alkaline pHs. At λ 280 nm excitation, both AfMGL and PpMGL have identical fluorescence emission spectra at λ 335 nm for the intrinsic tryptophan and λ 560 nm for the internal Schiff base. The maximum PLP tautomeric shift of ketoenamine to enolimine was detected at acidic pH causing complete enzyme unfolding, subunits dissociation and tautomeric shift of intrinsic PLP, rather than neutral-alkaline ones. The T m of AfMGL and PpMGL in presence of thermal stabilizer/ destabilizer was assayed by DSF. The T m of AfMGL and PpMGL was 73.1 °C and 74.4 °C, respectively, suggesting the higher proximity to the tertiary structure of both enzymes. The T m of AfMGL and PpMGL was slightly increased by trehalose and EDTA in contrast to guanidine HCl and urea. The active site and PLP-binding domains are identically conserved in both AfMGL and PpMGL.
Collapse
|
13
|
Cao H, Tan K, Wang F, Bigelow L, Yennamalli RM, Jedrzejczak R, Babnigg G, Bingman CA, Joachimiak A, Kharel MK, Singh S, Thorson JS, Phillips GN. Structural dynamics of a methionine γ-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2016; 3:034702. [PMID: 27191010 PMCID: PMC4851618 DOI: 10.1063/1.4948539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/21/2016] [Indexed: 06/05/2023]
Abstract
CalE6 from Micromonospora echinospora is a (pyridoxal 5' phosphate) PLP-dependent methionine γ-lyase involved in the biosynthesis of calicheamicins. We report the crystal structure of a CalE6 2-(N-morpholino)ethanesulfonic acid complex showing ligand-induced rotation of Tyr100, which stacks with PLP, resembling the corresponding tyrosine rotation of true catalytic intermediates of CalE6 homologs. Elastic network modeling and crystallographic ensemble refinement reveal mobility of the N-terminal loop, which involves both tetrameric assembly and PLP binding. Modeling and comparative structural analysis of PLP-dependent enzymes involved in Cys/Met metabolism shine light on the functional implications of the intrinsic dynamic properties of CalE6 in catalysis and holoenzyme maturation.
Collapse
Affiliation(s)
- Hongnan Cao
- Biosciences at Rice, Rice University , 6100 Main St., Houston, Texas 77005, USA
| | - Kemin Tan
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Fengbin Wang
- Biosciences at Rice, Rice University , 6100 Main St., Houston, Texas 77005, USA
| | - Lance Bigelow
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | | | - Robert Jedrzejczak
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Gyorgy Babnigg
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, USA
| | - Andrzej Joachimiak
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Madan K Kharel
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536, USA
| | - Shanteri Singh
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536, USA
| | - Jon S Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536, USA
| | - George N Phillips
- Biosciences at Rice, Rice University , 6100 Main St., Houston, Texas 77005, USA
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Anufrieva NV, Faleev NG, Morozova EA, Bazhulina NP, Revtovich SV, Timofeev VP, Tkachev YV, Nikulin AD, Demidkina TV. The role of active site tyrosine 58 in Citrobacter freundii methionine γ-lyase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1220-8. [PMID: 25584856 DOI: 10.1016/j.bbapap.2014.12.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 12/29/2014] [Accepted: 12/30/2014] [Indexed: 10/24/2022]
Abstract
In the spatial structure of methionine γ-lyase (MGL, EC 4.4.1.11) from Citrobacter freundii, Tyr58 is located at H-bonding distance to the oxygen atom of the phosphate "handle" of pyridoxal 5'-phosphate (PLP). It was replaced for phenylalanine by site-directed mutagenesis. The X-ray structure of the mutant enzyme was determined at 1.96Å resolution. Comparison of spatial structures and absorption spectra of wild-type and mutant holoenzymes demonstrated that the replacement did not result in essential changes of the conformation of the active site Tyr58Phe MGL. The Kd value of PLP for Tyr58Phe MGL proved to be comparable to the Kd value for the wild-type enzyme. The replacement led to a decrease of catalytic efficiencies in both γ- and β-elimination reactions of about two orders of magnitude as compared to those for the wild-type enzyme. The rates of exchange of C-α- and C-β- protons of inhibitors in D2O catalyzed by the mutant form are comparable with those for the wild-type enzyme. Spectral data on the complexes of the mutant form with the substrates and inhibitors showed that the replacement led to a change of rate the limiting step of the physiological reaction. The results allowed us to conclude that Tyr58 is involved in an optimal positioning of the active site Lys210 at some stages of γ- and β-elimination reactions. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications.
Collapse
Affiliation(s)
- Natalya V Anufrieva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow 119991, Russia
| | - Nicolai G Faleev
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, ul. Vavilova 28, Moscow 117813, Russia
| | - Elena A Morozova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow 119991, Russia
| | - Natalia P Bazhulina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow 119991, Russia
| | - Svetlana V Revtovich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow 119991, Russia
| | - Vladimir P Timofeev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow 119991, Russia
| | - Yaroslav V Tkachev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow 119991, Russia
| | - Alexei D Nikulin
- Institute of Protein Research, Russian Academy of Sciences, ul. Institutskaya 4, Pushchino, Moscow Region 142290, Russia
| | - Tatyana V Demidkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow 119991, Russia.
| |
Collapse
|
16
|
Kuznetsov NA, Faleev NG, Kuznetsova AA, Morozova EA, Revtovich SV, Anufrieva NV, Nikulin AD, Fedorova OS, Demidkina TV. Pre-steady-state kinetic and structural analysis of interaction of methionine γ-lyase from Citrobacter freundii with inhibitors. J Biol Chem 2014; 290:671-81. [PMID: 25398880 DOI: 10.1074/jbc.m114.586511] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Methionine γ-lyase (MGL) catalyzes the γ-elimination of l-methionine and its derivatives as well as the β-elimination of l-cysteine and its analogs. These reactions yield α-keto acids and thiols. The mechanism of chemical conversion of amino acids includes numerous reaction intermediates. The detailed analysis of MGL interaction with glycine, l-alanine, l-norvaline, and l-cycloserine was performed by pre-steady-state stopped-flow kinetics. The structure of side chains of the amino acids is important both for their binding with enzyme and for the stability of the external aldimine and ketimine intermediates. X-ray structure of the MGL·l-cycloserine complex has been solved at 1.6 Å resolution. The structure models the ketimine intermediate of physiological reaction. The results elucidate the mechanisms of the intermediate interconversion at the stages of external aldimine and ketimine formation.
Collapse
Affiliation(s)
- Nikita A Kuznetsov
- From the Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, the Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090
| | | | - Alexandra A Kuznetsova
- From the Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, the Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090
| | - Elena A Morozova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, and
| | - Svetlana V Revtovich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, and
| | - Natalya V Anufrieva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, and
| | - Alexei D Nikulin
- the Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Olga S Fedorova
- From the Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, the Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090,
| | - Tatyana V Demidkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, and
| |
Collapse
|
17
|
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.
Collapse
|