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Wu QF, Wang WS, Chen SB, Xu B, Li YD, Chen JH. Crystal Structure of Inorganic Pyrophosphatase From Schistosoma japonicum Reveals the Mechanism of Chemicals and Substrate Inhibition. Front Cell Dev Biol 2021; 9:712328. [PMID: 34458268 PMCID: PMC8386120 DOI: 10.3389/fcell.2021.712328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/15/2021] [Indexed: 11/13/2022] Open
Abstract
Soluble inorganic pyrophosphatases (PPases) are essential for facilitating the growth and development of organisms, making them attractive functional proteins. To provide insight into the molecular basis of PPases in Schistosoma japonicum (SjPPase), we expressed the recombinant SjPPase, analyzed the hydrolysis mechanism of inorganic pyrophosphate (PPi), and measured its activity. Moreover, we solved the crystal structure of SjPPase in complex with orthophosphate (Pi) and performed PPi and methylene diphosphonic acid (MDP) docking into the active site. Our results suggest that the SjPPase possesses PPi hydrolysis activity, and the activity declines with increased MDP or NaF concentration. However, the enzyme shows unexpected substrate inhibition properties. Through PPi metabolic pathway analysis, the physiological action of substrate inhibition might be energy saving, adaptably cytoprotective, and biosynthetic rate regulating. Furthermore, the structure of apo-SjPPase and SjPPase with Pi has been solved at 2.6 and 2.3 Å, respectively. The docking of PPi into the active site of the SjPPase-Pi complex revealed that substrate inhibition might result from blocking Pi exit due to excess PPi in the SjPPase-Pi complex of the catalytic cycle. Our results revealed the structural features of apo-SjPPase and the SjPPase-Pi complex by X-ray crystallography, providing novel insights into the physiological functions of PPase in S. japonicum without the PPi transporter and the mechanism of its substrate inhibition.
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Affiliation(s)
- Qun-Feng Wu
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China.,NHC Key Laboratory of Parasite and Vector Biology, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Shanghai, China.,Key Laboratory of Organo-Pharmaceutical Chemistry of Jiangxi Province, Chemistry and Chemical Engineering College, Gannan Normal University, Ganzhou, China
| | - Wei-Si Wang
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China.,NHC Key Laboratory of Parasite and Vector Biology, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Shanghai, China
| | - Shen-Bo Chen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China.,NHC Key Laboratory of Parasite and Vector Biology, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Shanghai, China
| | - Bin Xu
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China.,NHC Key Laboratory of Parasite and Vector Biology, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Shanghai, China
| | - Yong-Dong Li
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China.,NHC Key Laboratory of Parasite and Vector Biology, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Shanghai, China.,Key Laboratory of Organo-Pharmaceutical Chemistry of Jiangxi Province, Chemistry and Chemical Engineering College, Gannan Normal University, Ganzhou, China
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China.,NHC Key Laboratory of Parasite and Vector Biology, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Shanghai, China.,The School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Cruz CS, Costa EP, Machado JA, Silva JN, Romeiro NC, Moraes J, Silva JR, Fonseca RN, Vaz IS, Logullo C, Campos E. A soluble inorganic pyrophosphatase from the cattle tick Rhipicephalus microplus capable of hydrolysing polyphosphates. INSECT MOLECULAR BIOLOGY 2018; 27:260-267. [PMID: 29271528 DOI: 10.1111/imb.12369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Polyphosphates have been found in all cell types examined to date and play diverse roles depending on the cell type. In eukaryotic organisms, polyphosphates have been investigated mainly in mammalian cells, and only a few studies have addressed arthropods. Pyrophosphatases have been shown to regulate polyphosphate metabolism. However, these studies were restricted to trypanosomatids. Here we focus on the tick Rhipicephalus microplus, a haematophagous ectoparasite that is highly harmful to cattle. We produced a recombinant R. microplus pyrophosphatase (rRmPPase) with the aim of investigating its kinetic parameters using polyphosphates as substrate. Molecular docking assays of RmPPase with polyphosphates were also carried out. The kinetic and Hill coefficient parameters indicated that rRmPPase has a greater affinity, higher catalytic efficiency and increased cooperativity for sodium phosphate glass type 15 (polyP15 ) than for sodium tripolyphosphate (polyP3 ). Through molecular docking, we found that polyP3 binds close to the Mg2+ atoms in the catalytic region of the protein, participating in their coordination network, whereas polyP15 interactions involve negatively charged phosphate groups and basic amino acid residues, such as Lys56, Arg58 and Lys193; polyP15 has a more favourable theoretical binding affinity than polyP3 , thus supporting the kinetic data. This study shows, for the first time in arthropods, a pyrophosphatase with polyphosphatase activity, suggesting its participation in polyphosphate metabolism.
