1
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Zhu S, Guo Q, Xue Y, Lu X, Lai T, Liang C, Tian J. Impaired glycosylation of GmPAP15a, a root-associated purple acid phosphatase, inhibits extracellular phytate-P utilization in soybean. PLANT, CELL & ENVIRONMENT 2024; 47:259-277. [PMID: 37691629 DOI: 10.1111/pce.14715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 07/25/2023] [Accepted: 08/01/2023] [Indexed: 09/12/2023]
Abstract
Phosphorus (P) is an essential nutrient, but easily fixed in soils. Therefore, most of soil P exists in the form of inaccessible organic phosphorus (Po), particularly phytate-P. Root-associated purple acid phosphatases (PAPs) are considered to play a crucial role in phosphate (Pi) scavenging in soils. However, evidence for regulating root-associated PAPs in utilization of extracellular phytate-P remain largely unknown in plants at both transcriptional and posttranslational levels. In this study, a Pi-starvation responsive GmPAP15a was identified in soybean (Glycine max). Overexpressing GmPAP15a led to significant increases in root-associated phytase activities, as well as total P content when phytate-P was supplied as the sole P resource in soybean hairy roots. Meanwhile, mass spectrometry (MS) analysis showed GmPAP15a was glycosylated at Asn144 and Asn502 , and its glycan structures of N-linked oligosaccharide chains exhibited microheterogeneity. Moreover, two homologues of AtPHR1, GmPHR9 and GmPHR32 were found to activate GmPAP15a transcription through luciferase activity analysis. Taken together, it is strongly suggested that GmPAP15a plays a vital role in phytate-P utilization in soybean, which might be regulated at both transcriptional and glycosylation modification levels. Our results highlight the GmPHR9/GmPHR32-GmPAP15a signalling pathway might present, and control phytate-P utilization in soybean.
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Affiliation(s)
- Shengnan Zhu
- Root Biology Center, Department of Plant Nutrition, College of Natural Resources and Environment, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Department of Bioscience, Life Science and Technology School, Lingnan Normal University, Zhanjiang, China
| | - Qi Guo
- Root Biology Center, Department of Plant Nutrition, College of Natural Resources and Environment, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Yingbin Xue
- Department of Agriculture, College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, China
| | - Xing Lu
- Root Biology Center, Department of Plant Nutrition, College of Natural Resources and Environment, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Tao Lai
- Root Biology Center, Department of Plant Nutrition, College of Natural Resources and Environment, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Cuiyue Liang
- Root Biology Center, Department of Plant Nutrition, College of Natural Resources and Environment, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Jiang Tian
- Root Biology Center, Department of Plant Nutrition, College of Natural Resources and Environment, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
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2
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Zhang J, Li J, Gong J, Liu J, Wang Y, Zhao F, Sun S, Wang W. A novel highly thermostable and stress resistant ROS scavenging metalloprotein from Paenibacillus. Arch Biochem Biophys 2024; 751:109837. [PMID: 38007074 DOI: 10.1016/j.abb.2023.109837] [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: 08/08/2023] [Revised: 10/19/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
Reactive oxygen species (ROS) are unstable metabolites produced during cellular respiration that can cause extensive damage to the body. Here we report a unique structural metalloprotein called RSAPp for the first time, which exhibits robust ROS-scavenging activity, high thermostability, and stress resistance. RSAPp is a previously uncharacterized DUF2935 (domain of unknown function, accession number: cl12705) family protein from Paenibacillus, containing a highly conserved four-helix bundle with binding sites for variable-valence metal ions (Mn2+/Fe2+/Zn2+). Enzymatic characterization results indicated that RSAPp displays the functionality of three different antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD). In particular, RSAPp exhibits a significant SOD-like activity that is remarkably effective in eliminating superoxide radicals (up to kcat/KM = 2.27 × 1011 mol-1 s-1), and maintains the catalytical active in a wide range of temperatures (25-100 °C) and pH (pH 2.0-9.0), as well as resistant to high temperature, alkali and acidic pH, and 55 different concentrations of detergent agents, chemical solvents, and inhibitors. These properties make RSAPp an attractive candidate for various industrial applications, including cosmetics, food, and pharmaceuticals.
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Affiliation(s)
- Jingjing Zhang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457, PR China
| | - Jiabin Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457, PR China
| | - Jingbo Gong
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457, PR China
| | - Jingjing Liu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457, PR China
| | - Yijia Wang
- Laboratory of Oncologic Molecular Medicine, Tianjin Union Medical Center, Nankai University, Tianjin, 300121, PR China
| | - Fang Zhao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457, PR China
| | - Shenmei Sun
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457, PR China
| | - Wei Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457, PR China; Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, 300457, PR China.
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3
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Sharma SK, Mohanty BP, Singh V, Bansal MP, Singhal NK, Sharma SK, Sandhir R. Trace elements dyshomeostasis in liver and brain of weanling mice under altered dietary selenium conditions. J Trace Elem Med Biol 2023; 80:127305. [PMID: 37778095 DOI: 10.1016/j.jtemb.2023.127305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 10/03/2023]
Abstract
BACKGROUND A balanced diet containing selenium (Se) and other trace elements is essential for normal development and growth. Se has been recognized as an essential trace element; however, its interaction with other elements has not been fully investigated. In the present study, sodium (Na), magnesium (Mg), potassium (K), calcium (Ca), chromium (Cr), manganese (Mn), iron (Fe), cobalt (Co), copper (Cu), zinc (Zn), Se and rubidium (Rb), were analysed in liver and brain regions under altered dietary Se intake in weanling mice to identify major discriminatory elements. METHODS The study investigated the effects of different levels of Se intake on the elemental composition in liver and brain tissues of weaned mice. After 24 weeks of feeding with Se adequate, deficient, and excess diets, elemental analysis was performed on the harvested tissues using Inductively coupled plasma mass spectrometry (ICP-MS). Statistical analysis that included analysis of covariance (ANCOVA), correlation coefficient analysis, principal component analysis, and partial least squares discriminant analysis were performed. RESULTS The ANCOVA showed statistically significant changes and correlations among the analysed elements under altered dietary Se status. The multivariate analysis showed differential changes in elements in liver and brain regions. The results suggest that long-term dietary Se alternations lead to dyshomeostasis in trace elements that are required in higher concentrations compared to Se. It was observed that changes in the Fe, Co, and Rb levels were similar in all the tissues studied, whereas the changes in Mg, Cr, and Mn levels were different among the tissues under altered dietary Se status. Additionally, the changes in Rb levels correlated with the dietary Se intake but had no relation with the tissue Se levels. CONCLUSIONS The findings suggest interactions between Mg, Cr, Mn, Fe, Co, and Se under altered Se status may impact cellular functions during postnatal development. However, the possible biological significance of alterations in Rb levels under different dietary Se paradigms needs to be further explored.
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Affiliation(s)
| | | | - Vishal Singh
- National Agri-Food Biotechnology Institute, Sector 81, S.A.S. Nagar 140306, India
| | | | - Nitin Kumar Singhal
- National Agri-Food Biotechnology Institute, Sector 81, S.A.S. Nagar 140306, India
| | | | - Rajat Sandhir
- Department of Biochemistry, Panjab University, Chandigarh 160014, India.
