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Crystal structure of DNA cytidine deaminase ABOBEC3G catalytic deamination domain suggests a binding mode of full-length enzyme to single-stranded DNA.

Lu X, Zhang T, Xu Z, Liu S, Zhao B, Lan W, Wang C, Ding J, Cao C
J Biol Chem 290 4010-21 (2015)
Cited: 39 times
EuropePMC logo PMID: 25542899

Abstract

APOBEC3G (A3G) is a DNA cytidine deaminase (CD) that demonstrates antiviral activity against human immunodeficiency virus 1 (HIV-1) and other pathogenic virus. It has an inactive N-terminal CD1 virus infectivity factor (Vif) protein binding domain (A3G-CD1) and an actively catalytic C-terminal CD2 deamination domain (A3G-CD2). Although many studies on the structure of A3G-CD2 and enzymatic properties of full-length A3G have been reported, the mechanism of how A3G interacts with HIV-1 single-stranded DNA (ssDNA) is still not well characterized. Here, we reported a crystal structure of a novel A3G-CD2 head-to-tail dimer (in which the N terminus of the monomer H (head) interacts with the C terminus of monomer T (tail)), where a continuous DNA binding groove was observed. By constructing the A3G-CD1 structural model, we found that its overall fold was almost identical to that of A3G-CD2. We mutated the residues located in or along the groove in monomer H and the residues in A3G-CD1 that correspond to those seated in or along the groove in monomer T. Then, by performing enzymatic assays, we confirmed the reported key elements and the residues in A3G necessary to the catalytic deamination. Moreover, we identified more than 10 residues in A3G essential to DNA binding and deamination reaction. Therefore, this dimer structure may represent a structural model of full-length A3G, which indicates a possible binding mode of A3G to HIV-1 ssDNA.

Reviews - 4rov mentioned but not cited (1)

  1. New targets for HIV drug discovery. Puhl AC, Garzino Demo A, Makarov VA, Ekins S. Drug Discov Today 24 1139-1147 (2019)

Articles - 4rov mentioned but not cited (8)

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  6. Crystal Structure of a Soluble APOBEC3G Variant Suggests ssDNA to Bind in a Channel that Extends between the Two Domains. Maiti A, Myint W, Delviks-Frankenberry KA, Hou S, Kanai T, Balachandran V, Sierra Rodriguez C, Tripathi R, Kurt Yilmaz N, Pathak VK, Schiffer CA, Matsuo H. J Mol Biol 432 6042-6060 (2020)
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Reviews citing this publication (8)

  1. The APOBEC Protein Family: United by Structure, Divergent in Function. Salter JD, Bennett RP, Smith HC. Trends Biochem Sci 41 578-594 (2016)
  2. Dissecting How CD4 T Cells Are Lost During HIV Infection. Doitsh G, Greene WC. Cell Host Microbe 19 280-291 (2016)
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  6. The Role of APOBECs in Viral Replication. Xu WK, Byun H, Dudley JP. Microorganisms 8 E1899 (2020)
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  8. Insights into the Structures and Multimeric Status of APOBEC Proteins Involved in Viral Restriction and Other Cellular Functions. Chen XS. Viruses 13 497 (2021)

Articles citing this publication (22)