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Affiliation(s)
- C S Cruz
- Laboratório Integrado de Bioquímica - Hatisaburo Masuda, UFRJ, NUPEM, São José do Barreto, Macaé, Rio de Janeiro, Brazil
| | - E P Costa
- Laboratório de Química e Função de Proteínas e Peptídeos and Unidade de Experimentação Animal - CBB - UENF, Horto, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - J A Machado
- Laboratório de Química e Função de Proteínas e Peptídeos and Unidade de Experimentação Animal - CBB - UENF, Horto, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - J N Silva
- Laboratório de Química e Função de Proteínas e Peptídeos and Unidade de Experimentação Animal - CBB - UENF, Horto, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - N C Romeiro
- Laboratório de Química e Função de Proteínas e Peptídeos and Unidade de Experimentação Animal - CBB - UENF, Horto, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - J Moraes
- Laboratório Integrado de Bioquímica - Hatisaburo Masuda, UFRJ, NUPEM, São José do Barreto, Macaé, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia - Entomologia Molecular, Rio de Janeiro, Brazil
| | - J R Silva
- Laboratório Integrado de Bioquímica - Hatisaburo Masuda, UFRJ, NUPEM, São José do Barreto, Macaé, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia - Entomologia Molecular, Rio de Janeiro, Brazil
| | - R N Fonseca
- Laboratório Integrado de Bioquímica - Hatisaburo Masuda, UFRJ, NUPEM, São José do Barreto, Macaé, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia - Entomologia Molecular, Rio de Janeiro, Brazil
| | - I S Vaz
- Instituto Nacional de Ciência e Tecnologia - Entomologia Molecular, Rio de Janeiro, Brazil
- Centro de Biotecnologia e Faculdade de Veterinária, UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - C Logullo
- Laboratório de Química e Função de Proteínas e Peptídeos and Unidade de Experimentação Animal - CBB - UENF, Horto, Campos dos Goytacazes, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia - Entomologia Molecular, Rio de Janeiro, Brazil
| | - E Campos
- Laboratório Integrado de Bioquímica - Hatisaburo Masuda, UFRJ, NUPEM, São José do Barreto, Macaé, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia - Entomologia Molecular, Rio de Janeiro, Brazil
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Costa EP, Façanha AR, Cruz CS, Silva JN, Machado JA, Carvalho GM, Fernandes MR, Martins R, Campos E, Romeiro NC, Githaka NW, Konnai S, Ohashi K, Vaz IS, Logullo C. A novel mechanism of functional cooperativity regulation by thiol redox status in a dimeric inorganic pyrophosphatase. Biochim Biophys Acta Gen Subj 2016; 1861:2922-2933. [PMID: 27664315 DOI: 10.1016/j.bbagen.2016.09.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 08/30/2016] [Accepted: 09/18/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND Inorganic PPases are essential metal-dependent enzymes that convert pyrophosphate into orthophosphate. This reaction is quite exergonic and provides a thermodynamic advantage for many ATP-driven biosynthetic reactions. We have previously demonstrated that cytosolic PPase from R. microplus embryos is an atypical Family I PPase. Here, we explored the functional role of the cysteine residues located at the homodimer interface, its redox sensitivity, as well as structural and kinetic parameters related to thiol redox status. METHODS In this work, we used prokaryotic expression system for recombinant protein overexpression, biochemical approaches to assess kinetic parameters, ticks embryos and computational approaches to analyze and predict critical amino acids as well as physicochemical properties at the homodimer interface. RESULTS Cysteine 339, located at the homodimer interface, was found to play an important role in stabilizing a functional cooperativity between the two catalytic sites, as indicated by kinetics and Hill coefficient analyses of the WT-rBmPPase. WT-rBmPPase activity was up-regulated by physiological antioxidant molecules such as reduced glutathione and ascorbic acid. On the other hand, hydrogen peroxide at physiological concentrations decreased the affinity of WT-rBmPPase for its substrate (PPi), probably by inducing disulfide bridge formation. CONCLUSIONS Our results provide a new angle in understanding redox control by disulfide bonds formation in enzymes from hematophagous arthropods. The reversibility of the down-regulation is dependent on hydrophobic interactions at the dimer interface. GENERAL SIGNIFICANCE This study is the first report on a soluble PPase where dimeric cooperativity is regulated by a redox mechanism, according to cysteine redox status.