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4
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Jayasinghe-Arachchige VM, Serafim LF, Hu Q, Ozen C, Moorkkannur SN, Schenk G, Prabhakar R. Elucidating the Roles of Distinct Chemical Factors in the Hydrolytic Activities of Hetero- and Homonuclear Synthetic Analogues of Binuclear Metalloenzymes. ACS Catal 2023. [DOI: 10.1021/acscatal.2c05758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Affiliation(s)
| | - Leonardo F. Serafim
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Qiaoyu Hu
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Cihan Ozen
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Sreerag N. Moorkkannur
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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5
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Costa LMO, Reis IS, Fernandes C, Marques MM, Resende JALC, Krenske EH, Schenk G, Gahan LR, Horn A. Synthesis, characterization and computational investigation of the phosphatase activity of a dinuclear Zinc(II) complex containing a new heptadentate asymmetric ligand. J Inorg Biochem 2023; 239:112064. [PMID: 36410306 DOI: 10.1016/j.jinorgbio.2022.112064] [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: 08/23/2022] [Revised: 10/24/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022]
Abstract
We report the synthesis of a new asymmetric heptadentate ligand based on the 1,3-diaminopropan-2-ol backbone. The ligand 3-[[3-(bis-pyridin-2-ylmethyl-amino)-2-hydroxy-propyl]-(2-carbamoyl-ethyl)-amino]-propionamide (HL1) contains two amide and two pyridine groups attached to the 1,3-diaminopropan-2-ol core. Reaction between HL1 and Zn(ClO4)2.6H2O resulted in the formation of the dinuclear [Zn2(L1)(μ-OAc)](ClO4)2 complex, characterized by single crystal X-ray diffraction, 1H, 13C and 15N NMR, ESI-(+)-MS, CHN elemental analysis as well as infrared spectroscopy. The phosphatase activity of the complex was studied in the pH range 6-11 employing pyridinium bis(2,4-dinitrophenyl)phosphate (py(BDNPP)) as substrate. The complex exhibited activity dependent on the pH, presenting an asymmetric bell shape profile with the highest activity at pH 9; at high pH ligand exchange is rate-limiting. The hydrolysis of BDNPP- at pH 9 displayed behavior characteristic of Michaelis-Menten kinetics, with kcat = 5.06 × 10-3 min-1 and Km = 5.7 ± 1.0 mM. DFT calculations map out plausible reaction pathways and identify a terminal, Zn(II)-bound hydroxide as likely nucleophile.
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Affiliation(s)
- Luel M O Costa
- Laboratório de Ciências Químicas, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ 28013-602, Brazil
| | - Iago S Reis
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, SC 88040-900, Brazil
| | - Christiane Fernandes
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, SC 88040-900, Brazil
| | - Marcelo M Marques
- Colégio Universitário Geraldo Reis, Universidade Federal Fluminense, Niterói, RJ 24210-200, Brazil
| | - Jackson A L C Resende
- Instituto de Ciências Exatas e da Terra, Universidade Federal de Mato Grosso, Pontal do Araguaia, MT, Brazil
| | - Elizabeth H Krenske
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia; Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland, Australia, 4072; Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Lawrence R Gahan
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Adolfo Horn
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, SC 88040-900, Brazil.
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6
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Wilson LA, Pedroso MM, Peralta RA, Gahan LR, Schenk G. Biomimetics for purple acid phosphatases: A historical perspective. J Inorg Biochem 2023; 238:112061. [PMID: 36371912 DOI: 10.1016/j.jinorgbio.2022.112061] [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: 09/27/2022] [Revised: 10/23/2022] [Accepted: 10/29/2022] [Indexed: 11/06/2022]
Abstract
Biomimetics hold potential for varied applications in biotechnology and medicine but have also attracted particular interest as benchmarks for the functional study of their more complex biological counterparts, e.g. metalloenzymes. While many of the synthetic systems adequately mimic some structural and functional aspects of their biological counterparts the catalytic efficiencies displayed are mostly far inferior due to the smaller size and the associated lower complexity. Nonetheless they play an important role in bioinorganic chemistry. Numerous examples of biologically inspired and informed artificial catalysts have been reported, designed to mimic a plethora of chemical transformations, and relevant examples are highlighted in reviews and scientific reports. Herein, we discuss biomimetics of the metallohydrolase purple acid phosphatase (PAP), examples of which have been used to showcase synergistic research advances for both the biological and synthetic systems. In particular, we focus on the seminal contribution of our colleague Prof. Ademir Neves, and his group, pioneers in the design and optimization of suitable ligands that mimic the active site of PAP.
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Affiliation(s)
- Liam A Wilson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Marcelo M Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Rosely A Peralta
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, SC 88040-900, Brazil
| | - Lawrence R Gahan
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia; Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia; Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia.
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7
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Luiz E, Farias G, Bortoluzzi AJ, Neves A, de Melo Mattos LM, Pereira MD, Xavier FR, Peralta RA. Hydrolytic activity of new bioinspired Mn IIIMn II and Fe IIIMn II complexes as mimetics of PAPs: Biological and environmental interest. J Inorg Biochem 2022; 236:111965. [PMID: 35988388 DOI: 10.1016/j.jinorgbio.2022.111965] [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: 06/06/2022] [Revised: 08/01/2022] [Accepted: 08/10/2022] [Indexed: 12/15/2022]
Abstract
Coordination compounds that mimic Purple Acid Phosphatases (PAPs) have drawn attention in the bioinorganic field due to their capacity to cleave phosphodiester bonds. However, their catalytic activity upon phosphate triesters is still unexplored. Thus, we report the synthesis and characterization of two binuclear complexes, [MnIIMnIII(L1)(OAc)2]BF4 (1) and [MnIIFeIII(L1)(OAc)2]BF4 (2) (H2L1 = 2-[N,N-bis-(2- pyridilmethyl)aminomethyl]-4-methyl-6-[N-(2-hydroxy-3-formyl-5-methylbenzyl)-N-(2-pyridylmethyl)aminomethyl]phenol), their hydrolytic activity and antioxidant potential. The complexes were fully characterized, including the X-Ray diffraction (XRD) of 1. Density functional theory (DFT) calculations were performed to better understand their electronic and structural properties and phosphate conjugates. The catalytic activity was analyzed for two model substrates, a diester (BDNPP) and a triester phosphate (DEDNPP). The results suggest enhancement of the hydrolysis reaction by 170 to 1500 times, depending on the substrate and complex. It was possible to accompany the catalytic reaction of DEDNPP hydrolysis by phosphorus nuclear magnetic resonance (31P NMR), showing that both 1 and 2 are efficient catalysts. Moreover, we also addressed that 1 and 2 present a relevant antioxidant potential, protecting the yeast Saccharomyces cerevisiae, used as eukaryotic model of study, against the exposure of cells to acute oxidative stress.
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Affiliation(s)
- Edinara Luiz
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil
| | - Giliandro Farias
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil
| | - Adailton J Bortoluzzi
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil
| | - Ademir Neves
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil
| | - Larissa Maura de Melo Mattos
- Instituto de Química, Departamento de Bioquímica, Universidade Federal do Rio de Janeiro, 21941-909, Brazil; Rede Micologia RJ - FAPERJ
| | - Marcos Dias Pereira
- Instituto de Química, Departamento de Bioquímica, Universidade Federal do Rio de Janeiro, 21941-909, Brazil; Rede Micologia RJ - FAPERJ
| | - Fernando R Xavier
- Departamento de Química, Universidade do Estado de Santa Catarina, Joinville, Santa Catarina 89219-710, Brazil.
| | - Rosely A Peralta
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil.
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8
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Feder D, Mohd-Pahmi SH, Hussein WM, Guddat LW, McGeary RP, Schenk G. Rational Design of Potent Inhibitors of a Metallohydrolase Using a Fragment-Based Approach. ChemMedChem 2021; 16:3342-3359. [PMID: 34331400 DOI: 10.1002/cmdc.202100486] [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: 07/12/2021] [Indexed: 11/08/2022]
Abstract
Metallohydrolases form a large group of enzymes that have fundamental importance in a broad range of biological functions. Among them, the purple acid phosphatases (PAPs) have gained attention due to their crucial role in the acquisition and use of phosphate by plants and also as a promising target for novel treatments of bone-related disorders and cancer. To date, no crystal structure of a mammalian PAP with drug-like molecules bound near the active site is available. Herein, we used a fragment-based design approach using structures of a mammalian PAP in complex with the MaybridgeTM fragment CC063346, the amino acid L-glutamine and the buffer molecule HEPES, as well as various solvent molecules to guide the design of highly potent and efficient mammalian PAP inhibitors. These inhibitors have improved aqueous solubility when compared to the clinically most promising PAP inhibitors available to date. Furthermore, drug-like fragments bound in newly discovered binding sites mapped out additional scaffolds for further inhibitor discovery, as well as scaffolds for the design of inhibitors with novel modes of action.
