1
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Qoura LA, Balakin KV, Hoffman RM, Pokrovsky VS. The potential of methioninase for cancer treatment. Biochim Biophys Acta Rev Cancer 2024:189122. [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] [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.
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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.
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2
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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.
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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
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3
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Bekker GJ, Yokochi M, Suzuki H, Ikegawa Y, Iwata T, Kudou T, Yura K, Fujiwara T, Kawabata T, Kurisu G. Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data. Protein Sci 2021; 31:173-186. [PMID: 34664328 PMCID: PMC8740847 DOI: 10.1002/pro.4211] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 11/25/2022]
Abstract
Protein Data Bank Japan (PDBj), a founding member of the worldwide Protein Data Bank (wwPDB) has accepted, processed and distributed experimentally determined biological macromolecular structures for 20 years. During that time, we have continuously made major improvements to our query search interface of PDBj Mine 2, the BMRBj web interface, and EM Navigator for PDB/BMRB/EMDB entries. PDBj also serves PDB‐related secondary database data, original web‐based modeling services such as Homology modeling of complex structure (HOMCOS), visualization services and utility tools, which we have continuously enhanced and expanded throughout the years. In addition, we have recently developed several unique archives, BSM‐Arc for computational structure models, and XRDa for raw X‐ray diffraction images, both of which promote open science in the structural biology community. During the COVID‐19 pandemic, PDBj has also started to provide feature pages for COVID‐19 related entries across all available archives at PDBj from raw experimental data and PDB structural data to computationally predicted models, while also providing COVID‐19 outreach content for high school students and teachers.
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Affiliation(s)
- Gert-Jan Bekker
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Masashi Yokochi
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Hirofumi Suzuki
- School of Advanced Science and Engineering, Waseda University, Shinjuku, Tokyo, Japan
| | - Yasuyo Ikegawa
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Takeshi Iwata
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Takahiro Kudou
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Kei Yura
- School of Advanced Science and Engineering, Waseda University, Shinjuku, Tokyo, Japan.,Graduate School of Humanities and Sciences, Ochanoizu University, Bunkyo, Tokyo, Japan
| | | | - Takeshi Kawabata
- Protein Research Foundation, Minoh, Osaka, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
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4
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Ikeda K, Kezuka Y, Nonaka T, Yonezawa T, Osawa M, Katoh E. Comprehensive Approach of 19F Nuclear Magnetic Resonance, Enzymatic, and In Silico Methods for Site-Specific Hit Selection and Validation of Fragment Molecules that Inhibit Methionine γ-Lyase Activity. J Med Chem 2021; 64:14299-14310. [PMID: 34582207 DOI: 10.1021/acs.jmedchem.1c00766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fragment-based screening using 19F NMR (19F-FS) is an efficient method for exploring seed and lead compounds for drug discovery. Here, we demonstrate the utility and merits of using 19F-FS for methionine γ-lyase-binding fragments, together with a 19F NMR-based competition and mutation assay, as well as enzymatic and in silico methods. 19F NMR-based assays provided useful information on binding between 19F-FS hit fragments and target proteins. Although the 19F-FS and enzymatic assay were weakly correlated, they show that the 19F-FS hit fragments contained compounds with inhibitory activity. Furthermore, we found that in silico calculations partially account for the differences in activity levels between the 19F-FS hits as per NMR analysis. A comprehensive approach combining the 19F-FS and other methods not only identified fragment hits but also distinguished structural differences in chemical groups with diverse activity levels.
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Affiliation(s)
- Kazuyoshi Ikeda
- Division of Physics for Life Functions, Keio University Faculty of Pharmacy, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Yuichiro Kezuka
- Division of Structural Biology, Department of Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate 028-3694, Japan
| | - Takamasa Nonaka
- Division of Structural Biology, Department of Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate 028-3694, Japan
| | - Tomoki Yonezawa
- Division of Physics for Life Functions, Keio University Faculty of Pharmacy, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Masanori Osawa
- Division of Physics for Life Functions, Keio University Faculty of Pharmacy, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Etsuko Katoh
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
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5
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Catalytic specificity of the Lactobacillus plantarum cystathionine γ-lyase presumed by the crystallographic analysis. Sci Rep 2020; 10:14886. [PMID: 32913258 PMCID: PMC7483736 DOI: 10.1038/s41598-020-71756-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/05/2020] [Indexed: 11/17/2022] Open
Abstract
The reverse transsulfuration pathway, which is composed of cystathionine β-synthase (CBS) and cystathionine γ-lyase (CGL), plays a role to synthesize l-cysteine using l-serine and the sulfur atom in l-methionine. A plant-derived lactic acid bacterium Lactobacillus plantarum SN35N has been previously found to harbor the gene cluster encoding the CBS- and CGL-like enzymes. In addition, it has been demonstrated that the L. plantarum CBS can synthesize cystathionine from O-acetyl-l-serine and l-homocysteine. The aim of this study is to characterize the enzymatic functions of the L. plantarum CGL. We have found that the enzyme has the high γ-lyase activity toward cystathionine to generate l-cysteine, together with the β-lyase activity toward l-cystine to generate l-cysteine persulfide. By the crystallographic analysis of the inactive CGL K194A mutant complexed with cystathionine, we have found the residues which recognize the distal amino and carboxyl groups of cystathionine or l-cystine. The PLP-bound substrates at the active site may take either the binding pose for the γ- or β-elimination reaction, with the former being the major reaction in the case of cystathionine.