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Affiliation(s)
- Evenilton P Costa
- Laboratório de Química e Função de Proteínas e Peptídeos, Laboratório de Biologia Tecidual e Celular and Unidade de Experimentação Animal, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Brazil
| | - Arnoldo R Façanha
- Laboratório de Química e Função de Proteínas e Peptídeos, Laboratório de Biologia Tecidual e Celular and Unidade de Experimentação Animal, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Brazil
| | - Criscila S Cruz
- Laboratório de Química e Função de Proteínas e Peptídeos, Laboratório de Biologia Tecidual e Celular and Unidade de Experimentação Animal, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Brazil; Laboratório Integrado de Bioquímica Hatisaburo Masuda, Laboratório Integrado de Computação Científica, Núcleo de Pesquisas em Ecologia e Desenvolvimento Sócio-Ambiental de Macaé (NUPEM), Universidade Federal do Rio de Janeiro, Macaé, Brazil
| | - Jhenifer N Silva
- Laboratório de Química e Função de Proteínas e Peptídeos, Laboratório de Biologia Tecidual e Celular and Unidade de Experimentação Animal, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Brazil
| | - Josias A Machado
- Laboratório de Química e Função de Proteínas e Peptídeos, Laboratório de Biologia Tecidual e Celular and Unidade de Experimentação Animal, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Brazil
| | - Gabriel M Carvalho
- Laboratório de Química e Função de Proteínas e Peptídeos, Laboratório de Biologia Tecidual e Celular and Unidade de Experimentação Animal, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Brazil
| | - Mariana R Fernandes
- Laboratório de Química e Função de Proteínas e Peptídeos, Laboratório de Biologia Tecidual e Celular and Unidade de Experimentação Animal, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Brazil
| | - Renato Martins
- Laboratório de Química e Função de Proteínas e Peptídeos, Laboratório de Biologia Tecidual e Celular and Unidade de Experimentação Animal, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Brazil
| | - Eldo Campos
- Laboratório Integrado de Bioquímica Hatisaburo Masuda, Laboratório Integrado de Computação Científica, Núcleo de Pesquisas em Ecologia e Desenvolvimento Sócio-Ambiental de Macaé (NUPEM), Universidade Federal do Rio de Janeiro, Macaé, Brazil
| | - Nelilma C Romeiro
- Laboratório Integrado de Bioquímica Hatisaburo Masuda, Laboratório Integrado de Computação Científica, Núcleo de Pesquisas em Ecologia e Desenvolvimento Sócio-Ambiental de Macaé (NUPEM), Universidade Federal do Rio de Janeiro, Macaé, Brazil
| | - Naftaly W Githaka
- Tick Unit, International Livestock Research Institute, P.O. Box 30709, Nairobi, Kenya
| | - Satoru Konnai
- Laboratory of Infectious Diseases, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Japan
| | - Kazuhiko Ohashi
- Laboratory of Infectious Diseases, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Japan
| | - Itabajara S Vaz
- Faculdade de Veterinária e Centro de Biotecnologia do Estado do Rio Grande do Sul, Universidade Federal do Rio Grande do Sul, Brazil
| | - Carlos Logullo
- Laboratório de Química e Função de Proteínas e Peptídeos, Laboratório de Biologia Tecidual e Celular and Unidade de Experimentação Animal, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Brazil.
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