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Petrišič N, Adamek M, Kežar A, Hočevar SB, Žagar E, Anderluh G, Podobnik M. Structural basis for the unique molecular properties of broad-range phospholipase C from Listeria monocytogenes. Nat Commun 2023; 14:6474. [PMID: 37838694 PMCID: PMC10576769 DOI: 10.1038/s41467-023-42134-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 09/28/2023] [Indexed: 10/16/2023] Open
Abstract
Listeriosis is one of the most serious foodborne diseases caused by the intracellular bacterium Listeria monocytogenes. Its two major virulence factors, broad-range phospholipase C (LmPC-PLC) and the pore-forming toxin listeriolysin O (LLO), enable the bacterium to spread in the host by destroying cell membranes. Here, we determine the crystal structure of LmPC-PLC and complement it with the functional analysis of this enzyme. This reveals that LmPC-PLC has evolved several structural features to regulate its activity, including the invariant position of the N-terminal tryptophan (W1), the structurally plastic active site, Zn2+-dependent activity, and the tendency to form oligomers with impaired enzymatic activity. We demonstrate that the enzymatic activity of LmPC-PLC can be specifically inhibited by its propeptide added in trans. Furthermore, we show that the phospholipase activity of LmPC-PLC facilitates the pore-forming activity of LLO and affects the morphology of LLO oligomerization on lipid membranes, revealing the multifaceted synergy of the two virulence factors.
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Affiliation(s)
- Nejc Petrišič
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- PhD Program 'Biosciences', Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Maksimiljan Adamek
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Andreja Kežar
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Samo B Hočevar
- Department of Analytical Chemistry, National Institute of Chemistry, Ljubljana, Slovenia
| | - Ema Žagar
- Department of Polymer Chemistry and Technology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia.
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Lin SF, Li CK, Chung YP. Identification of a novel lactose oxidase in Myrmecridium flexuosum NUK-21. FEBS Open Bio 2019; 9:364-373. [PMID: 30761260 PMCID: PMC6356164 DOI: 10.1002/2211-5463.12582] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 11/16/2022] Open
Abstract
Lactobionic acid (O‐β‐galactosyl‐(1‐4)‐gluconic acid) (LBA) is a high‐value lactose derivative, produced via oxidation of the reducing terminal of lactose. LBA can be produced by fermentation using certain microorganisms, although subsequent purification is challenging. Therefore, we have attempted to identify an enzyme for possible use in LBA production. Here, we purified a novel lactose oxidase (LOD) to homogeneity from a wheat bran culture of a soil‐isolated fungal strain, Myrmecridium flexuosum NUK‐21. Maximal activity was observed on the wheat bran solid culture after 3 days of NUK‐21 growth, following release from cells at 0.66 unit·mL−1 culture filtrate. This new sugar oxidase was composed of a single polypeptide chain with a molecular mass of 47.2 kDa and was found to contain 2.0 zinc ions per mole of enzyme but no flavin adenine dinucleotide or heme. This enzyme was stable in the pH range 5.5–9.0, with an optimal reaction pH of 7.5. Its optimal reaction temperature was 40 °C, and it was stable up to 50 °C for 1 h at pH 7.5. LOD oxidized disaccharides with reducing‐end glucosyl residues linked by an α or β‐1,4 glucosidic bond. The relative activity of LOD toward lactose, cellobiose and maltose was 100 : 83 : 4, respectively. To the best of our knowledge, this is the first report on the discovery of an LOD based on coenzyme moiety and enzyme substrate specificity.
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Affiliation(s)
- Shuen-Fuh Lin
- Department of Life Sciences National University of Kaohsiung Taiwan
| | - Cheng-Ke Li
- Department of Life Sciences National University of Kaohsiung Taiwan
| | - Yi-Pei Chung
- Department of Life Sciences National University of Kaohsiung Taiwan
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Serum Albumin Binding and Esterase Activity: Mechanistic Interactions with Organophosphates. Molecules 2017; 22:molecules22071201. [PMID: 28718803 PMCID: PMC6151986 DOI: 10.3390/molecules22071201] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 06/30/2017] [Accepted: 07/12/2017] [Indexed: 12/23/2022] Open
Abstract
The albumin molecule, in contrast to many other plasma proteins, is not covered with a carbohydrate moiety and can bind and transport various molecules of endogenous and exogenous origin. The enzymatic activity of albumin, the existence of which many scientists perceive skeptically, is much less studied. In toxicology, understanding the mechanistic interactions of organophosphates with albumin is a special problem, and its solution could help in the development of new types of antidotes. In the present work, the history of the issue is briefly examined, then our in silico data on the interaction of human serum albumin with soman, as well as comparative in silico data of human and bovine serum albumin activities in relation to paraoxon, are presented. Information is given on the substrate specificity of albumin and we consider the possibility of its affiliation to certain classes in the nomenclature of enzymes.