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Affiliation(s)
- Daniel Feder
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia.,Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Siti H Mohd-Pahmi
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Waleed M Hussein
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ross P McGeary
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia.,Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
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9
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Srivastava R, Akash, Parida AP, Chauhan PK, Kumar R. Identification, structure analysis, and transcript profiling of purple acid phosphatases under Pi deficiency in tomato (Solanum lycopersicum L.) and its wild relatives. Int J Biol Macromol 2020; 165:2253-2266. [PMID: 33098900 DOI: 10.1016/j.ijbiomac.2020.10.080] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/12/2020] [Accepted: 10/11/2020] [Indexed: 11/26/2022]
Abstract
Purple acid phosphatases (PAPs), a family of metallo-phosphoesterase enzymes, are involved in phosphorus nutrition in plants. In this study, we report that the tomato genome encodes 25 PAP members. Physio-biochemical analyses revealed relatively lower total root-associated acid phosphatase activity in the seedlings of Solanum pimpinellifolium than their cultivated tomato seedlings under Pi deficiency. Scrutiny of their transcript abundance shows that most of PAPs are activated, although to varying levels, under Pi deficiency in tomato. Further investigation demonstrates that the magnitude of induction of phosphate starvation inducible root-associated PAP homologs remains lower in the Pi-starved S. pimpinellifolium seedlings, hence, accounting for the lower acid phosphatase activity in this wild relative. Examination of their amino acid sequences revealed significant variation in their substrate-specificity defining residues. Among all members, only SlPAP15 possesses the critical lysine residue (R337) and atypical REKA motif in its C-terminal region. Homology modeling and docking studies revealed that ADP and ATP are preferred substrates of SlPAP15. We also identified other amino acid residues present in the vicinity of the active site, possibly facilitating such physical interactions. Altogether, the results presented here will help in the functional characterization of these genes in the tomato in the future.
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Affiliation(s)
- Rajat Srivastava
- PTRL, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Akash
- PTRL, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Adwaita Prasad Parida
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Pankaj Kumar Chauhan
- PTRL, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Rahul Kumar
- PTRL, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
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10
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Feder D, McGeary RP, Mitić N, Lonhienne T, Furtado A, Schulz BL, Henry RJ, Schmidt S, Guddat LW, Schenk G. Structural elements that modulate the substrate specificity of plant purple acid phosphatases: Avenues for improved phosphorus acquisition in crops. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 294:110445. [PMID: 32234228 DOI: 10.1016/j.plantsci.2020.110445] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 02/12/2020] [Indexed: 05/11/2023]
Abstract
Phosphate acquisition by plants is an essential process that is directly implicated in the optimization of crop yields. Purple acid phosphatases (PAPs) are ubiquitous metalloenzymes, which catalyze the hydrolysis of a wide range of phosphate esters and anhydrides. While some plant PAPs display a preference for ATP as the substrate, others are efficient in hydrolyzing phytate or 2-phosphoenolpyruvate (PEP). PAP from red kidney bean (rkbPAP) is an efficient ATP- and ADPase, but has no activity towards phytate. Crystal structures of this enzyme in complex with ATP analogues (to 2.20 and 2.60 Å resolution, respectively) complement the recent structure of rkbPAP with a bound ADP analogue (ChemBioChem 20 (2019) 1536). Together these complexes provide the first structural insight of a PAP in complex with molecules that mimic biologically relevant substrates. Homology modeling was used to generate three-dimensional structures for the active sites of PAPs from tobacco (NtPAP) and thale cress (AtPAP26) that are efficient in hydrolyzing phytate and PEP as preferred substrates, respectively. The combining of crystallographic data, substrate docking simulations and a phylogenetic analysis of 49 plant PAP sequences (including the first PAP sequences reported from Eucalyptus) resulted in the identification of several active site residues that are important in defining the substrate specificities of plant PAPs; of particular relevance is the identification of a motif ("REKA") that is characteristic for plant PAPs that possess phytase activity. These results may inform bioengineering studies aimed at identifying and incorporating suitable plant PAP genes into crops to improve phosphorus acquisition and use efficiency. Organic phosphorus sources increasingly supplement or replace inorganic fertilizer, and efficient phosphorus use of crops will lower the environmental footprint of agriculture while enhancing food production.
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Affiliation(s)
- Daniel Feder
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ross P McGeary
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Natasa Mitić
- Department of Chemistry, Maynooth University, Maynooth Co. Kildare, Ireland
| | - Thierry Lonhienne
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Susanne Schmidt
- School of Agriculture and Food Science, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, QLD 4072, Australia; Sustainable Minerals Institute, The University of Queensland, St. Lucia, QLD 4072, Australia.
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11
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Sharma G, Jayasinghe-Arachchige VM, Hu Q, Schenk G, Prabhakar R. Effect of Chemically Distinct Substrates on the Mechanism and Reactivity of a Highly Promiscuous Metallohydrolase. ACS Catal 2020. [DOI: 10.1021/acscatal.9b04847] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Gaurav Sharma
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | | | - Qiaoyu Hu
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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12
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Synthesis, evaluation and structural investigations of potent purple acid phosphatase inhibitors as drug leads for osteoporosis. Eur J Med Chem 2019; 182:111611. [DOI: 10.1016/j.ejmech.2019.111611] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/31/2019] [Accepted: 08/09/2019] [Indexed: 12/18/2022]
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13
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Guanidine- and purine-functionalized ligands of FeIIIZnII complexes: effects on the hydrolysis of DNA. J Biol Inorg Chem 2019; 24:675-691. [DOI: 10.1007/s00775-019-01680-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 06/21/2019] [Indexed: 01/01/2023]
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14
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Feder D, Gahan LR, McGeary RP, Guddat LW, Schenk G. The Binding Mode of an ADP Analogue to a Metallohydrolase Mimics the Likely Transition State. Chembiochem 2019; 20:1536-1540. [DOI: 10.1002/cbic.201900077] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Daniel Feder
- School of Chemistry and Molecular Biosciences The University of Queensland St. Lucia QLD 4072 Australia
| | - Lawrence R. Gahan
- School of Chemistry and Molecular Biosciences The University of Queensland St. Lucia QLD 4072 Australia
| | - Ross P. McGeary
- School of Chemistry and Molecular Biosciences The University of Queensland St. Lucia QLD 4072 Australia
| | - Luke W. Guddat
- School of Chemistry and Molecular Biosciences The University of Queensland St. Lucia QLD 4072 Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences The University of Queensland St. Lucia QLD 4072 Australia
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15
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Ghahremani M, Tran H, Biglou SG, O'Gallagher B, She YM, Plaxton WC. A glycoform of the secreted purple acid phosphatase AtPAP26 co-purifies with a mannose-binding lectin (AtGAL1) upregulated by phosphate-starved Arabidopsis. PLANT, CELL & ENVIRONMENT 2019; 42:1139-1157. [PMID: 30156702 DOI: 10.1111/pce.13432] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 05/08/2023]
Abstract
The purple acid phosphatase AtPAP26 plays a central role in Pi-scavenging by Pi-starved (-Pi) Arabidopsis. Mass spectrometry (MS) of AtPAP26-S1 and AtPAP26-S2 glycoforms secreted by -Pi suspension cells demonstrated that N-glycans at Asn365 and Asn422 were modified in AtPAP26-S2 to form high-mannose glycans. A 55-kDa protein that co-purified with AtPAP26-S2 was identified as a Galanthus nivalis agglutinin-related and apple domain lectin-1 (AtGAL1; At1g78850). MS revealed that AtGAL1 was bisphosphorylated at Tyr38 and Thr39 and glycosylated at four conserved Asn residues. When AtGAL was incubated in the presence of a thiol-reducing reagent prior to immunoblotting, its cross-reactivity with anti-AtGAL1-IgG was markedly attenuated (consistent with three predicted disulfide bonds in AtGAL1's apple domain). Secreted AtGAL1 polypeptides were upregulated to a far greater extent than AtGAL1 transcripts during Pi deprivation, indicating posttranscriptional control of AtGAL1 expression. Growth of a -Pi atgal1 mutant was unaffected, possibly due to compensation by AtGAL1's closest paralog, AtGAL2 (At1g78860). Nevertheless, AtGAL1's induction by numerous stresses combined with the broad distribution of AtGAL1-like lectins in diverse species implies an important function for AtGAL1 orthologs within the plant kingdom. We hypothesize that binding of AtPAP26-S2's high-mannose glycans by AtGAL1 enhances AtPAP26 function to facilitate Pi-scavenging by -Pi Arabidopsis.
