1
|
Matoba Y, Oda K, Wataeda M, Kanemori H, Matsuo K. pH-dependent regulation of an acidophilic O-acetylhomoserine sulfhydrylase from Lactobacillus plantarum. Appl Environ Microbiol 2024; 90:e0011824. [PMID: 38568076 PMCID: PMC11107162 DOI: 10.1128/aem.00118-24] [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: 01/23/2024] [Accepted: 03/16/2024] [Indexed: 05/22/2024] Open
Abstract
Bacteria have two routes for the l-methionine biosynthesis. In one route called the direct sulfuration pathway, acetylated l-homoserine is directly converted into l-homocysteine. The reaction using H2S as the second substrate is catalyzed by a pyridoxal 5'-phosphate-dependent enzyme, O-acetylhomoserine sulfhydrylase (OAHS). In the present study, we determined the enzymatic functions and the structures of OAHS from Lactobacillus plantarum (LpOAHS). The LpOAHS enzyme exhibited the highest catalytic activity under the weak acidic pH condition. In addition, crystallographic analysis revealed that the enzyme takes two distinct structures, open and closed forms. In the closed form, two acidic residues are sterically clustered. The proximity may cause the electrostatic repulsion, inhibiting the formation of the closed form under the neutral to the basic pH conditions. We concluded that the pH-dependent regulation mechanism using the two acidic residues contributes to the acidophilic feature of the enzyme. IMPORTANCE In the present study, we can elucidate the pH-dependent regulation mechanism of the acidophilic OAHS. The acidophilic feature of the enzyme is caused by the introduction of an acidic residue to the neighborhood of the key acidic residue acting as a switch for the structural interconversion. The strategy may be useful in the field of protein engineering to change the optimal pH of the enzymes. In addition, this study may be useful for the development of antibacterial drugs because the l-methionine synthesis essential for bacteria is inhibited by the OAHS inhibitors. The compounds that can inhibit the interconversion between the open and closed forms of OAHS may become antibacterial drugs.
Collapse
Affiliation(s)
- Yasuyuki Matoba
- Faculty of Pharmacy, Yasuda Women’s University, Hiroshima, Japan
| | - Kosuke Oda
- Faculty of Pharmacy, Yasuda Women’s University, Hiroshima, Japan
| | - Maho Wataeda
- Faculty of Pharmacy, Yasuda Women’s University, Hiroshima, Japan
| | - Hina Kanemori
- Faculty of Pharmacy, Yasuda Women’s University, Hiroshima, Japan
| | - Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Hiroshima, Japan
| |
Collapse
|
2
|
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
|
3
|
Kuznetsova AA, Faleev NG, Morozova EA, Anufrieva NV, Gogoleva OI, Tsvetikova MA, Fedorova OS, Demidkina TV, Kuznetsov NA. Analyses of pre-steady-state kinetics and isotope effects of the γ-elimination reaction catalyzed by Citrobacter freundii methionine γ-lyase. Biochimie 2022; 201:157-167. [PMID: 35691533 DOI: 10.1016/j.biochi.2022.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/18/2022] [Accepted: 06/06/2022] [Indexed: 11/29/2022]
Abstract
Methionine γ-lyase (MGL) is a pyridoxal 5'-phosphate-dependent enzyme catalyzing γ-elimination in l-methionine. Pyridoxal 5'-phosphate-dependent enzymes have unique spectral properties that allow to monitor sequential formation and decomposition of various intermediates via the detection of absorbance changes. The kinetic mechanism of the γ-elimination reaction catalyzed by Citrobacter freundii MGL was elucidated here by fast stopped-flow kinetic analysis. Single-wavelength detection of characteristic absorbance changes enabled us to compare transformations of intermediates in the course of the reaction with different substrates. The influence of various γ-substituents in the substrate on the formation of key intermediates was estimated. Kinetic isotope effects of α- and β-protons were determined using deuterium-substituted l-methionine. Contributions of amino acid residues Tyr113 and Tyr58 located in the active site on the formation and decomposition of reaction intermediates were identified too. α-Aminocrotonate formation is the rate-limiting step of the enzymatic γ-elimination reaction. Kinetic isotope effects strongly support concerted reaction mechanisms of transformation between an external aldimine and a ketimine intermediate as well as a ketimine intermediate and an unsaturated ketimine.