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Recent research progress with phospholipase C from Bacillus cereus. Biotechnol Lett 2015; 38:23-31. [DOI: 10.1007/s10529-015-1962-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 09/22/2015] [Indexed: 10/23/2022]
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Blomberg MRA, Borowski T, Himo F, Liao RZ, Siegbahn PEM. Quantum chemical studies of mechanisms for metalloenzymes. Chem Rev 2014; 114:3601-58. [PMID: 24410477 DOI: 10.1021/cr400388t] [Citation(s) in RCA: 436] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
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Liao RZ, Yu JG, Himo F. Reaction Mechanism of the Trinuclear Zinc Enzyme Phospholipase C: A Density Functional Theory Study. J Phys Chem B 2010; 114:2533-40. [PMID: 20121060 DOI: 10.1021/jp910992f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Rong-Zhen Liao
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden, and College of Chemistry, Beijing Normal University, Beijing, 100875, People’s Republic of China
| | - Jian-Guo Yu
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden, and College of Chemistry, Beijing Normal University, Beijing, 100875, People’s Republic of China
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden, and College of Chemistry, Beijing Normal University, Beijing, 100875, People’s Republic of China
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Zhang L, Hellgren LI, Xu X. Enzymatic production of ceramide from sphingomyelin. J Biotechnol 2005; 123:93-105. [PMID: 16337303 DOI: 10.1016/j.jbiotec.2005.10.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2005] [Revised: 10/10/2005] [Accepted: 10/24/2005] [Indexed: 11/16/2022]
Abstract
Due to its major role in maintaining the water-retaining properties of the epidermis, ceramide is of great commercial potentials in cosmetic and pharmaceutical industries such as in hair and skin care products. Chemical synthesis of ceramide is a costly process, and developments of alternative cost-efficient production methods are of great interest. Present study was the first attempt to perform a systematic study on the production of ceramide through enzymatic hydrolysis of sphingomyelin. Sphingomyelin hydrolysis proved to be more efficient in two-phase (water:organic solvent) system than in one-phase (water-saturated organic solvent) system. Among the screened phospholipase C, the Clostridium perfringens enzyme had the highest sphingomyelin conversion rate, with very small temperature dependence. Addition of ethanol to the system markedly enhanced the rate of ceramide formation, and a mixture of ethylacetate:hexane (50:50) was the best organic solvent tested. Other factors such as (NH(4))(2)SO(4), NaCl and CaCl(2) were also tested but excluded for further consideration. On the basis of the initial experiments, the reaction system was optimized using response surface methodology including five factors (enzyme amount, water amount, ethanol amount, reaction time and the hexane ratio of organic solvent). Water content and enzyme amount was shown to have the most significant influence on the hydrolysis reaction in the fitted quadratic model. The efficiency of sphingomyelin hydrolysis was dramatically improved through system evaluation and optimization, with the optimal conditions at 75 min reaction time, 3 Uml(-1) enzyme amount, 6% water amount, 1.8% ethanol amount and 46% hexane in ethylacetate.
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Affiliation(s)
- Long Zhang
- BioCentrum-DTU and Center for Advanced Food Studies, Technical University of Denmark, Søltofts Plads, Building 221, DK 2800 Lyngby, Denmark.
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Weston J. Mode of action of bi- and trinuclear zinc hydrolases and their synthetic analogues. Chem Rev 2005; 105:2151-74. [PMID: 15941211 DOI: 10.1021/cr020057z] [Citation(s) in RCA: 272] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jennie Weston
- Institut für Organische und Makromolekulare Chemie, Friedrich-Schiller-Universität, Jena, Germany.