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Affiliation(s)
| | - Hue Tran
- Oncolytics Biotech Inc., Calgary, Canada
| | - Sanaz G Biglou
- Department of Biology, Queen's University, Kingston, Canada
| | | | - Yi-Min She
- Centre for Biologics Evaluation, Biologics and Genetic Therapies Directorate, Health Canada, Ottawa, Canada
| | - William C Plaxton
- Department of Biology, Queen's University, Kingston, Canada
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
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16
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Hussein WM, Feder D, Schenk G, Guddat LW, McGeary RP. Synthesis and evaluation of novel purple acid phosphatase inhibitors. MEDCHEMCOMM 2018; 10:61-71. [PMID: 30774855 DOI: 10.1039/c8md00491a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 11/09/2018] [Indexed: 11/21/2022]
Abstract
Transgenic studies in animals have demonstrated a direct association between the level of expression of purple acid phosphatase (PAP; also known as tartrate-resistant acid phosphatase) and the progression of osteoporosis. Consequently, PAP has emerged as a promising target for the development of novel therapeutic agents to treat this debilitating disorder. PAPs are binuclear hydrolases that catalyse the hydrolysis of phosphorylated substrates under acidic to neutral conditions. A series of phenyltriazole carboxylic acids, prepared by the reactions of azide derivatives with propiolic acid through copper(i)-catalysed azide-alkyne cycloaddition click reactions, has been assessed for their inhibitory effect on the catalytic activity of pig and red kidney bean PAPs. The binding mode of most of these compounds is purely uncompetitive with K iuc values as low as ∼23 μM for the mammalian enzyme. Molecular modelling has been used to examine the binding modes of these triazole compounds in the presence of a substrate in the active site of the enzyme in order to rationalise their activities and to design more potent and specific derivatives.
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Affiliation(s)
- Waleed M Hussein
- The University of Queensland , School of Chemistry and Molecular Biosciences , Brisbane , QLD 4072 , Australia . ; Tel: +61 7 33653955.,Helwan University , Pharmaceutical Organic Chemistry Department , Faculty of Pharmacy , Ein Helwan , Helwan , Egypt
| | - Daniel Feder
- The University of Queensland , School of Chemistry and Molecular Biosciences , Brisbane , QLD 4072 , Australia . ; Tel: +61 7 33653955
| | - Gerhard Schenk
- The University of Queensland , School of Chemistry and Molecular Biosciences , Brisbane , QLD 4072 , Australia . ; Tel: +61 7 33653955.,The University of Queensland , Australian Centre for Ecogenomics , Brisbane , QLD 4072 , Australia
| | - Luke W Guddat
- The University of Queensland , School of Chemistry and Molecular Biosciences , Brisbane , QLD 4072 , Australia . ; Tel: +61 7 33653955
| | - Ross P McGeary
- The University of Queensland , School of Chemistry and Molecular Biosciences , Brisbane , QLD 4072 , Australia . ; Tel: +61 7 33653955
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17
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Horn Jr. A, Englert D, Roberts AE, Comba P, Schenk G, Krenske EH, Gahan LR. Synthesis, Magnetic Properties, and Catalytic Properties of a Nickel(II)-Dependent Biomimetic of Metallohydrolases. Front Chem 2018; 6:441. [PMID: 30320072 PMCID: PMC6168013 DOI: 10.3389/fchem.2018.00441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 09/05/2018] [Indexed: 11/13/2022] Open
Abstract
A dinickel(II) complex of the ligand 1,3-bis(bis(pyridin-2-ylmethyl)amino)propan-2-ol (HL1) has been prepared and characterized to generate a functional model for nickel(II) phosphoesterase enzymes. The complex, [Ni2(L1)(μ-OAc)(H2O)2](ClO4)2·H2O, was characterized by microanalysis, X-ray crystallography, UV-visible, and IR absorption spectroscopy and solid state magnetic susceptibility measurements. Susceptibility studies show that the complex is antiferromagnetically coupled with the best fit parameters J = -27.4 cm-1, g = 2.29, D = 28.4 cm-1, comparable to corresponding values measured for the analogous dicobalt(II) complex [Co2(L1)(μ-OAc)](ClO4)2·0.5 H2O (J = -14.9 cm-1 and g = 2.16). Catalytic measurements with the diNi(II) complex using the substrate bis(2,4-dinitrophenyl)phosphate (BDNPP) demonstrated activity toward hydrolysis of the phosphoester substrate with K m ~10 mM, and k cat ~0.025 s-1. The combination of structural and catalytic studies suggests that the likely mechanism involves a nucleophilic attack on the substrate by a terminal nucleophilic hydroxido moiety.
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Affiliation(s)
- Adolfo Horn Jr.
