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Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.

Wu J, Samara NL, Kuraoka I, Yang W
Mol Cell 76 44-56.e3 (2019)
Related entries: 6oze, 6ozf, 6ozg, 6ozh, 6ozi, 6ozj, 6ozk, 6ozl, 6ozm, 6ozn, 6ozo, 6ozq, 6ozr, 6ozs

Cited: 18 times
EuropePMC logo PMID: 31444105

Abstract

Endonuclease V (EndoV) cleaves the second phosphodiester bond 3' to a deaminated adenosine (inosine). Although highly conserved, EndoV homologs change substrate preference from DNA in bacteria to RNA in eukaryotes. We have characterized EndoV from six different species and determined crystal structures of human EndoV and three EndoV homologs from bacteria to mouse in complex with inosine-containing DNA/RNA hybrid or double-stranded RNA (dsRNA). Inosine recognition is conserved, but changes in several connecting loops in eukaryotic EndoV confer recognition of 3 ribonucleotides upstream and 7 or 8 bp of dsRNA downstream of the cleavage site, and bacterial EndoV binds only 2 or 3 nt flanking the scissile phosphate. In addition to the two canonical metal ions in the active site, a third Mn2+ that coordinates the nucleophilic water appears necessary for product formation. Comparison of EndoV with its homologs RNase H1 and Argonaute reveals the principles by which these enzymes recognize RNA versus DNA.

Reviews - 6ozp mentioned but not cited (1)

  1. Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase-RNA complexes. Jones SP, Goossen C, Lewis SD, Delaney AM, Gleghorn ML. J Struct Biol X 6 100066 (2022)


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  1. Function and Molecular Mechanism of the DNA Damage Response in Immunity and Cancer Immunotherapy. Ye Z, Shi Y, Lees-Miller SP, Tainer JA. Front Immunol 12 797880 (2021)
  2. Regulation and functions of non-m6A mRNA modifications. Sun H, Li K, Liu C, Yi C. Nat Rev Mol Cell Biol 24 714-731 (2023)
  3. Protein-based molecular recognition tools for detecting and profiling RNA modifications. Knutson SD, Heemstra JM. Curr Opin Struct Biol 69 1-10 (2021)
  4. Flipons and small RNAs accentuate the asymmetries of pervasive transcription by the reset and sequence-specific microcoding of promoter conformation. Herbert A. J Biol Chem 299 105140 (2023)
  5. Do RNA modifications contribute to modulation of immune responses in allergic diseases? Kudrin P, Rebane A. Front Allergy 4 1277244 (2023)

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  1. Structural basis for two metal-ion catalysis of DNA cleavage by Cas12i2. Huang X, Sun W, Cheng Z, Chen M, Li X, Wang J, Sheng G, Gong W, Wang Y. Nat Commun 11 5241 (2020)
  2. In crystallo observation of three metal ion promoted DNA polymerase misincorporation. Chang C, Lee Luo C, Gao Y. Nat Commun 13 2346 (2022)
  3. Exploring C-to-G and A-to-Y Base Editing in Rice by Using New Vector Tools. Zeng D, Zheng Z, Liu Y, Liu T, Li T, Liu J, Luo Q, Xue Y, Li S, Chai N, Yu S, Xie X, Liu YG, Zhu Q. Int J Mol Sci 23 7990 (2022)
  4. Structural basis for recognition of distinct deaminated DNA lesions by endonuclease Q. Shi K, Moeller NH, Banerjee S, McCann JL, Carpenter MA, Yin L, Moorthy R, Orellana K, Harki DA, Harris RS, Aihara H. Proc Natl Acad Sci U S A 118 e2021120118 (2021)
  5. Structural and biochemical basis for DNA and RNA catalysis by human Topoisomerase 3β. Yang X, Saha S, Yang W, Neuman KC, Pommier Y. Nat Commun 13 4656 (2022)
  6. Visualization of mutagenic nucleotide processing by Escherichia coli MutT, a Nudix hydrolase. Nakamura T, Yamagata Y. Proc Natl Acad Sci U S A 119 e2203118119 (2022)
  7. Direct Immunodetection of Global A-to-I RNA Editing Activity with a Chemiluminescent Bioassay. Knutson SD, Arthur RA, Johnston HR, Heemstra JM. Angew Chem Int Ed Engl 60 17009-17017 (2021)
  8. Pan-Genome Portrait of Bacillus mycoides Provides Insights into the Species Ecology and Evolution. Fiedoruk K, Drewnowska JM, Mahillon J, Zambrzycka M, Swiecicka I. Microbiol Spectr 9 e0031121 (2021)
  9. Arabidopsis thaliana endonuclease V is a ribonuclease specific for inosine-containing single-stranded RNA. Endo M, Kim JI, Shioi NA, Iwai S, Kuraoka I. Open Biol 11 210148 (2021)
  10. Biochemical and mutational studies of an endonuclease V from the hyperthermophilic crenarchaeon Sulfolobus islandicus REY15A. Yin Y, Shi J, Zhang L, Liu Q, Gong Y, Oger P, Liu X. World J Microbiol Biotechnol 39 90 (2023)
  11. In crystallo observation of active site dynamics and transient metal ion binding within DNA polymerases. Chang C, Zhou G, Gao Y. Struct Dyn 10 034702 (2023)
  12. Visualizing the three-metal-ion-dependent cleavage of a mutagenic nucleotide. Samara NL. Proc Natl Acad Sci U S A 119 e2207180119 (2022)


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