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Zheng S, Zheng C, Chen S, Guo J, Huang L, Huang Z, Xu S, Wu Y, Li S, Lin J, You Y, Hu F. Structural and biochemical characterization of active sites mutant in human inorganic pyrophosphatase. Biochim Biophys Acta Gen Subj 2024; 1868:130594. [PMID: 38428647 DOI: 10.1016/j.bbagen.2024.130594] [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: 09/27/2023] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 03/03/2024]
Abstract
Inorganic pyrophosphatases (PPases) are enzymes that catalyze the conversion of inorganic pyrophosphate (PPi) into phosphate (Pi). Human inorganic pyrophosphatase 1 (Hu-PPase) exhibits high expression levels in a variety of tumors and plays roles in cell proliferation, apoptosis, invasion and metastasis, making it a promising prognostic biomarker and a target for cancer therapy. Despite its widespread presence, the catalytic mechanism of Hu-PPase in humans remains inadequately understood. The signature motif amino acid sequence (DXDPXD) within the active sites of PPases is preserved across different species. In this research, an enzymatic activity assay revealed that mutations led to a notable reduction in enzymatic function, although the impact of the four amino acids on the activity of the pocket varied. To investigate the influence of these residues on the substrate binding and enzymatic function of PPase, the crystal structure of the Hu-PPase-ED quadruple mutant (D116A/D118A/P119A/D121A) was determined at 1.69 Å resolution. The resulting structure maintained a barrel-like shape similar to that of the wild-type, albeit lacking Mg2+ ions. Molecular docking analysis demonstrated a decreased ability of Hu-PPase-ED to bind to PPi. Further, molecular dynamics simulation analysis indicated that the mutation rendered the loop of Mg2+ ion-binding residues less stable. Therefore, the effect on enzyme activity did not result from a change in the gross protein structure but rather from a mutation that abolished the Mg2+-coordinating groups, thereby eliminating Mg2+ binding and leading to the loss of enzyme activity.
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Affiliation(s)
- Shuping Zheng
- Public Technology Service Center, Fujian Medical University, Fuzhou, China
| | - Chenhua Zheng
- Experiment Teaching Center of Basic Medical Sciences, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Sishi Chen
- Public Technology Service Center, Fujian Medical University, Fuzhou, China
| | - Jianpeng Guo
- Department of Pharmacology, School of Pharmacy, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Drug Target Discovery and Structural and Functional Research, Fujian Medical University, Fuzhou, China
| | - Lirui Huang
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Zhenhong Huang
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Sunting Xu
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Yihan Wu
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Shunfa Li
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Junjin Lin
- Public Technology Service Center, Fujian Medical University, Fuzhou, China
| | - Yiqing You
- Key Laboratory of Diagnostic Medicine Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Fen Hu
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.
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Issa AA, Ibraheem HH, El-Sayed DS. Computational innovation of in situ metallic elements with zirconia as a novel possible carrier for chemotherapeutic medication. J Mol Model 2023; 30:14. [PMID: 38148383 DOI: 10.1007/s00894-023-05815-x] [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: 11/08/2023] [Accepted: 12/19/2023] [Indexed: 12/28/2023]
Abstract
CONTEXT Electronic sustainable behavior on the material surface and in situ metal configuration were accompted with some metal atoms like Li, Na, and K elements. Metal-doped ZrO2 crystal exported modified characteristics related to electronic conduction and exhibited some dynamic modification around the surface of the metal oxide. Computational perturbations were considered to discuss the modification behavior in addition to the studied Li, Na, and K metals. Optimization of the three doping systems was achieved followed by generating DOS and electronic band structure maps. A dynamic simulation was performed with temperature over 2000 k: the presence of the metal on the surface and prediction of its ZrO2 inclusion leading to access adsorption behavior, besides generating predictive designed models described the adsorption affinity on the solid-state surface. It cannot be neglected the importance of various metals as a main role in chemotherapy. Molecular docking investigation was considered to predict the binding behavior of the studied metal ZrO2 carrier system as an anticancer agent. Also, docking affinity was helpful in comparing the active sites binding for the studied metals, resulting in a notable binding affinity for both Li- and Na-zirconia incorporation. METHODS The program PWSCF, which is a component of the quantum ESPRESSO suite for quantum simulation of materials, was used to construct geometric systems. The generalized gradient approximation in the Perdew-Burke-Ernzerhof (GGA/PBE) function with D3 correction (Becke-Jonson damping) was applied to the exchange-correlation energy. As the last step in the DFT postulation and design, adsorption locator annealing was carried out on the convergent models using the Materials Studio simulation package. The main roles played by metal atoms are in protein binding and the suppression of bio-active regions. For the docking process, the protein was produced using AutoDock 4.2 and Discovery Studio software in accordance with the usual methodology. Chimera and Discovery Studio were used to examine the docking data that was processed after generating specific grid box dimensions for 7BTN.
