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Solution structure of the HIV-1 integrase-binding domain in LEDGF/p75

Nature Structural & Molecular Biology volume 12, pages 526–532 (2005)Cite this article

Abstract

Lens epithelium-derived growth factor (LEDGF)/p75 is the dominant binding partner of HIV-1 integrase (IN) in human cells. We have determined the NMR structure of the integrase-binding domain (IBD) in LEDGF and identified amino acid residues essential for the interaction. The IBD is a compact right-handed bundle composed of five α-helices. Based on folding topology, the IBD is structurally related to a diverse family of α-helical proteins that includes eukaryotic translation initiation factor eIF4G and karyopherin-β. LEDGF residues essential for the interaction with IN were localized to interhelical loop regions of the bundle structure. Interaction-defective IN mutants were previously shown to cripple replication although they retained catalytic function. The initial structure determination of a host cell factor that tightly binds to a retroviral enzyme lays the groundwork for understanding enzyme-host interactions important for viral replication.

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Figure 1: NMR structure of the LEDGF IBD.
Figure 2: Mapping the IN-binding interface.
Figure 3: Asp366 is essential for the binding of full-length LEDGF to IN and for stimulation of IN activity.
Figure 4: Effect of IN mutations on binding to LEDGF in vitro.

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Protein Data Bank

References

  1. Nishizawa, Y., Usukura, J., Singh, D.P., Chylack, L.T., Jr. & Shinohara, T. Spatial and temporal dynamics of two alternatively spliced regulatory factors, lens epithelium-derived growth factor (ledgf/p75) and p52, in the nucleus. Cell Tissue Res. 305, 107–114 (2001).

    Article  CAS  PubMed  Google Scholar 

  2. Cherepanov, P. et al. HIV-1 integrase forms stable tetramers and associates with LEDGF/p75 protein in human cells. J. Biol. Chem. 278, 372–381 (2003).

    Article  CAS  PubMed  Google Scholar 

  3. Ge, H., Si, Y. & Roeder, R.G. Isolation of cDNAs encoding novel transcription coactivators p52 and p75 reveals an alternate regulatory mechanism of transcriptional activation. EMBO J. 17, 6723–6729 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Ganapathy, V., Daniels, T. & Casiano, C.A. LEDGF/p75: a novel nuclear autoantigen at the crossroads of cell survival and apoptosis. Autoimmun. Rev. 2, 290–297 (2003).

    Article  CAS  PubMed  Google Scholar 

  5. Morerio, C. et al. t(9;11)(p22;p15) with NUP98-LEDGF fusion gene in pediatric acute myeloid leukemia. Leuk. Res. 29, 467–470 (2005).

    Article  CAS  PubMed  Google Scholar 

  6. Goff, S.P. Genetic control of retrovirus susceptibility in mammalian cells. Annu. Rev. Genet. 38, 61–85 (2004).

    Article  CAS  PubMed  Google Scholar 

  7. Craigie, R. Retroviral DNA integration. In Mobile DNA II (eds. Craig, N.L., Craigie, R., Gellert, M. & Lambowitz, A.M.) 613–630 (ASM Press, Washington, DC, 2002).

    Chapter  Google Scholar 

  8. Turlure, F., Devroe, E., Silver, P.A. & Engelman, A. Human cell proteins and human immunodeficiency virus DNA integration. Front. Biosci. 9, 3187–3208 (2004).

    Article  CAS  PubMed  Google Scholar 

  9. Maertens, G. et al. LEDGF/p75 is essential for nuclear and chromosomal targeting of HIV-1 integrase in human cells. J. Biol. Chem. 278, 33528–33539 (2003).

    Article  CAS  PubMed  Google Scholar 

  10. Llano, M. et al. LEDGF/p75 determines cellular trafficking of diverse lentiviral but not murine oncoretroviral integrase proteins and is a component of functional lentiviral preintegration complexes. J. Virol. 78, 9524–9537 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Llano, M., Delgado, S., Vanegas, M. & Poeschla, E.M. LEDGF/p75 prevents proteasomal degradation of HIV-1 integrase. J. Biol. Chem. 279, 55570–55577 (2004).