Collapse
Affiliation(s)
- Aleksandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Nicolai G Faleev
- Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Elena A Morozova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Natalya V Anufrieva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Olga I Gogoleva
- Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Marina A Tsvetikova
- Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Olga S Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Tatyana V Demidkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| |
Collapse
|
4
|
Hauth F, Buck H, Stanoppi M, Hartig JS. Canavanine utilization via homoserine and hydroxyguanidine by a PLP-dependent γ-lyase in Pseudomonadaceae and Rhizobiales. RSC Chem Biol 2022; 3:1240-1250. [PMID: 36320885 PMCID: PMC9533460 DOI: 10.1039/d2cb00128d] [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: 05/24/2022] [Accepted: 08/18/2022] [Indexed: 12/02/2022] Open
Abstract
Canavanine, the δ-oxa-analogue of arginine, is produced as one of the main nitrogen storage compounds in legume seeds and has repellent properties. Its toxicity originates from incorporation into proteins as well as arginase-mediated hydrolysis to canaline that forms stable oximes with carbonyls. So far no pathway or enzyme has been identified acting specifically on canavanine. Here we report the characterization of a novel PLP-dependent enzyme, canavanine-γ-lyase, that catalyzes the elimination of hydroxyguanidine from canavanine to subsequently yield homoserine. Homoserine-dehydrogenase, aspartate–semialdehyde–dehydrogenase and ammonium–aspartate–lyase activities are also induced for facilitating canavanine utilization. We demonstrate that this novel pathway is found in certain Pseudomonas species and the Rhizobiales symbionts of legumes. The findings broaden the diverse reactions that the versatile class of PLP-dependent enzymes is able to catalyze. Since canavanine utilization is found prominently in root-associated bacteria, it could have important implications for the establishment and maintenance of the legume rhizosphere. A novel degradation pathway enables rhizosphere-associated bacteria to utilize canavanine.![]()
Collapse
Affiliation(s)
- Franziskus Hauth
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Hiltrun Buck
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Marco Stanoppi
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Jörg S. Hartig
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| |
Collapse
|
5
|
Devi S, Tomar P, Faisal Tarique K, Gourinath S. Inhibiting Pyridoxal Kinase of Entamoeba histolytica Is Lethal for This Pathogen. Front Cell Infect Microbiol 2021; 11:660466. [PMID: 33937101 PMCID: PMC8085340 DOI: 10.3389/fcimb.2021.660466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/29/2021] [Indexed: 11/19/2022] Open
Abstract
Pyridoxal 5’-phosphate (PLP) functions as a cofactor for hundreds of different enzymes that are crucial to the survival of microorganisms. PLP-dependent enzymes have been extensively characterized and proposed as drug targets in Entamoeba histolytica. This pathogen is unable to synthesize vitamin B6via de-novo pathway and relies on the uptake of vitamin B6 vitamers from the host which are then phosphorylated by the enzyme pyridoxal kinase to produce PLP, the active form of vitamin B6. Previous studies from our lab shows that EhPLK is essential for the survival and growth of this protozoan parasite and its active site differs significantly with respect to its human homologue making it a potential drug target. In-silico screening of EhPLK against small molecule libraries were performed and top five ranked molecules were shortlisted on the basis of docking scores. These compounds dock into the PLP binding site of the enzyme such that binding of these compounds hinders the binding of substrate. Of these five compounds, two compounds showed inhibitory activity with IC50 values between 100-250 μM when tested in-vitro. The effect of these compounds proved to be extremely lethal for Entamoeba trophozoites in cultured cells as the growth was hampered by 91.5% and 89.5% when grown in the presence of these compounds over the period of 72 hours.