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Affiliation(s)
- Ali Abdullah Issa
- Department of Applied Sciences, University of Technology, Baghdad, Iraq
| | - Hiba H Ibraheem
- Department of Applied Sciences, University of Technology, Baghdad, Iraq
| | - Doaa S El-Sayed
- Chemistry Department, Faculty of Science, Alexandria University, Baghdad Street, Moharam Bey, P.O. Box 21511, Alexandria, Egypt.
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Wang S, Wei J, Li S, Luo Y, Li Y, Wang X, Shen W, Luo D, Liu D. PPA1, an energy metabolism initiator, plays an important role in the progression of malignant tumors. Front Oncol 2022; 12:1012090. [PMID: 36505776 PMCID: PMC9733535 DOI: 10.3389/fonc.2022.1012090] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 11/07/2022] [Indexed: 11/27/2022] Open
Abstract
Inorganic pyrophosphatase (PPA1) encoded by PPA1 gene belongs to Soluble Pyrophosphatases (PPase) family and is expressed widely in various tissues of Homo sapiens, as well as significantly in a variety of malignancies. The hydrolysis of inorganic pyrophosphate (PPi) to produce orthophosphate (Pi) not only dissipates the negative effects of PPi accumulation, but the energy released by this process also serves as a substitute for ATP. PPA1 is highly expressed in a variety of tumors and is involved in proliferation, invasion, and metastasis during tumor development, through the JNK/p53, Wnt/β-catenin, and PI3K/AKT/GSK-3β signaling pathways. Because of its remarkable role in tumor development, PPA1 may serve as a biological target for adjuvant therapy of tumor malignancies. Further, PPA1 is a potential biomarker to predict survival in patients with cancer, where the assessment of its transcriptional regulation can provide an in-depth understanding. Herein, we describe the signaling pathways through which PPA1 regulates malignant tumor progression and provide new insights to establish PPA1 as a biomarker for tumor diagnosis.
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Affiliation(s)
- Shuying Wang
- Department of Oncology, The Third Affiliated Hospital of Zunyi Medical University (The First People’s Hospital of Zunyi), Zunyi, China,College of Clinical Medicine, Zunyi Medical University, Zunyi, China
| | - Jianmei Wei
- Department of Clinical Pharmacy, The Third Affiliated Hospital of Zunyi Medical University (The First People' s Hospital of Zunyi), Zunyi, China
| | - Shunwei Li
- Department of Oncology, The Third Affiliated Hospital of Zunyi Medical University (The First People’s Hospital of Zunyi), Zunyi, China
| | - Yuyin Luo
- Department of Oncology, The Third Affiliated Hospital of Zunyi Medical University (The First People’s Hospital of Zunyi), Zunyi, China,College of Clinical Medicine, Zunyi Medical University, Zunyi, China
| | - Yifei Li
- College of Clinical Medicine, Jining Medical University, Jining, China
| | - Xianglin Wang
- Department of Oncology, The Third Affiliated Hospital of Zunyi Medical University (The First People’s Hospital of Zunyi), Zunyi, China,College of Clinical Medicine, Zunyi Medical University, Zunyi, China
| | - Wenzhi Shen
- Key Laboratory of Precision Oncology in Universities of Shandong, Institute of Precision Medicine, Jining Medical University, Jining, China,*Correspondence: Daishun Liu, ; Dehong Luo, ; Wenzhi Shen,
| | - Dehong Luo
- Department of Oncology, The Third Affiliated Hospital of Zunyi Medical University (The First People’s Hospital of Zunyi), Zunyi, China,*Correspondence: Daishun Liu, ; Dehong Luo, ; Wenzhi Shen,
| | - Daishun Liu
- College of Clinical Medicine, Zunyi Medical University, Zunyi, China,*Correspondence: Daishun Liu, ; Dehong Luo, ; Wenzhi Shen,