- Laboratório de Ciências Químicas, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Daniel Englert
- Anorganisch-Chemisches Institut and Interdisciplinary Center of Scientific Computing, Universität Heidelberg, Heidelberg, Germany
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Asha E. Roberts
- Anorganisch-Chemisches Institut and Interdisciplinary Center of Scientific Computing, Universität Heidelberg, Heidelberg, Germany
| | - Peter Comba
- Anorganisch-Chemisches Institut and Interdisciplinary Center of Scientific Computing, Universität Heidelberg, Heidelberg, Germany
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Elizabeth H. Krenske
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Lawrence R. Gahan
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
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18
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Hussein WM, Feder D, Schenk G, Guddat LW, McGeary RP. Purple acid phosphatase inhibitors as leads for osteoporosis chemotherapeutics. Eur J Med Chem 2018; 157:462-479. [DOI: 10.1016/j.ejmech.2018.08.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/14/2018] [Accepted: 08/01/2018] [Indexed: 11/24/2022]
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19
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Dutta N, Haldar S, Vijaykumar G, Paul S, Chattopadhyay AP, Carrella L, Bera M. Phosphatase-like Activity of Tetranuclear Iron(III) and Zinc(II) Complexes. Inorg Chem 2018; 57:10802-10820. [PMID: 30130107 DOI: 10.1021/acs.inorgchem.8b01441] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nityananda Dutta
- Department of Chemistry, University of Kalyani, Kalyani, West Bengal-741235, India
| | - Shobhraj Haldar
- Department of Chemistry, University of Kalyani, Kalyani, West Bengal-741235, India
| | - Gonela Vijaykumar
- Department of Chemical Sciences, Indian Institute of Science Education & Research Kolkata, Mohanpur, West Bengal-741246, India
| | - Suvendu Paul
- Department of Chemistry, University of Kalyani, Kalyani, West Bengal-741235, India
| | | | - Luca Carrella
- Institut fur Anorganische Chemie und Analytische Chemie, Johannes-Gutenberg Universitat Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Manindranath Bera
- Department of Chemistry, University of Kalyani, Kalyani, West Bengal-741235, India
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20
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Monteiro Pedroso M, Selleck C, Bilyj J, Harmer JR, Gahan LR, Mitić N, Standish AJ, Tierney DL, Larrabee JA, Schenk G. Reaction mechanism of the metallohydrolase CpsB from Streptococcus pneumoniae, a promising target for novel antimicrobial agents. Dalton Trans 2018; 46:13194-13201. [PMID: 28573276 DOI: 10.1039/c7dt01350g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
CpsB is a metal ion-dependent hydrolase involved in the biosynthesis of capsular polysaccharides in bacterial organisms. The enzyme has been proposed as a promising target for novel chemotherapeutics to combat antibiotic resistance. The crystal structure of CpsB indicated the presence of as many as three closely spaced metal ions, modelled as Mn2+, in the active site. While the preferred metal ion composition in vivo is obscure Mn2+ and Co2+ have been demonstrated to be most effective in reconstituting activity. Using isothermal titration calorimetry (ITC) we have demonstrated that, in contrast to the crystal structure, only two Mn2+ or Co2+ ions bind to a monomer of CpsB. This observation is in agreement with magnetic circular dichroism (MCD) and electron paramagnetic resonance (EPR) data that indicate the presence of two weakly ferromagnetically coupled Co2+ ions in the active site of catalytically active CpsB. While CpsB is known to be a phosphoesterase we have also been able to demonstrate that this enzyme is efficient in hydrolyzing the β-lactam substrate nitrocefin. Steady-state and stopped-flow kinetics measurements further indicated that phosphoesters and nitrocefin undergo catalysis in a conserved manner with a metal ion-bridging hydroxide acting as a nucleophile. Thus, the combined physicochemical studies demonstrate that CpsB is a novel member of the dinuclear metallohydrolase family.
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Affiliation(s)
- Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia.
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21
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Chagas MA, Pereira ES, Godinho MPB, Da Silva JCS, Rocha WR. Base Mechanism to the Hydrolysis of Phosphate Triester Promoted by the Cd2+/Cd2+ Active site of Phosphotriesterase: A Computational Study. Inorg Chem 2018; 57:5888-5902. [DOI: 10.1021/acs.inorgchem.8b00361] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Marcelo A. Chagas
- LQC-MM: Laboratório de Química Computacional e Modelagem Molecular Departamento de Química, ICEx, Universidade Federal de Minas Gerais 31270-901 Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Eufrásia S. Pereira
- LQC-MM: Laboratório de Química Computacional e Modelagem Molecular Departamento de Química, ICEx, Universidade Federal de Minas Gerais 31270-901 Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Marina P. B. Godinho
- LQC-MM: Laboratório de Química Computacional e Modelagem Molecular Departamento de Química, ICEx, Universidade Federal de Minas Gerais 31270-901 Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Júlio Cosme S. Da Silva
- LQC-MM: Laboratório de Química Computacional e Modelagem Molecular Departamento de Química, ICEx, Universidade Federal de Minas Gerais 31270-901 Pampulha, Belo Horizonte, Minas Gerais, Brazil
- GQC: Grupo de Química Computacional Instituto de Química e Biotecnologia, IQB, Universidade Federal de Alagoas Campus A. C. Simões, 57072-900 Maceió, Alagoas, Brazil
| | - Willian R. Rocha
- LQC-MM: Laboratório de Química Computacional e Modelagem Molecular Departamento de Química, ICEx, Universidade Federal de Minas Gerais 31270-901 Pampulha, Belo Horizonte, Minas Gerais, Brazil
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22
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Paul TJ, Schenk G, Prabhakar R. Formation of Catalytically Active Binuclear Center of Glycerophosphodiesterase: A Molecular Dynamics Study. J Phys Chem B 2018; 122:5797-5808. [DOI: 10.1021/acs.jpcb.8b02046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thomas J. Paul
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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23
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Stoian SA, Peng YR, Beedle CC, Chung YJ, Lee GH, Yang EC, Hill S. Structural, Spectroscopic, and Theoretical Investigation of a T-Shaped [Fe 3(μ 3-O)] Cluster. Inorg Chem 2017; 56:10861-10874. [PMID: 28845975 DOI: 10.1021/acs.inorgchem.7b00455] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The synthesis, X-ray crystal and electronic structures of [Fe3(μ3-O)(mpmae)2(OAc)2 Cl3], 1, where mpmae-H = 2-(N-methyl-N-((pyridine-2-yl)methyl)amino)ethanol, are described. This cluster comprises three high-spin ferric ions and exhibits a T-shaped site topology. Variable-frequency electron paramagnetic resonance measurements performed on single crystals of 1 demonstrate a total spin ST = 5/2 ground state, characterized by a small, negative, and nearly axial zero-field splitting tensor D = -0.49 cm-1, E/D ≈ 0.055. Analysis of magnetic susceptibility, magnetization, and magneto-structural correlations further corroborate the presence of a sextet ground-spin state. The observed ground state originates from the strong anti-ferromagnetic interaction of two iron(III) spins, with J = 115(5) cm-1, that, in turn, are only weakly coupled to the spin of the third site, with j = 7(1) cm-1. These exchange interactions lead to a ground state with magnetic properties that are essentially entirely determined by the weakly coupled site. The contributions of the individual spins to the total ground state of the cluster were monitored using variable-field 57Fe Mössbauer spectroscopy. Field-dependent spectra reveal that, while one of the iron sites exhibits a large negative internal field, typical of ferric ions, the other two sites exhibit small, but not null, negative and positive internal fields. A theoretical analysis reveals that these small internal fields originate from the mixing of the lowest ST = 5/2 excited state into the ground state which, in turn, is induced by a minute structural distortion.