Collapse
Affiliation(s)
- Suneeta Devi
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Priya Tomar
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Khaja Faisal Tarique
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.,Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Samudrala Gourinath
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| |
Collapse
|
6
|
Foo TC, Meacham JE, Terentis AC, Venkatachalam KV. Gamma cleavage is a rate-determining step in the gamma-elimination reaction of L-methionine analogues catalyzed by methionine-gamma-lyase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140652. [PMID: 33746063 DOI: 10.1016/j.bbapap.2021.140652] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/12/2021] [Accepted: 03/17/2021] [Indexed: 11/15/2022]
Abstract
Methionine-γ-lyase (MGL) is a pyridoxal-5'-phosphate dependent enzyme found in bacteria and protozoa that catalyzes a variety of reactions, including the γ-elimination of L-methionine (L-Met). Here we report experimental kinetic data and density functional theory (DFT) computational data for the γ-elimination reaction of L-Met and several other substrate analogues by a recombinant MGL from P. gingivalis (MGL_Pg). UV-Visible spectrophotometry experiments revealed a heavily populated species with maximum absorbance at 478 nm during steady-state catalysis of L-Met, L-ethionine, L-methionine sulfone and L-homoserine, which we assign to a late crotonate intermediate formed after the γ-cleavage step in the reaction and thus common to all substrates. A more red-shifted (498 nm) species was observed during the reaction of L-homoserine lactone, which we assign to an early quinonoid intermediate with the aid of time-dependent self-consistent field calculations. Significant differences in both binding and the rate of turnover were observed for the substrates. MGL_Pg's highest catalytic efficiency was recorded for L-vinylglycine (kcat/Km = 6455 s-1 M-1), exceeding that of L-Met (kcat/Km = 4211 s-1 M-1), while L-Met sulfone displayed the largest turnover number (kcat = 1638 min-1). A direct correlation between experimental kcat values and DFT-calculated γ-cleavage Gibbs activation energies was identified for the various substrates. In light of these data, we propose that the γ-cleavage step in the catalytic reaction pathway is rate-limiting. This conclusion has direct implications for the rational design of substrates or inhibitors aimed at regulating MGL activity.
Collapse
Affiliation(s)
- Timothy C Foo
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, United States
| | - Jesse E Meacham
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, United States
| | - Andrew C Terentis
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, United States.
| | - Kallidaikurichi V Venkatachalam
- Division of Biochemistry, College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, United States.
| |
Collapse
|
7
|
Tarique KF, Devi S, Tomar P, Ali MF, Rehman SAA, Gourinath S. Characterization and functional insights into the Entamoeba histolytica pyridoxal kinase, an enzyme essential for its survival. J Struct Biol 2020; 212:107645. [PMID: 33045383 DOI: 10.1016/j.jsb.2020.107645] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/29/2020] [Accepted: 10/06/2020] [Indexed: 01/18/2023]
Abstract
Pyridoxal 5'-phosphate (PLP) is the active form of vitamin B6 and a cofactor for more than 140 enzymes. This coenzyme plays a pivotal role in catalysis of various enzymatic reactions that are critical for the survival of organisms. Entamoeba histolytica depends on the uptake of pyridoxal (PL), a B6 vitamer from the external environment which is then phosphorylated by pyridoxal kinase (EhPLK) to form PLP via the salvage pathway. E. histolytica cannot synthesise vitamin B6de-novo, and also lacks pyridoxine 5'-phosphate oxidase, a salvage pathway enzyme required to produce PLP from pyridoxine phosphate (PNP) and pyridoxamine phosphate (PMP). Analysing the importance of PLK in E. histolytica, we have determined the high-resolution crystal structures of the dimeric pyridoxal kinase in apo, ADP-bound, and PLP-bound states. These structures provided a snapshot of the transition state and help in understanding the reaction mechanism in greater detail. The EhPLK structure significantly differed from the human homologue at its PLP binding site, and the phylogenetic study also revealed its divergence from human PLK. Further, gene regulation of EhPLK using sense and antisense RNA showed that any change in optimal level is harmful to the pathogen. Biochemical and in vivo studies unveiled EhPLK to be essential for this pathogen, while the molecular differences with human PLK structure can be exploited for the structure-guided design of EhPLK inhibitors.