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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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Zhao A, Shen J, Ding Y, Sheng M, Zuo M, Lv H, Wang J, Shen Y, Wang H, Sun L. Long-read sequencing identified a novel nonsense and a de novo missense of PPA2 in trans in a Chinese patient with autosomal recessive infantile sudden cardiac failure. Clin Chim Acta 2021; 519:163-171. [PMID: 33826954 DOI: 10.1016/j.cca.2021.03.029] [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: 02/21/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND AND AIMS Biallelic missense variants in PPA2 gene cause infantile sudden cardiac failure (SCFI; OMIM #617222) characterized by sudden cardiac failure, sudden cardiac death in infants. Here, we present an unusual survivor with one inherited plus one de novo variant in PPA2. Since next-generation sequencing (NGS) fails to resolve variant phasing, which require long-read sequencing to clarify the diagnosis. MATERIALS AND METHODS Whole exome and Sanger sequencing were initially performed to identify the causative variants. PCR-based short tandem repeats (STRs) analysis and long-read single molecule real-time (SMRT) sequencing were further implemented for paternity testing and variant phasing. Pathogenicity evaluation of the biallelic variants in PPA2 was conducted according to the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) guidelines based on VarSome. RESULTS Whole exome and Sanger sequencing revealed two variants in PPA2, with one novel nonsense variant (c.524C > G; p.Ser175*) inherited from the mother and one de novo missense variant (c.379C > T; p.Arg127Cys). PCR-based STRs analysis verified the paternity. And long-read SMRT sequencing phased the two variants in trans and identified the paternal origin of the de novo variant. The genetic diagnosis clarified the genetic etiology of the proband and assisted in patient management and counseling. CONCLUSION We identified a rare combination of one inherited plus one de novo variant of PPA2 in a patient with autosomal recessive SCFI, which expanded the mutation spectrum of PPA2 and demonstrated the power of target long-read sequencing to make up the diagnostic gap of prevailing NGS.
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Affiliation(s)
- Arman Zhao
- Department of Clinical Laboratory, Children's Hospital of Soochow University, 92 Zhongnan Street, Suzhou Industrial Park, Suzhou 215025, Jiangsu, China.
| | - Jie Shen
- Department of Cardiology, Children's Hospital of Soochow University, 92 Zhongnan Street, Suzhou Industrial Park, Suzhou 215025, Jiangsu, China.
| | - Yueyue Ding
- Department of Cardiology, Children's Hospital of Soochow University, 92 Zhongnan Street, Suzhou Industrial Park, Suzhou 215025, Jiangsu, China.
| | - Mao Sheng
- Department of Radiology, Children's Hospital of Soochow University, 92 Zhongnan Street, Suzhou Industrial Park, Suzhou 215025, Jiangsu, China.
| | - Mengying Zuo
- Department of Cardiology, Children's Hospital of Soochow University, 92 Zhongnan Street, Suzhou Industrial Park, Suzhou 215025, Jiangsu, China.
| | - Haitao Lv
- Department of Cardiology, Children's Hospital of Soochow University, 92 Zhongnan Street, Suzhou Industrial Park, Suzhou 215025, Jiangsu, China.
| | - Jian Wang
- Department of Pediatric Surgery, Children's Hospital of Soochow University, 92 Zhongnan Street, Suzhou Industrial Park, Suzhou 215025, Jiangsu, China.
| | - Yiping Shen
- Department of Genetics and Metabolism, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, Guangxi, China; Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, United States; Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, United States.
| | - Hongying Wang
- Department of Clinical Laboratory, Children's Hospital of Soochow University, 92 Zhongnan Street, Suzhou Industrial Park, Suzhou 215025, Jiangsu, China; Department of Clinical Laboratory, Children's Hospital of Wujiang District, Suzhou, 169 Park Road, Wujiang District, Suzhou 215234, Jiangsu, China.
| | - Ling Sun
- Department of Cardiology, Children's Hospital of Soochow University, 92 Zhongnan Street, Suzhou Industrial Park, Suzhou 215025, Jiangsu, China.
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