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6
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Maggi M, Scotti C. Enzymes in Metabolic Anticancer Therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1148:173-199. [PMID: 31482500 DOI: 10.1007/978-981-13-7709-9_9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cancer treatment has greatly improved over the last 50 years, but it remains challenging in several cases. Useful therapeutic targets are normally unique peculiarities of cancer cells that distinguish them from normal cells and that can be tackled with appropriate drugs. It is now known that cell metabolism is rewired during tumorigenesis and metastasis as a consequence of oncogene activation and oncosuppressors inactivation, leading to a new cellular homeostasis typically directed towards anabolism. Because of these modifications, cells can become strongly or absolutely dependent on specific substrates, like sugars, lipids or amino acids. Cancer addictions are a relevant target for therapy, as removal of an essential substrate can lead to their selective cell-cycle arrest or even to cell death, leaving normal cells untouched. Enzymes can act as powerful agents in this respect, as demonstrated by asparaginase, which has been included in the treatment of Acute Lymphoblastic Leukemia for half a century. In this review, a short outline of cancer addictions will be provided, focusing on the main cancer amino acid dependencies described so far. Therapeutic enzymes which have been already experimented at the clinical level will be discussed, along with novel potential candidates that we propose as new promising molecules. The intrinsic limitations of their present molecular forms, along with molecular engineering solutions to explore, will also be presented.
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Affiliation(s)
- Maristella Maggi
- Department of Molecular Medicine, Unit of Immunology and General Pathology, University of Pavia, Pavia, Italy.
| | - Claudia Scotti
- Department of Molecular Medicine, Unit of Immunology and General Pathology, University of Pavia, Pavia, Italy
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7
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Suganya K, Govindan K, Prabha P, Murugan M. An extensive review on L-methioninase and its potential applications. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2017.09.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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8
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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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9
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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.
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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.
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10
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El-Sayed AS, Hassan AE, Shindia AA, Mohamed SG, Sitohy MZ. Aspergillus flavipes methionine γ-lyase-dextran conjugates with enhanced structural, proteolytic stability and anticancer efficiency. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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11
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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.
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12
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Muharram MM. Recombinant Engineering of L-Methioninase Using Two Different Promoter and Expression Systems and in vitro Analysis of Its Anticancer Efficacy on Different Human Cancer Cell Lines. Pak J Biol Sci 2016; 19:106-114. [PMID: 29023047 DOI: 10.3923/pjbs.2016.106.114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Recombinant methioninase (rMETase) is an enzyme that has antitumor activity. In this work, METase gene from Pseudomonas putida ATTCC 8209 was cloned to pT7-7 plasmid (yielded, PT7-METase-R7 clone) and expressed in E. coli strain BL21 (DE3). A protein band with a molecular massof 42 kDa was visualized by SDS-PAGE. The applied protocol yielded a total protein of 3.13 g with a recovery of 66.89% and a specific activity of 18.59 U mg-1 which considered as a low yield. However, when the METase gene was cloned to the vector (pTrc99A, clone: pTrc99A-MET-3) cells of E. coli JM109 yielded a total protein of 32.63 g with a recovery of 41.62% and a specific activity of 54.86 U mg-1 which revealed that the enhancement of METase gene expression by trc promoter was more than the T7 RNA polymerase promoter. The t1/2 of the rMETase was 2 h asanalyzed in mice by IV injection. Antitumor efficacy of rMETase was studied in five human cancer cell lines. At 1 U mL-1 the growth rate of treated colon cancer cell lines, Colo205 and SW620, with rMETase was 46 and 32% relative to control, respectively. With the ovarian cancer cell line (A2780) rMETase produced an inhibition effect of 54% at 1.5 U mL-1. In addition, the growth rate was reduced to 45 and 53% with the skin cancer cell line (A375) and the breast cancer cell line (MCF-7), respectively. These results indicate the feasibility of rMETase for use as a potent antitumor agent.
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Affiliation(s)
- M M Muharram
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Kingdom of Saudi Arabia
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13
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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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14
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Dauter Z, Wlodawer A. On the accuracy of unit-cell parameters in protein crystallography. ACTA ACUST UNITED AC 2015; 71:2217-26. [PMID: 26527139 DOI: 10.1107/s1399004715015503] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 08/19/2015] [Indexed: 11/10/2022]
Abstract
The availability in the Protein Data Bank (PDB) of a number of structures that are presented in space group P1 but in reality possess higher symmetry allowed the accuracy and precision of the unit-cell parameters of the crystals of macromolecules to be evaluated. In addition, diffraction images from crystals of several proteins, previously collected as part of in-house projects, were processed independently with three popular software packages. An analysis of the results, augmented by published serial crystallography data, suggests that the apparent precision of the presentation of unit-cell parameters in the PDB to three decimal points is not justified, since these parameters are subject to errors of not less than 0.2%. It was also noticed that processing data including full crystallographic symmetry does not lead to deterioration of the refinement parameters; thus, it is not beneficial to treat the crystals as belonging to space group P1 when higher symmetry can be seen.
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Affiliation(s)
- Zbigniew Dauter
- Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Alexander Wlodawer
- Protein Structure Section, MCL, National Cancer Institute, Frederick, MD 21702, USA
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15
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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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El-Sayed AS, Shouman SA, Nassrat HM. Pharmacokinetics, immunogenicity and anticancer efficiency of Aspergillus flavipes l-methioninase. Enzyme Microb Technol 2012; 51:200-10. [DOI: 10.1016/j.enzmictec.2012.06.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 04/19/2012] [Accepted: 06/20/2012] [Indexed: 12/31/2022]
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17
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The role of amino acid residues in the active site of L-methionine γ-lyase from Pseudomonas putida. Biosci Biotechnol Biochem 2012; 76:1275-84. [PMID: 22785484 DOI: 10.1271/bbb.110906] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cys116, Lys240*, and Asp241* (asterisks indicate residues from the second subunit of the active dimer) at the active site of L-methionine γ-lyase of Pseudomonas putida (MGL_Pp) are highly conserved among heterologous MGLs. In a previous study, we found that substitution of Cys116 for His led to a drastic increase in activity toward L-cysteine and a decrease in that toward L-methionine. In this study, we examined some properties of the C116H mutant by kinetic analysis and 3D structural analysis. We assumed that substitution of Cys116 for His broke the original hydrogen-bond network and that this induced a significant effect of Tyr114 as a general acid catalyst, possibly due to the narrow space in the active site. The C116H mutant acquired a novel β-elimination activity and lead a drastic conformation change in the histidine residue at position 116 by binding the substrate, suggesting that this His residue affects the reaction specificity of C116H. Furthermore, we suggest that Lys240* is important for substrate recognition and structural stability and that Asp241* is also involved in substrate specificity in the elimination reaction. Based on this, we suggest that the hydrogen-bond network among Cys116, Lys240*, and Asp241* contributes to substrate specificity that is, to L-methionine recognition at the active site in MGL_Pp.