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Affiliation(s)
| | - Yi-Ru Peng
- Department of Chemistry, Fu Jen Catholic University , Hsinchuang, New Taipei City, 24205 Taiwan, Republic of China
| | | | - Yi-Jung Chung
- Department of Chemistry, Fu Jen Catholic University , Hsinchuang, New Taipei City, 24205 Taiwan, Republic of China
| | - Gene-Hsiang Lee
- Instrumentation Centre, College of Science, National Taiwan University , Taipei, 106 Taiwan, Republic of China
| | - En-Che Yang
- Department of Chemistry, Fu Jen Catholic University , Hsinchuang, New Taipei City, 24205 Taiwan, Republic of China
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24
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Comba P, Eisenschmidt A, Gahan LR, Herten DP, Nette G, Schenk G, Seefeld M. Is CuIICoordinated to Patellamides insideProchloronCells? Chemistry 2017; 23:12264-12274. [DOI: 10.1002/chem.201700895] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Peter Comba
- Universität Heidelberg; Anorganisch-Chemisches Institut and Interdisciplinary Center for Scientific Computing (IWR); Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Annika Eisenschmidt
- Universität Heidelberg; Anorganisch-Chemisches Institut and Interdisciplinary Center for Scientific Computing (IWR); Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Lawrence R. Gahan
- School of Chemistry and Molecular Bioscience; University of Queensland; Brisbane, Queensland 4072 Australia
| | - Dirk-Peter Herten
- CellNetworks Cluster und Physikalisch-Chemisches Institut; Universität Heidelberg; 69120 Heidelberg Germany
| | - Geoffrey Nette
- Independent Marine Biochemistry Research (IMBCR Pty. Ltd.); Point Lookout, Queensland 4183 Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Bioscience; University of Queensland; Brisbane, Queensland 4072 Australia
| | - Martin Seefeld
- CellNetworks Cluster und Physikalisch-Chemisches Institut; Universität Heidelberg; 69120 Heidelberg Germany
- Biochemistry Center (BZH); Universität Heidelberg; Im Neuenheimer Feld 345 69120 Heidelberg Germany
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25
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Selleck C, Clayton D, Gahan LR, Mitić N, McGeary RP, Pedroso MM, Guddat LW, Schenk G. Visualization of the Reaction Trajectory and Transition State in a Hydrolytic Reaction Catalyzed by a Metalloenzyme. Chemistry 2017; 23:4778-4781. [DOI: 10.1002/chem.201700866] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Christopher Selleck
- School of Chemistry and Molecular Biosciences The University of Queensland, St. Lucia Queensland 4072 Australia
| | - Daniel Clayton
- School of Chemistry and Molecular Biosciences The University of Queensland, St. Lucia Queensland 4072 Australia
| | - Lawrence R. Gahan
- School of Chemistry and Molecular Biosciences The University of Queensland, St. Lucia Queensland 4072 Australia
| | - Nataša Mitić
- Department of Chemistry Maynooth University, Maynooth, Co. Kildare Ireland
| | - Ross P. McGeary
- School of Chemistry and Molecular Biosciences The University of Queensland, St. Lucia Queensland 4072 Australia
| | - Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences The University of Queensland, St. Lucia Queensland 4072 Australia
| | - Luke W. Guddat
- School of Chemistry and Molecular Biosciences The University of Queensland, St. Lucia Queensland 4072 Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences The University of Queensland, St. Lucia Queensland 4072 Australia
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26
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Promiscuous metallo-β-lactamases: MIM-1 and MIM-2 may play an essential role in quorum sensing networks. J Inorg Biochem 2016; 162:366-375. [DOI: 10.1016/j.jinorgbio.2015.12.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/04/2015] [Accepted: 12/16/2015] [Indexed: 11/21/2022]
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27
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Tadrowski S, Pedroso MM, Sieber V, Larrabee JA, Guddat LW, Schenk G. Metal Ions Play an Essential Catalytic Role in the Mechanism of Ketol-Acid Reductoisomerase. Chemistry 2016; 22:7427-36. [PMID: 27136273 DOI: 10.1002/chem.201600620] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Indexed: 01/13/2023]
Abstract
Ketol-acid reductoisomerase (KARI) is a Mg(2+) -dependent enzyme in the branched-chain amino acid biosynthesis pathway. It catalyses a complex two-part reaction: an alkyl migration followed by a NADPH-dependent reduction. Both reactions occur within the one active site, but in particular, the mechanism of the isomerisation step is poorly understood. Here, using a combination of kinetic, thermodynamic and spectroscopic techniques, the reaction mechanisms of both Escherichia coli and rice KARI have been investigated. We propose a conserved mechanism of catalysis, whereby a hydroxide, bridging the two Mg(2+) ions in the active site, initiates the reaction by abstracting a proton from the C2 alcohol group of the substrate. While the μ-hydroxide-bridged dimetallic centre is pre-assembled in the bacterial enzyme, in plant KARI substrate binding leads to a reduction of the metal-metal distance with the concomitant formation of a hydroxide bridge. Only Mg(2+) is capable of promoting the isomerisation reaction, likely to be due to non-competent substrate binding in the presence of other metal ions.
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Affiliation(s)
- Sonya Tadrowski
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Marcelo M Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Volker Sieber
- Straubing Center of Science, Technische Universität München, Straubing, Germany
| | - James A Larrabee
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, 05753, USA
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia.
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia.
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28
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Mendes LL, Englert D, Fernandes C, Gahan LR, Schenk G, Horn A. Metallohydrolase biomimetics with catalytic and structural flexibility. Dalton Trans 2016; 45:18510-18521. [DOI: 10.1039/c6dt03200a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The phosphatase activity of zinc complexes containing six- and seven-dentate ligands was evaluated through kinetic and31P NMR studies.
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Affiliation(s)
- Luisa L. Mendes
- Laboratório de Ciências Químicas
- Universidade Estadual do Norte Fluminense
- Campos dos Goytacazes/RJ
- Brazil
| | - Daniel Englert
- Anorganisch-Chemisches Institut
- Universität Heidelberg
- 69120 Heidelberg
- Germany
| | - Christiane Fernandes
- Laboratório de Ciências Químicas
- Universidade Estadual do Norte Fluminense
- Campos dos Goytacazes/RJ
- Brazil
| | - Lawrence R. Gahan
- School of Chemistry and Molecular Biosciences
- The University of Queensland
- Brisbane
- Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences
- The University of Queensland
- Brisbane
- Australia
| | - Adolfo Horn
- Laboratório de Ciências Químicas
- Universidade Estadual do Norte Fluminense
- Campos dos Goytacazes/RJ
- Brazil
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29
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Luong TKN, Shestakova P, Parac-Vogt TN. Kinetic studies of phosphoester hydrolysis promoted by a dimeric tetrazirconium(iv) Wells–Dawson polyoxometalate. Dalton Trans 2016; 45:12174-80. [DOI: 10.1039/c6dt02211a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The kinetic and thermodynamic studies of p-nitrophenyl phosphate hydrolysis promoted by a Zr(iv)-substituted Wells–Dawson polyoxometalate, Na14[Zr4(P2W16O59)2 (μ3-O)2(OH)2(H2O)4]·57H2O, were fully presented.
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Affiliation(s)
| | - Pavletta Shestakova
- NMR Laboratory
- Institute of Organic Chemistry with Centre of Phytochemistry
- Bulgarian Academy of Sciences
- 1113 Sofia
- Bulgaria
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30
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Sugrue E, Hartley CJ, Scott C, Jackson CJ. The Evolution of New Catalytic Mechanisms for Xenobiotic Hydrolysis in Bacterial Metalloenzymes. Aust J Chem 2016. [DOI: 10.1071/ch16426] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
An increasing number of bacterial metalloenzymes have been shown to catalyse the breakdown of xenobiotics in the environment, while others exhibit a variety of promiscuous xenobiotic-degrading activities. Several different evolutionary processes have allowed these enzymes to gain or enhance xenobiotic-degrading activity. In this review, we have surveyed the range of xenobiotic-degrading metalloenzymes, and discuss the molecular and catalytic basis for the development of new activities. We also highlight how our increased understanding of the natural evolution of xenobiotic-degrading metalloenzymes can be been applied to laboratory enzyme design.
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Yang K, Kim MY, Um IH. S NAr Reactions of 1-Halo-2,4-dinitrobenzenes with Alkali-Metal Ethoxides: Differential Stabilization of Ground State and Transition State Determines Alkali-Metal Ion Catalysis or Inhibition. B KOREAN CHEM SOC 2015. [DOI: 10.1002/bkcs.10344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Kiyull Yang
- Department of Chemistry Education; Gyeongsang National University; Jinju 660-701 Korea
| | - Min-Young Kim
- Department of Chemistry and Nano Science; Ewha Womans University; Seoul 120-750 Korea
| | - Ik-Hwan Um
- Department of Chemistry and Nano Science; Ewha Womans University; Seoul 120-750 Korea
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Roberts AE, Schenk G, Gahan LR. A Heterodinuclear FeIIIZnIIComplex as a Mimic for Purple Acid Phosphatase with Site-Specific ZnIIBinding. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201500351] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Mitić N, Miraula M, Selleck C, Hadler KS, Uribe E, Pedroso MM, Schenk G. Catalytic mechanisms of metallohydrolases containing two metal ions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 97:49-81. [PMID: 25458355 DOI: 10.1016/bs.apcsb.2014.07.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
At least one-third of enzymes contain metal ions as cofactors necessary for a diverse range of catalytic activities. In the case of polymetallic enzymes (i.e., two or more metal ions involved in catalysis), the presence of two (or more) closely spaced metal ions gives an additional advantage in terms of (i) charge delocalisation, (ii) smaller activation barriers, (iii) the ability to bind larger substrates, (iv) enhanced electrostatic activation of substrates, and (v) decreased transition-state energies. Among this group of proteins, enzymes that catalyze the hydrolysis of ester and amide bonds form a very prominent family, the metallohydrolases. These enzymes are involved in a multitude of biological functions, and an increasing number of them gain attention for translational research in medicine and biotechnology. Their functional versatility and catalytic proficiency are largely due to the presence of metal ions in their active sites. In this chapter, we thus discuss and compare the reaction mechanisms of several closely related enzymes with a view to highlighting the functional diversity bestowed upon them by their metal ion cofactors.