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Smith DM, Daniel KG, Wang Z, Guida WC, Chan TH, Dou QP. Docking studies and model development of tea polyphenol proteasome inhibitors: applications to rational drug design. Proteins 2004; 54:58-70. [PMID: 14705024 DOI: 10.1002/prot.10504] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Previously, we demonstrated that natural and synthetic ester bond-containing green tea polyphenols were potent and specific non-peptide proteasome inhibitors. However, the molecular mechanism of inhibition is currently unknown. Here, we report that inhibition of the chymotrypsin activity of the 20S proteasome by (-)-epigallocatechin-3-gallate (EGCG) is time-dependent and irreversible, implicating acylation of the beta5-subunit's catalytic N-terminal threonine (Thr 1). This knowledge is used, along with in silico docking experiments, to aid in the understanding of binding and inhibition. On the basis of these docking experiments, we propose that (-)-EGCG binds the chymotrypsin site in an orientation and conformation that is suitable for a nucleophilic attack by Thr 1. Consistently, the distance from the electrophilic carbonyl carbon of (-)-EGCG to the hydroxyl group of Thr 1 was measured as 3.18 A. Furthermore, the A ring of (-)-EGCG acts as a tyrosine mimic, binding to the hydrophobic S1 pocket of the beta5-subunit. In the process, the (-)-EGCG scissile bond may become strained, which could lower the activation energy for attack by the hydroxyl group of Thr 1. This model is validated by comparison of predicted and actual activities of several EGCG analogs, either naturally occurring, previously synthesized, or rationally synthesized.
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Affiliation(s)
- David M Smith
- Drug Discovery Program, H. Lee Moffitt Cancer Center and Research Institute, and Department of Biochemistry and Molecular Biology, College of Medicine, University of South Florida, Tampa, Florida, USA
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Epperson JD, Ming LJ. Cobalt(II) and copper(II) binding of Bacillus cereus trinuclear phospholipase C: a novel 1H NMR spectrum of a 'Tri-Cu(II)' center in protein. J Inorg Biochem 2001; 87:149-56. [PMID: 11730896 DOI: 10.1016/s0162-0134(01)00341-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The phosphatidylcholine-preferring phospholipase C from Bacillus cereus (PC-PLC(Bc)) is a tri-Zn enzyme with two 'tight binding' and one 'loose binding' sites. The Zn2+ ions can be replaced with Co2+ and Cu2+ to afford metal-substituted derivatives. Two Cu2+-substituted derivatives are detected by means of 1H NMR spectroscopy, a 'transient' derivative and a 'stable' derivative. The detection of sharp hyperfine-shifted 1H NMR signals in the 'transient' derivative indicates the formation of a magnetically coupled di-Cu2+ center, which concludes that the Zn2+ ions in the dinuclear (Zn1 and Zn3) sites are more easily replaced by Cu2+ than that in the Zn2 site. This might possibly be the case for Co2+ binding. Complete replacement of the three Zn2+ ions can be achieved by extensive dialysis of the enzyme against excess Cu2+ to yield the final 'stable' derivative. This derivative has been determined to have five-coordinated His residues and an overall S'=1/2 spin state with NMR and EPR, consistent with the formation of a tri-Cu2+ center (i.e. a di-Cu2+/mono-Cu2+ center) in this enzyme. The binding of substrate to the inert tri-Cu2+ center to form an enzyme-substrate (ES) complex is clearly seen in the 1H NMR spectrum, which is not obtainable in the case of the native enzyme. The change in the spectral features indicates that the substrate binds directly to the trinuclear metal center. The studies reported here suggest that 1H NMR spectroscopy can be a valuable tool for the characterization of di- and multi-nuclear metalloproteins using the 'NMR friendly' magnetically coupled Cu2+ as a probe.
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Affiliation(s)
- J D Epperson
- Department of Chemistry and Institute for Biomolecular Science, University of South Florida, 4202 Fowler Ave., CHE305, Tampa, FL 33620-5250, USA
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Phosphatidylcholine-Preferring Phospholipase C from B. cereus. Function, Structure, and Mechanism. Top Curr Chem (Cham) 2000. [DOI: 10.1007/3-540-45035-1_5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Nagahama M, Michiue K, Mukai M, Ochi S, Sakurai J. Mechanism of membrane damage by Clostridium perfringens alpha-toxin. Microbiol Immunol 1998; 42:533-8. [PMID: 9776394 DOI: 10.1111/j.1348-0421.1998.tb02321.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effect of Clostridium perfringens alpha-toxin on liposomes prepared from phosphatidylcholine (PC) containing the fatty acyl residues of 18 carbon atoms was investigated. The toxin-induced carboxyfluorescein (CF) leakage and phosphorylcholine release from multilamellar liposomes increased as the phase transition temperature of the phosphatidylcholines containing unsaturated fatty acyl residues decreased. However, there was no difference between the sensitivity of the different phosphatidylcholines solubilized by deoxycholate to the phospholipase C (PLC) activity of the toxin. However, the toxin did not hydrolyze solubilized distearoyl-L-alpha-phosphatidylcholine (DSPC) or phosphatidylcholine containing saturated fatty acyl residue, and caused no effect on liposomes composed of DSPC. These results suggest that the activity of the toxin is closely related to the membrane fluidity and double bond in PC. The N-terminal domain of alpha-toxin (AT1-246) and variant H148G did not induce CF leakage from liposomes composed of dioleoyl-L-alpha-phosphatidylcholine (DOPC). H148G bound to the liposomes, but AT1-246 did not. However, the C-terminal domain (AT251-370) conferred binding to liposomes and the membrane-damaging activity on AT1-246. These observations suggest that the membrane-damaging action of alpha-toxin is due to the binding of the C-terminal domain of the toxin to the double bond in the PC in the bilayer and hydrolysis of the PC by the N-terminal domain.