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18
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Li H, Huang Y, Zhang J, Du J, Tan H, Lu Y, Zhou S. Identification and characterization of a novel methionine γ-lyase gene from deep-sea sediment metagenomic library. World J Microbiol Biotechnol 2011. [DOI: 10.1007/s11274-011-0748-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Tran TH, Krishnamoorthy K, Begley TP, Ealick SE. A novel mechanism of sulfur transfer catalyzed by O-acetylhomoserine sulfhydrylase in the methionine-biosynthetic pathway of Wolinella succinogenes. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:831-8. [PMID: 21931214 PMCID: PMC3176619 DOI: 10.1107/s0907444911028010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 07/12/2011] [Indexed: 11/10/2022]
Abstract
O-Acetylhomoserine sulfhydrylase (OAHS) is a pyridoxal 5'-phosphate (PLP) dependent sulfide-utilizing enzyme in the L-cysteine and L-methionine biosynthetic pathways of various enteric bacteria and fungi. OAHS catalyzes the conversion of O-acetylhomoserine to homocysteine using sulfide in a process known as direct sulfhydrylation. However, the source of the sulfur has not been identified and no structures of OAHS have been reported in the literature. Here, the crystal structure of Wolinella succinogenes OAHS (MetY) determined at 2.2 Å resolution is reported. MetY crystallized in space group C2 with two monomers in the asymmetric unit. Size-exclusion chromatography, dynamic light scattering and crystal packing indicate that the biological unit is a tetramer in solution. This is further supported by the crystal structure, in which a tetramer is formed using a combination of noncrystallographic and crystallographic twofold axes. A search for structurally homologous proteins revealed that MetY has the same fold as cystathionine γ-lyase and methionine γ-lyase. The active sites of these enzymes, which are also PLP-dependent, share a high degree of structural similarity, suggesting that MetY belongs to the γ-elimination subclass of the Cys/Met metabolism PLP-dependent family of enzymes. The structure of MetY, together with biochemical data, provides insight into the mechanism of sulfur transfer to a small molecule via a protein thiocarboxylate intermediate.
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Affiliation(s)
- Timothy H. Tran
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA
| | | | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, TX 77842, USA
| | - Steven E. Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA
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20
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Yin J, Garen CR, Bateman K, Yu M, Alipio Lyon EZ, Habel J, Kim H, Hung LW, Kim CY, James MNG. Expression, purification and preliminary crystallographic analysis of O-acetylhomoserine sulfhydrylase from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:959-63. [PMID: 21821905 PMCID: PMC3151138 DOI: 10.1107/s1744309111017611] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 05/10/2011] [Indexed: 11/11/2022]
Abstract
The gene product of the open reading frame Rv3340 from Mycobacterium tuberculosis is annotated as encoding a probable O-acetylhomoserine (OAH) sulfhydrylase (MetC), an enzyme that catalyzes the last step in the biosynthesis of methionine, which is an essential amino acid in bacteria and plants. Following overexpression in Escherichia coli, the M. tuberculosis MetC enzyme was purified and crystallized using the hanging-drop vapor-diffusion method. Native diffraction data were collected from crystals belonging to space group P2(1) and were processed to a resolution of 2.1 Å.
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Affiliation(s)
- Jiang Yin
- Protein Structure and Function Group, Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Craig R. Garen
- Protein Structure and Function Group, Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Katherine Bateman
- Protein Structure and Function Group, Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Minmin Yu
- E. O. Lawrence Berkeley National Laboratory, University of California at Berkeley, California 94720, USA
| | - Emily Z. Alipio Lyon
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jeff Habel
- E. O. Lawrence Berkeley National Laboratory, University of California at Berkeley, California 94720, USA
| | - Heungbok Kim
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Li-wei Hung
- E. O. Lawrence Berkeley National Laboratory, University of California at Berkeley, California 94720, USA
| | - Chang-Yub Kim
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Michael N. G. James
- Protein Structure and Function Group, Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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21
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El-Sayed AS, Shindia AA. Characterization and immobilization of purified Aspergillus flavipesl-methioninase: continuous production of methanethiol. J Appl Microbiol 2011; 111:54-69. [PMID: 21466637 DOI: 10.1111/j.1365-2672.2011.05027.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS To immobilize the purified Aspergillus flavipesl-methioninase on solid carriers for continuous production of methanethiol with high purity, by the enzymatic methods. METHODS AND RESULTS The purified l-methioninase was immobilized using different methods, and physicochemical and kinetic studies for the potent immobilized enzyme were conducted parallel to the soluble one. The activity of the purified extracellular enzyme was 1·8-fold higher than intracellular one from submerged cultures of A. flavipes. Among the tested methods, polyacrylamide (42·2%), Ca-alginate (40·9%) and chitin (40·8%) displayed the highest immobilization efficiency. The thermal inactivation rate was strongly decreased for chitin-immobilized enzyme (0·222 s⁻¹) comparing to soluble enzyme (0·51 s⁻¹). Enzyme immobilization efficiency was greatly improved using 4·0% glutaraldehyde and 41·6/6·3 (T/C) as spacers for chitin and polyacrylamide-enzyme conjugates, comparing to their controls. Also the incorporation of lysine, glutathione, cysteine and dithiothreitol as active site protectants significantly enhance the catalytic efficiency of immobilized enzyme. The activity of enzyme was increased by 4·5- and 3·5-fold using glutathione plus DDT and glutathione plus methionine, for chitin and polyacrylamide enzyme, respectively. CONCLUSION Chitin enzyme gave a plausible stability till fourth cycle for production of methanethiol under controlled system. Applying GC and HNMR analysis, methanethiol has identical chemical structure to the standard compound. SIGNIFICANCE AND IMPACT OF THE STUDY Technically, a new method for continuous production of pure methanethiol, with broad applications, was developed using a simple low expenses method.