  1. Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity. Kouno T, Silvas TV, Hilbert BJ, Shandilya SMD, Bohn MF, Kelch BA, Royer WE, Somasundaran M, Kurt Yilmaz N, Matsuo H, Schiffer CA. Nat Commun 8 15024 (2017)
  2. Crystal structures of APOBEC3G N-domain alone and its complex with DNA. Xiao X, Li SX, Yang H, Chen XS. Nat Commun 7 12193 (2016)
  3. The double-domain cytidine deaminase APOBEC3G is a cellular site-specific RNA editing enzyme. Sharma S, Patnaik SK, Taggart RT, Baysal BE. Sci Rep 6 39100 (2016)
  4. APOBEC3H structure reveals an unusual mechanism of interaction with duplex RNA. Bohn JA, Thummar K, York A, Raymond A, Brown WC, Bieniasz PD, Hatziioannou T, Smith JL. Nat Commun 8 1021 (2017)
  5. Dimerization regulates both deaminase-dependent and deaminase-independent HIV-1 restriction by APOBEC3G. Morse M, Huo R, Feng Y, Rouzina I, Chelico L, Williams MC. Nat Commun 8 597 (2017)
  6. 1.92 Angstrom Zinc-Free APOBEC3F Catalytic Domain Crystal Structure. Shaban NM, Shi K, Li M, Aihara H, Harris RS. J Mol Biol 428 2307-2316 (2016)
  7. Cytidine deaminase efficiency of the lentiviral viral restriction factor APOBEC3C correlates with dimerization. Adolph MB, Ara A, Feng Y, Wittkopp CJ, Emerman M, Fraser JS, Chelico L. Nucleic Acids Res 45 3378-3394 (2017)
  8. Computational Model and Dynamics of Monomeric Full-Length APOBEC3G. Gorle S, Pan Y, Sun Z, Shlyakhtenko LS, Harris RS, Lyubchenko YL, Vuković L. ACS Cent Sci 3 1180-1188 (2017)
  9. APOBEC3G Interacts with ssDNA by Two Modes: AFM Studies. Shlyakhtenko LS, Dutta S, Banga J, Li M, Harris RS, Lyubchenko YL. Sci Rep 5 15648 (2015)
  10. Molecular Interactions of a DNA Modifying Enzyme APOBEC3F Catalytic Domain with a Single-Stranded DNA. Fang Y, Xiao X, Li SX, Wolfe A, Chen XS. J Mol Biol 430 87-101 (2018)
  11. Structural Analysis of the Active Site and DNA Binding of Human Cytidine Deaminase APOBEC3B. Hou S, Silvas TV, Leidner F, Nalivaika EA, Matsuo H, Kurt Yilmaz N, Schiffer CA. J Chem Theory Comput 15 637-647 (2019)
  12. Moloney leukemia virus 10 (MOV10) inhibits the degradation of APOBEC3G through interference with the Vif-mediated ubiquitin-proteasome pathway. Chen C, Ma X, Hu Q, Li X, Huang F, Zhang J, Pan T, Xia J, Liu C, Zhang H. Retrovirology 14 56 (2017)
  13. Nanoscale Characterization of Interaction of APOBEC3G with RNA. Pan Y, Sun Z, Maiti A, Kanai T, Matsuo H, Li M, Harris RS, Shlyakhtenko LS, Lyubchenko YL. Biochemistry 56 1473-1481 (2017)
  14. Structural basis of substrate specificity in human cytidine deaminase family APOBEC3s. Hou S, Lee JM, Myint W, Matsuo H, Kurt Yilmaz N, Schiffer CA. J Biol Chem 297 100909 (2021)
  15. DNA mutagenic activity and capacity for HIV-1 restriction of the cytidine deaminase APOBEC3G depend on whether DNA or RNA binds to tyrosine 315. Polevoda B, Joseph R, Friedman AE, Bennett RP, Greiner R, De Zoysa T, Stewart RA, Smith HC. J Biol Chem 292 8642-8656 (2017)
  16. MiR-141-3p and miR-200a-3p are involved in Th17 cell differentiation by negatively regulating RARB expression. Bahmani L, Baghi M, Peymani M, Javeri A, Ghaedi K. Hum Cell 34 1375-1387 (2021)
  17. Characterization of an A3G-VifHIV-1-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host-Pathogen Complexes. Kaake RM, Echeverria I, Kim SJ, Von Dollen J, Chesarino NM, Feng Y, Yu C, Ta H, Chelico L, Huang L, Gross J, Sali A, Krogan NJ. Mol Cell Proteomics 20 100132 (2021)
  18. Characterization of the Deamination Coupled with Sliding along DNA of Anti-HIV Factor APOBEC3G on the Basis of the pH-Dependence of Deamination Revealed by Real-Time NMR Monitoring. Kamba K, Nagata T, Katahira M. Front Microbiol 7 587 (2016)
  19. Insight into dynamics of APOBEC3G protein in complexes with DNA assessed by high speed AFM. Pan Y, Shlyakhtenko LS, Lyubchenko YL. Nanoscale Adv 1 4016-4024 (2019)
  20. Two different kinds of interaction modes of deaminase APOBEC3A with single-stranded DNA in solution detected by nuclear magnetic resonance. Liu Y, Lan W, Wang C, Cao C. Protein Sci 31 443-453 (2022)
  21. Computational Investigation of APOBEC3H Substrate Orientation and Selectivity. Hix MA, Cisneros GA. J Phys Chem B 124 3903-3908 (2020)
  22. ICBS 2017 in Shanghai-Illuminating Life with Chemical Innovation. Zhang Q, Zhang J, Gavathiotis E. ACS Chem Biol 13 1111-1122 (2018)


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