    Article  CAS  PubMed  Google Scholar 

  12. Maertens, G., Vercammen, J., Debyser, Z. & Engelborghs, Y. Measuring protein-protein interactions inside living cells using single color fluorescence correlation spectroscopy. Application to human immunodeficiency virus type 1 integrase and LEDGF/p75. FASEB J. Epub ahead of print, 23 March 2005 (10.1096/fj.04–3373fje).

  13. Pluymers, W., Cherepanov, P., Schols, D., De Clercq, E. & Debyser, Z. Nuclear localization of human immunodeficiency virus type 1 integrase expressed as a fusion protein with green fluorescent protein. Virology 258, 327–332 (1999).

    Article  CAS  PubMed  Google Scholar 

  14. Cherepanov, P. et al. High-level expression of active HIV-1 integrase from a synthetic gene in human cells. FASEB J. 14, 1389–1399 (2000).

    Article  CAS  PubMed  Google Scholar 

  15. Devroe, E., Engelman, A. & Silver, P.A. Intracellular transport of human immunodeficiency virus type 1 integrase. J. Cell Sci. 116, 4401–4408 (2003).

    Article  CAS  PubMed  Google Scholar 

  16. Maertens, G., Cherepanov, P., Debyser, Z., Engelborghs, Y. & Engelman, A. Identification and characterization of a functional nuclear localization signal in the HIV-1 integrase interactor LEDGF/p75. J. Biol. Chem. 279, 33421–33429 (2004).

    Article  CAS  PubMed  Google Scholar 

  17. Mulder, L.C. & Muesing, M.A. Degradation of HIV-1 integrase by the N-end rule pathway. J. Biol. Chem. 275, 29749–29753 (2000).

    Article  CAS  PubMed  Google Scholar 

  18. Cherepanov, P., Devroe, E., Silver, P.A. & Engelman, A. Identification of an evolutionarily conserved domain in human lens epithelium-derived growth factor/transcriptional co-activator p75 (LEDGF/p75) that binds HIV-1 integrase. J. Biol. Chem. 279, 48883–48892 (2004).

    Article  CAS  PubMed  Google Scholar 

  19. Busschots, K. et al. The interaction of LEDGF/p75 with integrase is lentiviral-specific and promotes DNA binding. J. Biol. Chem. Epub ahead of print, 4 March 2005 (10.1074/jbc.M411681200).

  20. Bushman, F.D. Targeting survival: integration site selection by retroviruses and LTR-retrotransposons. Cell 115, 135–138 (2003).

    Article  CAS  PubMed  Google Scholar 

  21. Engelman, A. The ups and downs of gene expression and retroviral DNA integration. Proc. Natl. Acad. Sci. USA 102, 1275–1276 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Vanegas, M. et al. Identification of the LEDGF/p75 HIV-1 integrase-interaction domain and NLS reveals NLS-independent chromatin tethering. J. Cell Sci. 118, 1733–1743 (2005).

    Article  CAS  PubMed  Google Scholar 

  23. Qiu, C., Sawada, K., Zhang, X. & Cheng, X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nat. Struct. Biol. 9, 217–224 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Sue, S.C., Chen, J.Y., Lee, S.C., Wu, W.G. & Huang, T.H. Solution structure and heparin interaction of human hepatoma-derived growth factor. J. Mol. Biol. 343, 1365–1377 (2004).

    Article  CAS  PubMed  Google Scholar 

  25. Kamtekar, S. & Hecht, M.H. Protein Motifs. 7. The four-helix bundle: what determines a fold? FASEB J. 9, 1013–1022 (1995).