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Affiliation(s)
- A S El-Sayed
- Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, Egypt.
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22
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Ronda L, Bazhulina NP, Morozova EA, Revtovich SV, Chekhov VO, Nikulin AD, Demidkina TV, Mozzarelli A. Exploring methionine γ-lyase structure-function relationship via microspectrophotometry and X-ray crystallography. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:834-42. [PMID: 20601224 DOI: 10.1016/j.bbapap.2010.06.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 06/17/2010] [Accepted: 06/18/2010] [Indexed: 11/26/2022]
Abstract
Pyridoxal 5'-phosphate (PLP) dependent methionine γ-lyase catalyzes the breakdown of L-methionine to α-ketobutyric acid, methanethiol and ammonia. This enzyme, present in anaerobic microorganisms, has biomedical interest both for its activity as antitumor agent, depleting methionine supply in methionine-dependent cancers, and as target in the treatment of human pathogen infections, activating the pro-drug trifluoromethionine. To validate the structure of the enzyme from Citrobacter freundii, crystallized from monomethyl ether polyethylene glycol 2000, for the development of lead compounds, the reactivity of the crystalline enzyme towards L-methionine, substrate analogs and inhibitors was determined by polarized absorption microspectrophotometry. Spectral data were also collected for enzyme crystals, grown in monomethyl ether polyethylene glycol 2000 in the presence of ammonium sulfate. The three-dimensional structure of these enzyme crystals, solved at 1.65Å resolution with R(free) 23.2%, revealed the surprising absence of the aldimine bond between the active site Lys210 and PLP. Different hypothesis are proposed and discussed in the light of spectral and structural data, pointing out to the relevance of the complementarity between X-ray crystallography and single crystal spectroscopy for the understanding of biological mechanisms at molecular level. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.
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Affiliation(s)
- Luca Ronda
- Department of Biochemistry and Molecular Biology, University of Parma, Parma, Italy
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23
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El-Sayed AS. Microbial l-methioninase: production, molecular characterization, and therapeutic applications. Appl Microbiol Biotechnol 2010; 86:445-67. [DOI: 10.1007/s00253-009-2303-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Revised: 10/08/2009] [Accepted: 10/10/2009] [Indexed: 10/19/2022]
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24
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Sato D, Nozaki T. Methionine gamma-lyase: The unique reaction mechanism, physiological roles, and therapeutic applications against infectious diseases and cancers. IUBMB Life 2009; 61:1019-28. [DOI: 10.1002/iub.255] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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25
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Methionine γ-lyase: Mechanistic deductions from the kinetic pH-effects. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1414-20. [DOI: 10.1016/j.bbapap.2009.06.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Revised: 05/22/2009] [Accepted: 06/01/2009] [Indexed: 11/19/2022]
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26
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Goyer A, Collakova E, Shachar-Hill Y, Hanson AD. Functional characterization of a methionine gamma-lyase in Arabidopsis and its implication in an alternative to the reverse trans-sulfuration pathway. PLANT & CELL PHYSIOLOGY 2007; 48:232-42. [PMID: 17169919 DOI: 10.1093/pcp/pcl055] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Methionine gamma-lyase (MGL) catalyzes the degradation of L-methionine to alpha-ketobutyrate, methanethiol and ammonia. The Arabidopsis (Arabidopsis thaliana) genome includes a single gene (At1g64660) encoding a protein (AtMGL) with approximately 35% identity to bacterial and protozoan MGLs. When overexpressed in Escherichia coli, AtMGL allowed growth on L-methionine as sole nitrogen source and conferred a high rate of methanethiol emission. The purified recombinant protein exhibited a spectrum typical of pyridoxal 5'-phosphate enzymes, and had high activity toward l-methionine, L-ethionine, L-homocysteine and seleno-L-methionine, but not L-cysteine. Quantitation of mRNA showed that the AtMGL gene is expressed in aerial organs and roots, and that its expression in leaves was increased 2.5-fold by growth on low sulfate medium. Emission of methanethiol from Arabidopsis plants supplied with 10 mM L-methionine was undetectable (<0.5 nmol min(-1) g(-1) FW), suggesting that AtMGL is not an important source of volatile methanethiol. Knocking out the AtMGL gene significantly increased leaf methionine content (9.2-fold) and leaf and root S-methylmethionine content (4.7- and 7-fold, respectively) under conditions of sulfate starvation, indicating that AtMGL carries a significant flux in vivo. In Arabidopsis plantlets fed L-[(35)S]methionine on a low sulfate medium, label was incorporated into protein-bound cysteine as well as methionine, but incorporation into cysteine was significantly (30%) less in the knockout mutant. These data indicate that plants possess an alternative to the reverse trans-sulfuration pathway (methionine-->homocysteine-->cystathionine-->cysteine) in which methanethiol is an intermediate.
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Affiliation(s)
- Aymeric Goyer
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA.