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Affiliation(s)
- M Nagahama
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Japan
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Zückert WR, Marquis H, Goldfine H. Modulation of enzymatic activity and biological function of Listeria monocytogenes broad-range phospholipase C by amino acid substitutions and by replacement with the Bacillus cereus ortholog. Infect Immun 1998; 66:4823-31. [PMID: 9746585 PMCID: PMC108596 DOI: 10.1128/iai.66.10.4823-4831.1998] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The secreted broad-range phosphatidylcholine (PC)-preferring phospholipase C (PC-PLC) of Listeria monocytogenes plays a role in the bacterium's ability to escape from phagosomes and spread from cell to cell. Based on comparisons with two orthologs, Clostridium perfringens alpha-toxin and Bacillus cereus PLC (PLCBc), we generated PC-PLC mutants with altered enzymatic activities and substrate specificities and analyzed them for biological function in tissue culture and mouse models of infection. Two of the conserved active-site zinc-coordinating histidines were confirmed by single amino acid substitutions H69G and H118G, which resulted in proteins inactive in broth culture and unstable intracellularly. Substitutions D4E and H56Y remodeled the PC-PLC active site to more closely resemble the PLCBc active site, while a gene replacement resulted in L. monocytogenes secreting PLCBc. All of these mutants yielded similar amounts of active enzyme as wild-type PC-PLC both in broth culture and intracellularly. D4E increased activity on and specificity for PC, while H56Y and D4E H56Y showed higher activity on both PC and sphingomyelin, with reduced specificity for PC. As expected, PLCBc expressed by L. monocytogenes was highly specific for PC. During early intracellular growth in human epithelial cells, the D4E mutant and the PLCBc-expressing strain performed significantly better than the wild type, while the H56Y and D4E H56Y mutants showed a significant defect. In assays for cell-to-cell spread, the H56Y and D4E mutants had close to wild-type characteristics, while the spreading efficiency of PLCBc was significantly lower. These studies emphasize the species-specific features of PC-PLC important for growth in mammalian cells.
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Affiliation(s)
- W R Zückert
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
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Christensen IT, Jørgensen FS. Molecular mechanics calculations of proteins. Comparison of different energy minimization strategies. J Biomol Struct Dyn 1997; 15:473-88. [PMID: 9439995 DOI: 10.1080/07391102.1997.10508959] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A general strategy for performing energy minimization of proteins using the SYBYL molecular modelling program has been developed. The influence of several variables including energy minimization procedure, solvation, dielectric function and dielectric constant have been investigated in order to develop a general method, which is capable of producing high quality protein structures. Avian pancreatic polypeptide (APP) and bovine pancreatic phospholipase A2 (BP PLA2) were selected for the calculations, because high quality X-ray structures exist and because all classes of secondary structure are represented in the structures. The energy minimized structures were evaluated relative to the corresponding X-ray structures. The overall similarity was checked by calculating RMS distances for all atom positions. Backbone conformation was checked by Ramachandran plots and secondary structure elements evaluated by the length on hydrogen bonds. The dimensions of active site in BP PLA2 is very dependent on electrostatic interactions, due to the presence of the positively charged calcium ion. Thus, the distances between calcium and the calcium-coordinating groups were used as a quality index for this protein. Energy minimized structures of the trimeric PLA2 from Indian cobra (N.n.n. PLA2) were used for assessing the impact of protein-protein interactions. Based on the above mentioned criteria, it could be concluded that using the following conditions: Dielectric constant epsilon = 4 or 20; a distance dependent dielectric function and stepwise energy minimization, it is possible to reproduce X-ray structures very accurately without including explicit solvent molecules.
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Affiliation(s)
- I T Christensen
- Department of Medicinal Chemistry, Royal Danish School of Pharmacy, Copenhagen, Denmark
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