Structure Characterization of Escherichia coli Pseudouridine Kinase PsuK
Pseudouridine (Ψ) is one of the most abundant RNA modifications in cellular RNAs that post-transcriptionally impact many aspects of RNA. However, the metabolic fate of modified RNA nucleotides has long been a question. A pseudouridine kinase (PsuK) and a pseudouridine monophosphate glycosylase (PsuG...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-06-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2022.926099/full |
| _version_ | 1828728424826404864 |
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| author | Xiaojia Li Xiaojia Li Kangjie Li Wenting Guo Yan Wen Yan Wen Chunyan Meng Baixing Wu |
| author_facet | Xiaojia Li Xiaojia Li Kangjie Li Wenting Guo Yan Wen Yan Wen Chunyan Meng Baixing Wu |
| author_sort | Xiaojia Li |
| collection | DOAJ |
| description | Pseudouridine (Ψ) is one of the most abundant RNA modifications in cellular RNAs that post-transcriptionally impact many aspects of RNA. However, the metabolic fate of modified RNA nucleotides has long been a question. A pseudouridine kinase (PsuK) and a pseudouridine monophosphate glycosylase (PsuG) in Escherichia coli were first characterized as involved in pseudouridine degradation by catalyzing the phosphorylation of pseudouridine to pseudouridine 5′-phosphate (ΨMP) and further hydrolyzing 5′-ΨMP to produce uracil and ribose 5′-phosphate. Recently, their homolog proteins in eukaryotes were also identified, which were named PUKI and PUMY in Arabidopsis. Here, we solved the crystal structures of apo-EcPsuK and its binary complex with Ψ or N1-methyl-pseudouridine (m1Ψ). The structure of EcPsuK showed a homodimer conformation assembled by its β-thumb region. EcPsuK has an appropriate binding site with a series of hydrophilic and hydrophobic interactions for Ψ. Moreover, our complex structure of EcPsuK-m1Ψ suggested the binding pocket has an appropriate capacity for m1Ψ. We also identified the monovalent ion-binding site and potential ATP-binding site. Our studies improved the understanding of the mechanism of Ψ turnover. |
| first_indexed | 2024-04-12T14:15:13Z |
| format | Article |
| id | doaj.art-4fb3a89509d343c6b03b19031b94f756 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-12T14:15:13Z |
| publishDate | 2022-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-4fb3a89509d343c6b03b19031b94f7562022-12-22T03:29:45ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2022-06-011310.3389/fmicb.2022.926099926099Structure Characterization of Escherichia coli Pseudouridine Kinase PsuKXiaojia Li0Xiaojia Li1Kangjie Li2Wenting Guo3Yan Wen4Yan Wen5Chunyan Meng6Baixing Wu7Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, RNA Biomedical Institute, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, ChinaDepartment of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, ChinaDepartment of Biopharmaceutical Technology, School of Life Sciences, Guangzhou University, Guangzhou, ChinaGuangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, RNA Biomedical Institute, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, ChinaGuangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, RNA Biomedical Institute, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, ChinaBreast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, ChinaGuangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, RNA Biomedical Institute, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, ChinaGuangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, RNA Biomedical Institute, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, ChinaPseudouridine (Ψ) is one of the most abundant RNA modifications in cellular RNAs that post-transcriptionally impact many aspects of RNA. However, the metabolic fate of modified RNA nucleotides has long been a question. A pseudouridine kinase (PsuK) and a pseudouridine monophosphate glycosylase (PsuG) in Escherichia coli were first characterized as involved in pseudouridine degradation by catalyzing the phosphorylation of pseudouridine to pseudouridine 5′-phosphate (ΨMP) and further hydrolyzing 5′-ΨMP to produce uracil and ribose 5′-phosphate. Recently, their homolog proteins in eukaryotes were also identified, which were named PUKI and PUMY in Arabidopsis. Here, we solved the crystal structures of apo-EcPsuK and its binary complex with Ψ or N1-methyl-pseudouridine (m1Ψ). The structure of EcPsuK showed a homodimer conformation assembled by its β-thumb region. EcPsuK has an appropriate binding site with a series of hydrophilic and hydrophobic interactions for Ψ. Moreover, our complex structure of EcPsuK-m1Ψ suggested the binding pocket has an appropriate capacity for m1Ψ. We also identified the monovalent ion-binding site and potential ATP-binding site. Our studies improved the understanding of the mechanism of Ψ turnover.https://www.frontiersin.org/articles/10.3389/fmicb.2022.926099/fullcrystal structruepseudouridine (Ψ)kinasenucleosideN1-methyl-pseudouridine |
| spellingShingle | Xiaojia Li Xiaojia Li Kangjie Li Wenting Guo Yan Wen Yan Wen Chunyan Meng Baixing Wu Structure Characterization of Escherichia coli Pseudouridine Kinase PsuK Frontiers in Microbiology crystal structrue pseudouridine (Ψ) kinase nucleoside N1-methyl-pseudouridine |
| title | Structure Characterization of Escherichia coli Pseudouridine Kinase PsuK |
| title_full | Structure Characterization of Escherichia coli Pseudouridine Kinase PsuK |
| title_fullStr | Structure Characterization of Escherichia coli Pseudouridine Kinase PsuK |
| title_full_unstemmed | Structure Characterization of Escherichia coli Pseudouridine Kinase PsuK |
| title_short | Structure Characterization of Escherichia coli Pseudouridine Kinase PsuK |
| title_sort | structure characterization of escherichia coli pseudouridine kinase psuk |
| topic | crystal structrue pseudouridine (Ψ) kinase nucleoside N1-methyl-pseudouridine |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2022.926099/full |
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