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27
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Ali V, Nozaki T. Current therapeutics, their problems, and sulfur-containing-amino-acid metabolism as a novel target against infections by "amitochondriate" protozoan parasites. Clin Microbiol Rev 2007; 20:164-87. [PMID: 17223627 PMCID: PMC1797636 DOI: 10.1128/cmr.00019-06] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The "amitochondriate" protozoan parasites of humans Entamoeba histolytica, Giardia intestinalis, and Trichomonas vaginalis share many biochemical features, e.g., energy and amino acid metabolism, a spectrum of drugs for their treatment, and the occurrence of drug resistance. These parasites possess metabolic pathways that are divergent from those of their mammalian hosts and are often considered to be good targets for drug development. Sulfur-containing-amino-acid metabolism represents one such divergent metabolic pathway, namely, the cysteine biosynthetic pathway and methionine gamma-lyase-mediated catabolism of sulfur-containing amino acids, which are present in T. vaginalis and E. histolytica but absent in G. intestinalis. These pathways are potentially exploitable for development of drugs against amoebiasis and trichomoniasis. For instance, L-trifluoromethionine, which is catalyzed by methionine gamma-lyase and produces a toxic product, is effective against T. vaginalis and E. histolytica parasites in vitro and in vivo and may represent a good lead compound. In this review, we summarize the biology of these microaerophilic parasites, their clinical manifestation and epidemiology of disease, chemotherapeutics, the modes of action of representative drugs, and problems related to these drugs, including drug resistance. We further discuss our approach to exploit unique sulfur-containing-amino-acid metabolism, focusing on development of drugs against E. histolytica.
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Affiliation(s)
- Vahab Ali
- Department of Parasitology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
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28
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Sato D, Yamagata W, Kamei K, Nozaki T, Harada S. Expression, purification and crystallization of L-methionine gamma-lyase 2 from Entamoeba histolytica. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:1034-6. [PMID: 17012806 PMCID: PMC2225178 DOI: 10.1107/s1744309106036694] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2006] [Accepted: 09/11/2006] [Indexed: 11/10/2022]
Abstract
L-Methionine gamma-lyase (MGL) is considered to be an attractive target for rational drug development because the enzyme is absent in mammalian hosts. To enable structure-based design of drugs targeting MGL, one of the two MGL isoenzymes (EhMGL2) was crystallized in the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 88.89, b = 102.68, c = 169.87 A. The crystal diffracted to a resolution of 2.0 A. The presence of a tetramer in the asymmetric unit (4 x 43.1 kDa) gives a Matthews coefficient of 2.2 A(3) Da(-1). The structure was solved by the molecular-replacement method and structure refinement is now in progress.
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Affiliation(s)
- Dan Sato
- Department of Parasitology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
| | - Wataru Yamagata
- Graduate School of Science and Technology, Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan
| | - Kaeko Kamei
- Graduate School of Science and Technology, Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan
| | - Tomoyoshi Nozaki
- Department of Parasitology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
| | - Shigeharu Harada
- Graduate School of Science and Technology, Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan
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29
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Manukhov IV, Mamaeva DV, Morozova EA, Rastorguev SM, Faleev NG, Demidkina TV, Zavilgelsky GB. L-methionine γ-lyase from Citrobacter freundii: Cloning of the gene and kinetic parameters of the enzyme. BIOCHEMISTRY (MOSCOW) 2006; 71:361-9. [PMID: 16615855 DOI: 10.1134/s0006297906040031] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
It is shown for the first time for the Enterobacteriaceae family that a gene encoding L-methionine gamma-lyase (MGL) is present in the genome of Citrobacter freundii. Homogeneous enzyme has been purified from C. freundii cells and its N-terminal sequence has been determined. The hybrid plasmid pUCmgl obtained from the C. freundii genomic library contains an EcoRI insert of about 3000 bp, which ensures the appearance of MGL activity when expressed in Escherichia coli TG1 cells. The nucleotide sequence of the EcoRI fragment contains two open reading frames. The first frame (the megL gene) encodes a protein of 398 amino acid residues that has sequence homology with MGLs from different sources. The second frame encodes a protein with sequence homology with proteins belonging to the family of permeases. To overexpress the megL gene it was cloned into pET-15b vector. Recombinant enzyme has been purified and its kinetic parameters have been determined. It is demonstrated that a presence of a hybrid plasmid pUCmgl, containing the megL gene in the E. coli K12 cells, leads to a decrease in efficiency of EcoKI-restriction. It seems likely that decomposition of L-methionine under the action of MGL leads to a decrease in the intracellular content of S-adenosylmethionine. Expression of the megL gene in the C. freundii genome occurs only upon induction by a significant amount of L-methionine.
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Affiliation(s)
- I V Manukhov
- State Research Institute of Genetics and Selection of Industrial Microorganisms, 117545 Moscow, Russia
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30
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Takakura T, Takimoto A, Notsu Y, Yoshida H, Ito T, Nagatome H, Ohno M, Kobayashi Y, Yoshioka T, Inagaki K, Yagi S, Hoffman RM, Esaki N. Physicochemical and Pharmacokinetic Characterization of Highly Potent Recombinant l-Methionine γ-Lyase Conjugated with Polyethylene Glycol as an Antitumor Agent. Cancer Res 2006; 66:2807-14. [PMID: 16510603 DOI: 10.1158/0008-5472.can-05-3910] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A highly potent recombinant L-methionine gamma-lyase (METase) conjugated with polyethylene glycol (PEG) was characterized physicochemically and pharmacokinetically in vivo and in vitro. Pegylated METase (PEG-METase), which contains pyridoxal 5'-phosphate (PLP) as a cofactor in the molecule, is a potent anticancer agent that can deplete L-methionine from plasma. Although pegylation decreased its specific activity, dithiothreitol (DTT) treatment increased it over three times with the detachment of one PEG moiety modified with a cysteine residue. We can produce DTT-treated PEG-METase on a large scale in sufficient quality for therapeutic use. The superiority of DTT-treated PEG-METase was confirmed by the enhancement of L-methionine depletion and amelioration of pharmacokinetics in mice. The holoenzyme of DTT-treated PEG-METase gave a several times larger area under the plasma concentration curve than that of DTT-untreated PEG-METase, not because of an increase of the half-life but because of high specific activity. Conversely, simultaneous PLP infusion led to a greatly increased half-life of the holoenzyme. DTT-treated PEG-METase administration with PLP infusion was the most useful combination for maximizing the potency of the enzyme. We showed that serum albumin interfered with holoenzyme activity in vitro. The decrease of holoenzyme activity was dependent on the type of serum albumin. We concluded that PLP was released from PEG-METase by serum albumin in vivo and in vitro. The deleterious effect of PLP dissociation from PEG-METase could be improved by supplementing PLP and oleic acid. Their synergistic effect in preventing a decrease of the holoenzyme activity was also observed.