    Article  CAS  PubMed  Google Scholar 

  26. Andrade, M.A., Petosa, C., O'Donoghue, S.I., Muller, C.W. & Bork, P. Comparison of ARM and HEAT protein repeats. J. Mol. Biol. 309, 1–18 (2001).

    Article  CAS  PubMed  Google Scholar 

  27. Marcotrigiano, J. et al. A conserved HEAT domain within eIF4G directs assembly of the translation initiation machinery. Mol. Cell 7, 193–203 (2001).

    Article  CAS  PubMed  Google Scholar 

  28. Chook, Y.M. & Blobel, G. Structure of the nuclear transport complex karyopherin-β2-Ran x GppNHp. Nature 399, 230–237 (1999).

    Article  CAS  PubMed  Google Scholar 

  29. Green, J.B., Gardner, C.D., Wharton, R.P. & Aggarwal, A.K. RNA recognition via the SAM domain of Smaug. Mol. Cell 11, 1537–1548 (2003).

    Article  CAS  PubMed  Google Scholar 

  30. Wei, Z. et al. Crystal structure of human eIF3k, the first structure of eIF3 subunits. J. Biol. Chem. 279, 34983–34990 (2004).

    Article  CAS  PubMed  Google Scholar 

  31. Bogan, A.A. & Thorn, K.S. Anatomy of hot spots in protein interfaces. J. Mol. Biol. 280, 1–9 (1998).

    Article  CAS  PubMed  Google Scholar 

  32. Cherepanov, P. et al. Activity of recombinant HIV-1 integrase on mini-HIV DNA. Nucleic Acids Res. 27, 2202–2210 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Engelman, A. In vivo analysis of retroviral integrase structure and function. Adv. Virus Res. 52, 411–426 (1999).

    Article  CAS  PubMed  Google Scholar 

  34. Bouyac-Bertoia, M. et al. HIV-1 infection requires a functional integrase NLS. Mol. Cell 7, 1025–1035 (2001).

    Article  CAS  PubMed  Google Scholar 

  35. Dvorin, J.D. et al. Reassessment of the roles of integrase and the central DNA flap in human immunodeficiency virus type 1 nuclear import. J. Virol. 76, 12087–12096 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Priet, S., Navarro, J.M., Querat, G. & Sire, J. Reversion of the lethal phenotype of an HIV-1 integrase mutant virus by overexpression of the same integrase mutant protein. J. Biol. Chem. 278, 20724–20730 (2003).

    Article  CAS  PubMed  Google Scholar 

  37. Lu, R. et al. Class II integrase mutants with changes in putative nuclear localization signals are primarily blocked at a postnuclear entry step of human immunodeficiency virus type 1 replication. J. Virol. 78, 12735–12746 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Jenkins, T.M., Engelman, A., Ghirlando, R. & Craigie, R. A soluble active mutant of HIV-1 integrase: involvement of both the core and carboxyl-terminal domains in multimerization. J. Biol. Chem. 271, 7712–7718 (1996).

    Article  CAS  PubMed  Google Scholar 

  39. Fatma, N., Singh, D.P., Shinohara, T. & Chylack, L.T., Jr. Transcriptional regulation of the antioxidant protein 2 gene, a thiol-specific antioxidant, by lens epithelium-derived growth factor to protect cells from oxidative stress. J. Biol. Chem. 276, 48899–48907 (2001).

    Article  CAS  PubMed  Google Scholar 

  40. Yung, E. et al. Specificity of interaction of INI1/hSNF5 with retroviral integrases and its functional significance. J. Virol. 78, 2222–2231 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Priet, S. et al. HIV-1-associated uracil DNA glycosylase activity controls dUTP misincorporation in viral DNA and is essential to the HIV-1 life cycle. Mol. Cell 17, 479–490 (2005).