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Affiliation(s)
- Nataša Mitić
- Department of Chemistry, National University of Ireland, Maynooth, Maynooth, Co. Kildare, Ireland.
| | - Manfredi Miraula
- Department of Chemistry, National University of Ireland, Maynooth, Maynooth, Co. Kildare, Ireland; School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Christopher Selleck
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Kieran S Hadler
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Elena Uribe
- Department of Biochemistry and Molecular Biology, University of Concepción, Concepción, Chile
| | - Marcelo M Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
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Um IH, Cho HJ, Kim MY, Buncel E. Alkali-metal ion catalysis and inhibition in SNAr displacement: relative stabilization of ground state and transition state determines catalysis and inhibition in SNAr reactivity. Chemistry 2014; 20:13337-44. [PMID: 25171659 DOI: 10.1002/chem.201404004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Indexed: 11/11/2022]
Abstract
We report here the first observation of alkali-metal ion catalysis and inhibition in SNAr reactions. The plot of kobsd versus [alkali-metal ethoxide] exhibits downward curvature for the reactions of 1-(4-nitrophenoxy)-2,4-dinitrobenzene with EtOLi, EtONa, and EtOK, but upward curvature for the corresponding reaction with EtOK in the presence of 18-crown-6-ether (18C6). Dissection of kobsd into the second-order rate constants for the reactions with the dissociated EtO(-) and the ion-paired EtOM (i.e., k EtO - and kEtOM , respectively) has revealed that the reactivity increases in the order EtOLi<EtONa<EtOK<EtO(-)<EtOK/18C6. This indicates that the reaction is inhibited by Li(+), Na(+), and K(+) ions but is catalyzed by 18C6 K(+) ion. The reactions of 1-(Y-substituted-phenoxy)-2,4-dinitrobenzenes have been proposed to proceed through a stepwise mechanism, in which expulsion of the leaving group occurs after the rate-determining step based on the kinetic result that σ(o) constants exhibit a much better Hammett correlation than σ(-) constants. Alkali-metal ion catalysis or inhibition has been discussed in terms of differential stabilization of ground-state and transition-state complexes through a qualitative energy profile. A π-complexed transition-state structure is proposed to account for the kinetic results.
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Affiliation(s)
- Ik-Hwan Um
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750 (Korea).
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Lee J, Kim MY, Um IH. Kinetic Study on Nucleophilic Substitution Reaction of 5-Nitro-8-quinolyl Benzoate, Picolinate, Nicotinate and Isonicotinate with Alkali Metal Ethoxide: Effect of Nonleaving Group on Reactivity and Transition State Structure. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.6.1789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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36
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Jeon SH, Yoon JH, Kim MY, Um IH. Alkali-Metal Ion Catalysis in Nucleophilic Substitution Reactions of 5-Nitro-8-quinolyl Picolinate with Alkali Metal Ethoxides: Effect of Modification of Nonleaving Group from Benzoyl to Picolinyl on Reactivity and Transition State Structure. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.5.1506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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37
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McGeary RP, Schenk G, Guddat LW. The applications of binuclear metallohydrolases in medicine: Recent advances in the design and development of novel drug leads for purple acid phosphatases, metallo-β-lactamases and arginases. Eur J Med Chem 2014; 76:132-44. [DOI: 10.1016/j.ejmech.2014.02.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 01/28/2014] [Accepted: 02/06/2014] [Indexed: 10/25/2022]
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38
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Das B, Daver H, Singh A, Singh R, Haukka M, Demeshko S, Meyer F, Lisensky G, Jarenmark M, Himo F, Nordlander E. A Heterobimetallic FeIIIMnIIComplex of an Unsymmetrical Dinucleating Ligand: A Structural and Functional Model Complex for the Active Site of Purple Acid Phosphatase of Sweet Potato. Eur J Inorg Chem 2014. [DOI: 10.1002/ejic.201301375] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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39
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Kim SI, Kim MY, Um IH. Kinetic Study on Nucleophilic Substitution Reactions of 4-Nitrophenyl X-Substituted-Benzoates with Potassium Ethoxide: Reaction Mechanism and Role of K+Ion. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.1.225] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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40
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Pedroso MM, Ely F, Lonhienne T, Gahan LR, Ollis DL, Guddat LW, Schenk G. Determination of the catalytic activity of binuclear metallohydrolases using isothermal titration calorimetry. J Biol Inorg Chem 2014; 19:389-98. [DOI: 10.1007/s00775-013-1079-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 12/12/2013] [Indexed: 11/28/2022]
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Daumann LJ, Schenk G, Ollis DL, Gahan LR. Spectroscopic and mechanistic studies of dinuclear metallohydrolases and their biomimetic complexes. Dalton Trans 2013; 43:910-28. [PMID: 24135968 DOI: 10.1039/c3dt52287c] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An enhanced understanding of the metal ion binding and active site structural features of phosphoesterases such as the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ), and the organophosphate degrading agent from Agrobacterium radiobacter (OpdA) have important consequences for potential applications. Coupled with investigations of the metalloenzymes, programs of study to synthesise and characterise model complexes based on these metalloenzymes can add to our understanding of structure and function of the enzymes themselves. This review summarises some of our work and illustrates the significance and contributions of model studies to knowledge in the area.
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Affiliation(s)
- Lena J Daumann
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
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42
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Identification and characterization of an unusual metallo-β-lactamase from Serratia proteamaculans. J Biol Inorg Chem 2013; 18:855-63. [DOI: 10.1007/s00775-013-1035-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 08/14/2013] [Indexed: 11/25/2022]
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43
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44
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Comba P, Gahan LR, Mereacre V, Hanson GR, Powell AK, Schenk G, Zajaczkowski-Fischer M. Spectroscopic Characterization of the Active FeIIIFeIII and FeIIIFeII Forms of a Purple Acid Phosphatase Model System. Inorg Chem 2012; 51:12195-209. [DOI: 10.1021/ic301347t] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Peter Comba
- Universität Heidelberg, Anorganisch-Chemisches Institut, INF 270,
D-69120 Heidelberg, Germany
| | - Lawrence R. Gahan
- School of Chemistry and Molecular
Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Valeriu Mereacre
- Institut für Anorganische
Chemie, Karlsruher Institut für Technologie, Enesserstrasse 15, D-76131 Karlsruhe, Germany
| | - Graeme R. Hanson
- Centre for Advanced Imaging, The University of Queensland, Brisbane, Queensland
4072, Australia
| | - Annie K. Powell
- Institut für Anorganische
Chemie, Karlsruher Institut für Technologie, Enesserstrasse 15, D-76131 Karlsruhe, Germany
| | - Gerhard Schenk
- School of Chemistry and Molecular
Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
- Department
of Chemistry, National University of Ireland, Maynooth, Co. Kildare,
Ireland
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45
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Schenk G, Mitić N, Gahan LR, Ollis DL, McGeary RP, Guddat LW. Binuclear metallohydrolases: complex mechanistic strategies for a simple chemical reaction. Acc Chem Res 2012; 45:1593-603. [PMID: 22698580 DOI: 10.1021/ar300067g] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Binuclear metallohydrolases are a large family of enzymes that require two closely spaced transition metal ions to carry out a plethora of hydrolytic reactions. Representatives include purple acid phosphatases (PAPs), enzymes that play a role in bone metabolism and are the only member of this family with a heterovalent binuclear center in the active form (Fe(3+)-M(2+), M = Fe, Zn, Mn). Other members of this family are urease, which contains a di-Ni(2+) center and catalyzes the breakdown of urea, arginase, which contains a di-Mn(2+) center and catalyzes the final step in the urea cycle, and the metallo-β-lactamases, which contain a di-Zn(2+) center and are virulence factors contributing to the spread of antibiotic-resistant pathogens. Binuclear metallohydrolases catalyze numerous vital reactions and are potential targets of drugs against a wide variety of human disorders including osteoporosis, various cancers, antibiotic resistance, and erectile dysfunctions. These enzymes also tend to catalyze more than one reaction. An example is an organophosphate (OP)-degrading enzyme from Enterobacter aerogenes (GpdQ). Although GpdQ is part of a pathway that is used by bacteria to degrade glycerolphosphoesters, it hydrolyzes a variety of other phosphodiesters and displays low levels of activity against phosphomono- and triesters. Such a promiscuous nature may have assisted the apparent recent evolution of some binuclear metallohydrolases to deal with situations created by human intervention such as OP pesticides in the environment. OP pesticides were first used approximately 70 years ago, and therefore the enzymes that bacteria use to degrade them must have evolved very quickly on the evolutionary time scale. The promiscuous nature of enzymes such as GpdQ makes them ideal candidates for the application of directed evolution to produce new enzymes that can be used in bioremediation and against chemical warfare. In this Account, we review the mechanisms employed by binuclear metallohydrolases and use PAP, the OP-degrading enzyme from Agrobacterium radiobacter (OPDA), and GpdQ as representative systems because they illustrate both the diversity and similarity of the reactions catalyzed by this family of enzymes. The majority of binuclear metallohydrolases utilize metal ion-activated water molecules as nucleophiles to initiate hydrolysis, while some, such as alkaline phosphatase, employ an intrinsic polar amino acid. Here we only focus on catalytic strategies applied by the former group.