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Affiliation(s)
- Tomoaki Takakura
- Discovery Research Laboratories, Shionogi & Co., Ltd., Osaka, Japan.
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31
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ATCUN-like metal-binding motifs in proteins: identification and characterization by crystal structure and sequence analysis. Proteins 2006; 58:211-21. [PMID: 15508143 DOI: 10.1002/prot.20265] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The amino terminal Cu(II)- and Ni(II)-binding (ATCUN) motif is a small metal-binding site found in the N-terminus of many naturally occurring proteins. The ATCUN motif has been implicated in DNA cleavage and has been shown to have antitumor activity. In proteins, the ATCUN motif is formed from a histidine in the third position, its preceding residue and the free N-terminus. Four nitrogen atoms from these three residues act as metal ligands. Knowledge of metal-binding geometry helps in the design of metal-binding peptides and in understanding of the mechanisms of metal-mediated functions. Since the N-terminus region of ATCUN-containing proteins is highly disordered, no geometrical features can be derived from the protein structures. However, the crystal structure of a small metal-bound ATCUN peptide shows that the nitrogen ligands form a distorted square planar geometry. Distance constraints derived from this designed peptide were used to search 1949 polypeptide chains to find ATCUN-like motifs in any position along the polypeptide chain. Only approximately 1.9% and approximately 0.3% of histidines are involved in partial and full ATCUN-like geometric features, respectively. These two datasets were compared with the dataset of all histidines. None of the ATCUN-like motifs occur in the middle of an alpha-helix or a beta-strand. Further sequence analysis revealed total conservation of ATCUN histidines in four proteins including the transcription factor TBX3, implicated in Ulnar-Mammary Syndrome. Our analysis suggests that the ATCUN-like motif in TBX3 is a potential metal-binding site, although a structural role was not completely ruled out. Metal-binding activity in TBX3, if confirmed, will help us to understand the role of metals in transcriptional regulation and is likely to cast light on the causes of some serious genetic disorders. A conformational role is suggested for ATCUN-like motifs in other proteins.
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32
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Takakura T, Ito T, Yagi S, Notsu Y, Itakura T, Nakamura T, Inagaki K, Esaki N, Hoffman RM, Takimoto A. High-level expression and bulk crystallization of recombinant L-methionine gamma-lyase, an anticancer agent. Appl Microbiol Biotechnol 2005; 70:183-92. [PMID: 16012835 DOI: 10.1007/s00253-005-0038-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2005] [Revised: 05/22/2005] [Accepted: 05/30/2005] [Indexed: 10/25/2022]
Abstract
L-Methionine gamma-lyase is a pyridoxal 5'-phosphate-dependent enzyme which has tumor selective anticancer activity. An efficient production process for the recombinant enzyme was constructed by using the overexpression plasmid in Escherichia coli, large-scale cultivation, and practical crystallization on an industrial scale. The plasmid was optimized with a promoter and the region of the ribosome-binding site. Plasmid pMGLTrc03, which has a trc promoter and a spacing of 12 nucleotides between the Shine-Dalgarno sequence and the ATG translation initiation codon, was selected as the most suitable plasmid. The transformants produced the enzyme, which intracellularly accumulated at 2.1 mg/ml as an active form and accounted for 43% of the total proteins in the soluble fraction by simple batch fermentation using a 500-l fermentor. The crystals were directly obtained from crude enzyme with 87% yield by a crystallization in the presence of 9.0% polyethylene glycol 6000, 3.6% ammonium sulfate, and 0.18 M sodium chloride using a 100-l crystallizer. After recrystallization, the enzyme was purified by anion-exchange column chromatography to remove endotoxins and by gel filtration for polishing. We prepared 600 g of purified enzyme with a low endotoxin content of sufficient quality for therapeutical use, with a 41% overall yield in the purification process.
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Affiliation(s)
- Tomoaki Takakura
- Discovery Research Laboratories, Shionogi & Co., Ltd., Amagasaki, Hyogo, Japan.
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33
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Mamaeva DV, Morozova EA, Nikulin AD, Revtovich SV, Nikonov SV, Garber MB, Demidkina TV. Structure of Citrobacter freundii L-methionine gamma-lyase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:546-9. [PMID: 16511092 PMCID: PMC1952331 DOI: 10.1107/s1744309105015447] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2005] [Accepted: 05/14/2005] [Indexed: 11/10/2022]
Abstract
L-Methionine gamma-lyase (MGL) is a pyridoxal 5'-phosphate (PLP) dependent enzyme that catalyzes gamma-elimination of L-methionine. The crystal structure of MGL from Citrobacter freundii has been determined at 1.9 A resolution. The spatial fold of the protein is similar to those of MGLs from Pseudomonas putida and Trichomonas vaginalis. The comparison of these structures revealed that there are differences in PLP-binding residues and positioning of the surrounding flexible loops.