Collapse
Affiliation(s)
- Khaja Faisal Tarique
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India; Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Suneeta Devi
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Priya Tomar
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mohammad Farhan Ali
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Syed Arif Abdul Rehman
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India; MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Samudrala Gourinath
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
| |
Collapse
|
8
|
Matoba Y, Noda M, Yoshida T, Oda K, Ezumi Y, Yasutake C, Izuhara-Kihara H, Danshiitsoodol N, Kumagai T, Sugiyama M. Catalytic specificity of the Lactobacillus plantarum cystathionine γ-lyase presumed by the crystallographic analysis. Sci Rep 2020; 10:14886. [PMID: 32913258 DOI: 10.1038/s51598-020-71756-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/05/2020] [Indexed: 05/22/2023] 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.
Collapse
Affiliation(s)
- Yasuyuki Matoba
- Faculty of Pharmacy, Yasuda Women's University, Yasuhigashi 6-13-1, Asaminami-ku, Hiroshima, 731-0153, Japan.
| | - Masafumi Noda
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima, 734-8551, Japan
| | - Tomoki Yoshida
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima, 734-8551, Japan
| | - Kosuke Oda
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima, 734-8551, Japan
| | - Yuka Ezumi
- Faculty of Pharmacy, Yasuda Women's University, Yasuhigashi 6-13-1, Asaminami-ku, Hiroshima, 731-0153, Japan
| | - Chiaki Yasutake
- Faculty of Pharmaceutical Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima, 734-8551, Japan
| | - Hisae Izuhara-Kihara
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima, 734-8551, Japan
| | - Narandarai Danshiitsoodol
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima, 734-8551, Japan
| | - Takanori Kumagai
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima, 734-8551, Japan
| | - Masanori Sugiyama
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima, 734-8551, Japan.
| |
Collapse
|
9
|
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.
Collapse
|
10
|
The investigation on ibuprofen methyl ester isomerization as a fundamental stage in the preparation of antipyretic medicine (R)-ibuprofen: a computational insight. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02618-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
11
|
|
12
|
Kana O, Brylinski M. Elucidating the druggability of the human proteome with eFindSite. J Comput Aided Mol Des 2019; 33:509-519. [PMID: 30888556 PMCID: PMC6516084 DOI: 10.1007/s10822-019-00197-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 03/12/2019] [Indexed: 01/12/2023]
Abstract
Identifying the viability of protein targets is one of the preliminary steps of drug discovery. Determining the ability of a protein to bind drugs in order to modulate its function, termed the druggability, requires a non-trivial amount of time and resources. Inability to properly measure druggability has accounted for a significant portion of failures in drug discovery. This problem is only further exacerbated by the large sample space of proteins involved in human diseases. With these barriers, the druggability space within the human proteome remains unexplored and has made it difficult to develop drugs for numerous diseases. Hence, we present a new feature developed in eFindSite that employs supervised machine learning to predict the druggability of a given protein. Benchmarking calculations against the Non-Redundant data set of Druggable and Less Druggable binding sites demonstrate that an AUC for druggability prediction with eFindSite is as high as 0.88. With eFindSite, we elucidated the human druggability space to be 10,191 proteins. Considering the disease space from the Open Targets Platform and excluding already known targets from the predicted data set reveal 2731 potentially novel therapeutic targets. eFindSite is freely available as a stand-alone software at https://github.com/michal-brylinski/efindsite .
Collapse
Affiliation(s)
- Omar Kana
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Michal Brylinski
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
- Center for Computation & Technology, Louisiana State University, Baton Rouge, LA, 70803, USA.
| |
Collapse
|