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Affiliation(s)
- Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Department of Chemistry, National University of Ireland—Maynooth, Maynooth, County Kildare, Ireland
| | - Nataša Mitić
- Department of Chemistry, National University of Ireland—Maynooth, Maynooth, County Kildare, Ireland
| | - Lawrence R. Gahan
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David L. Ollis
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Ross P. McGeary
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Luke W. Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
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46
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Xavier FR, Bortoluzzi AJ, Neves A. A Synthetic Pathway for an Unsymmetrical N5O2 Heptadentate Ligand and Its Heterodinuclear Iron(III)Zinc(II) Complex: A Biomimetic Model for the Purple Acid Phosphatases. Chem Biodivers 2012; 9:1794-805. [DOI: 10.1002/cbdv.201100436] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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47
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Daumann LJ, Gahan LR, Comba P, Schenk G. Cadmium(II) Complexes: Mimics of Organophosphate Pesticide Degrading Enzymes and Metallo-β-lactamases. Inorg Chem 2012; 51:7669-81. [DOI: 10.1021/ic300687y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lena J. Daumann
- School of
Chemistry and Molecular
Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lawrence. R. Gahan
- School of
Chemistry and Molecular
Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Peter Comba
- Anorganisch-Chemisches Institut, Universitat Heidelberg, Im Neuenheimer Feld 270, 69120
Heidelberg, Germany
| | - Gerhard Schenk
- School of
Chemistry and Molecular
Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Department
of Chemistry, National University of Ireland, Maynooth, County Kildare,
Ireland
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48
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Anand A, Srivastava PK. A molecular description of acid phosphatase. Appl Biochem Biotechnol 2012; 167:2174-97. [PMID: 22684363 DOI: 10.1007/s12010-012-9694-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 04/11/2012] [Indexed: 11/25/2022]
Abstract
Acid phosphatase is ubiquitous in distribution in various organisms. Although it catalyzes simple hydrolytic reactions, it is considered as an interesting enzyme in biological systems due to its involvement in different physiological activities. However, earlier reviews on acid phosphatase reveal some fragmentary information and do not give a holistic view on this enzyme. So, the present review summarizes studies on biochemical properties, structure, catalytic mechanism, and applications of acid phosphatase. Recent advancement of acid phosphatase in agricultural and clinical fields is emphasized where it is presented as potent agent for sustainable agricultural practices and diagnostic marker in bone metabolic disorders. Also, its significance in prostate cancer therapies as a therapeutic target has been discussed. At the end, current studies and prospects of immobilized acid phosphatase are included.
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Affiliation(s)
- Asha Anand
- Department of Biochemistry, Faculty of Science, Banaras Hindu University, Varanasi 221005, India
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49
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Daumann LJ, McCarthy BY, Hadler KS, Murray TP, Gahan LR, Larrabee JA, Ollis DL, Schenk G. Promiscuity comes at a price: catalytic versatility vs efficiency in different metal ion derivatives of the potential bioremediator GpdQ. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:425-32. [PMID: 22366468 DOI: 10.1016/j.bbapap.2012.02.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 01/26/2012] [Accepted: 02/03/2012] [Indexed: 10/28/2022]
Abstract
The glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) is a highly promiscuous dinuclear metallohydrolase with respect to both substrate specificity and metal ion composition. While this promiscuity may adversely affect the enzyme's catalytic efficiency its ability to hydrolyse some organophosphates (OPs) and by-products of OP degradation have turned GpdQ into a promising candidate for bioremedial applications. Here, we investigated both metal ion binding and the effect of the metal ion composition on catalysis. The prevalent in vivo metal ion composition for GpdQ is proposed to be of the type Fe(II)Zn(II), a reflection of natural abundance rather than catalytic optimisation. The Fe(II) appears to have lower binding affinity than other divalent metal ions, and the catalytic efficiency of this mixed metal center is considerably smaller than that of Mn(II), Co(II) or Cd(II)-containing derivatives of GpdQ. Interestingly, metal ion replacements do not only affect catalytic efficiency but also the optimal pH range for the reaction, suggesting that different metal ion combinations may employ different mechanistic strategies. These metal ion-triggered modulations are likely to be mediated via an extensive hydrogen bond network that links the two metal ion binding sites via residues in the substrate binding pocket. The observed functional diversity may be the cause for the modest catalytic efficiency of wild-type GpdQ but may also be essential to enable the enzyme to evolve rapidly to alter substrate specificity and enhance k(cat) values, as has recently been demonstrated in a directed evolution experiment. This article is part of a Special Issue entitled: Chemistry and mechanism of phosphatases, diesterases and triesterases.
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Affiliation(s)
- Lena J Daumann
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
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50
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Smith SJ, Peralta RA, Jovito R, Horn A, Bortoluzzi AJ, Noble CJ, Hanson GR, Stranger R, Jayaratne V, Cavigliasso G, Gahan LR, Schenk G, Nascimento OR, Cavalett A, Bortolotto T, Razzera G, Terenzi H, Neves A, Riley MJ. Spectroscopic and Catalytic Characterization of a Functional FeIIIFeII Biomimetic for the Active Site of Uteroferrin and Protein Cleavage. Inorg Chem 2012; 51:2065-78. [DOI: 10.1021/ic201711p] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | | | | | | | | | | | | | - Robert Stranger
- Research School of Chemistry, Australian National University, Canberra 0200, Australia
| | - Vidura Jayaratne
- Research School of Chemistry, Australian National University, Canberra 0200, Australia
| | - Germán Cavigliasso
- Research School of Chemistry, Australian National University, Canberra 0200, Australia
| | | | - Gerhard Schenk
- Department of Chemistry, National University of Ireland—Maynooth, Maynooth County, Kildare, Ireland
| | - Otaciro R. Nascimento
- Instituto de Física, Universidade de São Paulo, 13560-970 São
Carlos, São Paulo, Brazil
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