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Affiliation(s)
- D. V. Mamaeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia
| | - E. A. Morozova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia
| | - A. D. Nikulin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - S. V. Revtovich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia
| | - S. V. Nikonov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - M. B. Garber
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - T. V. Demidkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia
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Amarita F, Yvon M, Nardi M, Chambellon E, Delettre J, Bonnarme P. Identification and functional analysis of the gene encoding methionine-gamma-lyase in Brevibacterium linens. Appl Environ Microbiol 2005; 70:7348-54. [PMID: 15574935 PMCID: PMC535188 DOI: 10.1128/aem.70.12.7348-7354.2004] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The enzymatic degradation of L-methionine and subsequent formation of volatile sulfur compounds (VSCs) is believed to be essential for flavor development in cheese. L-methionine-gamma-lyase (MGL) can convert L-methionine to methanethiol (MTL), alpha-ketobutyrate, and ammonia. The mgl gene encoding MGL was cloned from the type strain Brevibacterium linens ATCC 9175 known to produce copious amounts of MTL and related VSCs. The disruption of the mgl gene, achieved in strain ATCC 9175, resulted in a 62% decrease in thiol-producing activity and a 97% decrease in total VSC production in the knockout strain. Our work shows that L-methionine degradation via gamma-elimination is a key step in the formation of VSCs in B. linens.
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Affiliation(s)
- Felix Amarita
- Unité Mixte de Recherches Génie et Microbiologie des Procédés Alimentaires, Institut National de la Recherche Agronomique, Thiverval-Grignon, France
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Nozaki T, Ali V, Tokoro M. Sulfur-Containing Amino Acid Metabolism in Parasitic Protozoa. ADVANCES IN PARASITOLOGY 2005; 60:1-99. [PMID: 16230102 DOI: 10.1016/s0065-308x(05)60001-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Sulfur-containing amino acids play indispensable roles in a wide variety of biological activities including protein synthesis, methylation, and biosynthesis of polyamines and glutathione. Biosynthesis and catabolism of these amino acids need to be carefully regulated to achieve the requirement of the above-mentioned activities and also to eliminate toxicity attributable to the amino acids. Genome-wide analyses of enzymes involved in the metabolic pathways of sulfur-containing amino acids, including transsulfuration, sulfur assimilatory de novo cysteine biosynthesis, methionine cycle, and degradation, using genome databases available from a variety of parasitic protozoa, reveal remarkable diversity between protozoan parasites and their mammalian hosts. Thus, the sulfur-containing amino acid metabolic pathways are a rational target for the development of novel chemotherapeutic and prophylactic agents against diseases caused by protozoan parasites. These pathways also demonstrate notable heterogeneity among parasites, suggesting that the metabolism of sulfur-containing amino acids reflects the diversity of parasitism among parasite species, and probably influences their biology and pathophysiology such as virulence competence and stress defense.
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Affiliation(s)
- Tomoyoshi Nozaki
- Department of Parasitology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
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Takakura T, Mitsushima K, Yagi S, Inagaki K, Tanaka H, Esaki N, Soda K, Takimoto A. Assay method for antitumor l-methionine γ-lyase: comprehensive kinetic analysis of the complex reaction with l-methionine. Anal Biochem 2004; 327:233-40. [PMID: 15051540 DOI: 10.1016/j.ab.2004.01.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2003] [Indexed: 10/26/2022]
Abstract
L-Methionine gamma-lyase (EC 4.4.1.11) is a pyridoxal 5'-phosphate-dependent multifunctional enzyme. Measuring the initial velocity of alpha-ketobutyrate production by alpha,gamma-elimination of L-methionine catalyzed by L-methionine gamma-lyase is not very feasible, because the enzyme simultaneously catalyzes both gamma-replacement and alpha,gamma-elimination. To develop an accurate enzyme assay, the comprehensive enzyme kinetics needed to be elucidated by progress curve analysis on the basis of a reaction model for conversion of L-methionine to alpha-ketobutyrate, methanethiol, and ammonia with pyridoxal 5'-phosphate as a cofactor. Kinetic parameters were determined by linear transformation using an approximation of a Maclaurin series from the whole velocity of alpha-ketobutyrate production including alpha,gamma-elimination and gamma-replacement. The significance of gamma-replacement was revealed both theoretically and practically by the kinetic analysis. The enzyme activity was standardized and represented as the Vmax value taking into consideration gamma-replacement in the presence of L-methionine at 37 degrees C and pH 8.0. The novel method that we proposed is accurate, sensitive, reproducible, and linear over a wide range for the determination of L-methionine gamma-lyase activity.
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Affiliation(s)
- Tomoaki Takakura
- Discovery Research Laboratories, Shionogi & Co., Ltd., 1-3, Kuise Terajima 2-chome, Amagasaki, Hyogo 660-0813, Japan.
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Bentley R, Chasteen TG. Environmental VOSCs--formation and degradation of dimethyl sulfide, methanethiol and related materials. CHEMOSPHERE 2004; 55:291-317. [PMID: 14987929 DOI: 10.1016/j.chemosphere.2003.12.017] [Citation(s) in RCA: 147] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2003] [Revised: 12/12/2003] [Accepted: 12/17/2003] [Indexed: 05/07/2023]
Abstract
Volatile organic sulfur compounds (VOSCs) play a major role in the global sulfur cycle. Two components, dimethyl sulfide (DMS) and methanethiol (MT) are formed in large amounts by living systems (e.g. algae, bacteria, plants), particularly in marine environments. A major route to DMS is by action of a lyase enzyme on dimethylsulfoniopropionate (DMSP). DMSP has other roles, for instance as an osmoprotectant and cryoprotectant. Demethiolation of DMSP and other materials leads to MT. A major transport process is release of DMS from the oceans to the atmosphere. Oxidation of DMS in the atmosphere by hydroxyl and nitrate radicals produces many degradation products including CO2, COS, dimethyl sulfoxide, dimethyl sulfone, organic oxyacids of sulfur, and sulfate. These materials also have roles in biotic processes and there are complex metabolic interrelationships between some of them. This review emphasizes the chemical reactions of the organic sulfur cycle. For biotic reactions, details of relevant enzymes are provided when possible.
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Affiliation(s)
- Ronald Bentley
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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Tokoro M, Asai T, Kobayashi S, Takeuchi T, Nozaki T. Identification and characterization of two isoenzymes of methionine gamma-lyase from Entamoeba histolytica: a key enzyme of sulfur-amino acid degradation in an anaerobic parasitic protist that lacks forward and reverse trans-sulfuration pathways. J Biol Chem 2003; 278:42717-27. [PMID: 12920135 DOI: 10.1074/jbc.m212414200] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To better understand the metabolism of sulfur-containing amino acids, which likely plays a key role in a variety of cell functions, in Entamoeba histolytica, we searched the genome data base for genes encoding putative orthologs of enzymes known to be involved in the metabolism. The search revealed that E. histolytica possesses only incomplete cysteine-methionine conversion pathways in both directions. Instead, this parasite possesses genes encoding two isoenzymes of methionine gamma-lyase (EC 4.4.1.11, EhMGL1/2), which has been implicated in the degradation of sulfur-containing amino acids. The two amebic MGL isoenzymes, showing 69% identity to each other, encode 389- and 392-amino acid polypeptides with predicted molecular masses of 42.3 and 42.7 kDa and pIs of 6.01 and 6.63, respectively. Amino acid comparison and phylogenetic analysis suggested that these amebic MGLs are likely to have been horizontally transferred from the Archaea, whereas an MGL from another anaerobic protist Trichomonas vaginalis has MGL isotypes that share a common ancestor with bacteria. Enzymological and immunoblot analyses of the partially purified native amebic MGL confirmed that both of the MGL isotypes are expressed in a comparable amount predominantly in the cytosol and form a homotetramer. Recombinant EhMGL1 and 2 proteins catalyzed degradation of L-methionine, DL-homocysteine, L-cysteine, and O-acetyl-L-serine to form alpha-keto acid, ammonia, and hydrogen sulfide or methanethiol, whereas activity toward cystathionine was negligible. These two isoenzymes showed notable differences in substrate specificity and pH optimum. In addition, we showed that EhMGL is an ideal target for the development of new chemotherapeutic agents against amebiasis by demonstrating an amebicidal effect of the methionine analog trifluoromethionine on trophozoites in culture (IC50 18 mum) and that this effect of trifluoromethionine was completely abolished by the addition of the MGL-specific inhibitor DL-propargylglycine.
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Affiliation(s)
- Masaharu Tokoro
- Department of Tropical Medicine and Parasitology, Keio University School of Medicine, Tokyo 160-8582, Japan
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Watkins LM, Rodriguez R, Schneider D, Broderick R, Cruz M, Chambers R, Ruckman E, Cody M, Mrachko GT. Purification and characterization of the aromatic desulfinase, 2-(2'-hydroxyphenyl)benzenesulfinate desulfinase. Arch Biochem Biophys 2003; 415:14-23. [PMID: 12801508 DOI: 10.1016/s0003-9861(03)00230-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
2-(2(')-Hydroxyphenyl)benzenesulfinate desulfinase (HPBS desulfinase) catalyzes the cleavage of the carbon-sulfur bond of 2-(2(')-hydroxyphenyl)benzenesulfinate (HPBS) to form hydroxybiphenyl and sulfite. This is the final step in the desulfurization of dibenzothiophene, the organosulfur compound used to study biodesulfurization of petroleum middle distillate. HPBS desulfinase was purified 1600-fold from Rhodococcus IGTS8. The purification was monitored using a spectrofluorimetric assay and SDS-PAGE. The pI of HPBS desulfinase is 5.6, the temperature optimum is 35 degrees C, and the pH optimum is 7.0. HPBS desulfinase has a K(m) of 0.90+/-0.15 microM and a k(cat) of 1.3+/-0.07 min(-1). Several analogs were tested for their ability to act as substrates or inhibitors of HPBS desulfinase. No alternative substrates and very few inhibitors were identified. HPBS desulfinase activity decreases in the presence of Cu(2+) and Zn(2+), while no metals significantly enhance enzyme activity. HPBS desulfinase is susceptible to tyrosine, tryptophan, and cysteine specific modification agents.
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Affiliation(s)
- L M Watkins
- Department of Chemistry and Biochemistry, Southwest Texas State University, 601 University Dr., San Marcos, TX 78666, USA.
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Kumasaka T, Yamamoto M, Yamashita E, Moriyama H, Ueki T. Trichromatic concept optimizes MAD experiments in synchrotron X-ray crystallography. Structure 2002; 10:1205-10. [PMID: 12220492 DOI: 10.1016/s0969-2126(02)00830-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The trichromatic concept is a new synchrotron beamline design that optimizes MAD experiments by reducing systematic experimental errors with three-colored and coaxial synchrotron X-ray beams produced by a tandem vertical undulator and trichromator. The concept enables rapid and flexible switching of three defined wavelengths, and extends the flexibility of experimental design for MAD data collection. Thus, we can collect MAD data taking into account time series effects such as radiation damage. The data based on the trichromatic concept gave a better quality electron density map than data collected by conventional methods. It was also revealed that multicolor diffraction using dichromatic or trichromatic X-ray beams is effective in rapid MAD data collection.
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Affiliation(s)
- Takashi Kumasaka
- X-Ray Coherent Optics Laboratory, RIKEN Harima Institute/SPring-8, Mikazuki, Sayo, Hyogo 679-5148, Japan
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