    Article  CAS  PubMed  Google Scholar 

  42. Schwartz, O., Marechal, V., Friguet, B., Arenzana-Seisdedos, F. & Heard, J.M. Antiviral activity of the proteasome on incoming human immunodeficiency virus type 1. J. Virol. 72, 3845–3850 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  43. Priet, S., Navarro, J.M., Gros, N., Querat, G. & Sire, J. Functional role of HIV-1 virion-associated uracil DNA glycosylase 2 in the correction of G:U mispairs to G:C pairs. J. Biol. Chem. 278, 4566–4571 (2003).

    Article  CAS  PubMed  Google Scholar 

  44. Hacein-Bey-Abina, S. et al. LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1. Science 302, 415–419 (2003).

    Article  CAS  PubMed  Google Scholar 

  45. Bram, R.J., Hung, D.T., Martin, P.K., Schreiber, S.L. & Crabtree, G.R. Identification of the immunophilins capable of mediating inhibition of signal transduction by cyclosporin A and FK506: roles of calcineurin binding and cellular location. Mol. Cell. Biol. 13, 4760–4769 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Hyberts, S.G. & Wagner, G. IBIS–a tool for automated sequential assignment of protein spectra from triple resonance experiments. J. Biomol. NMR 26, 335–344 (2003).

    Article  CAS  PubMed  Google Scholar 

  47. Clore, G.M. & Gronenborn, A.M. Multidimensional heteronuclear nuclear magnetic resonance of proteins. Methods Enzymol. 239, 349–363 (1994).

    Article  CAS  PubMed  Google Scholar 

  48. Ferentz, A.E. & Wagner, G. NMR spectroscopy: a multifaceted approach to macromolecular structure. Q. Rev. Biophys. 33, 29–65 (2000).

    Article  CAS  PubMed  Google Scholar 

  49. Szyperski, T., Neri, D., Leiting, B., Otting, G. & Wuthrich, K. Support of 1H NMR assignments in proteins by biosynthetically directed fractional 13C-labeling. J. Biomol. NMR 2, 323–334 (1992).

    Article  CAS  PubMed  Google Scholar 

  50. Cornilescu, G., Delaglio, F. & Bax, A. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR 13, 289–302 (1999).

    Article  CAS  PubMed  Google Scholar 

  51. Brünger, A.T. X-PLOR Version 3.851: A System for X-ray Crystallography and NMR (Yale University Press, New Haven, Connecticut, 1996).

    Google Scholar 

  52. Laskowski, R.A., Rullmannn, J.A., MacArthur, M.W., Kaptein, R. & Thornton, J.M. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8, 477–486 (1996).

    Article  CAS  PubMed  Google Scholar 

  53. Koradi, R., Billeter, M. & Wuthrich, K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51–55, 29–32 (1996).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We thank N. Vandegraaff for thoughtful discussions and comments on the manuscript and P. Dormitzer for stimulating discussion in the early phase of the project. We also thank J. Miranda, J. Al-Bassam and S. Harrison for the use of and help with the analytical ultracentrifuge. This work was supported by US National Institutes of Health grants GM47467 and AI37581 (G.W.), and AI39394 and AI62249 (A.E.).

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Authors and Affiliations

  1. Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, 44 Binney Street, Boston, 02115, Massachusetts, USA

    Peter Cherepanov, Shaila Rahman, Goedele Maertens & Alan Engelman

  2. Department of Pathology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, 02115, Massachusetts, USA

    Peter Cherepanov, Goedele Maertens & Alan Engelman

  3. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, 02115, Massachusetts, USA

    Zhen-Yu J Sun & Gerhard Wagner

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  1. Peter Cherepanov
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Correspondence to Alan Engelman.

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Supplementary information

Supplementary Fig. 1

Sedimentation equilibrium analysis of recombinant LEDGF. (PDF 292 kb)

Supplementary Fig. 2

Stereo view of an ensemble of 15 final NMR structures. (PDF 50 kb)

Supplementary Fig. 3

Structural similarity between the LEDGF IBD and HEAT repeats. (PDF 38 kb)

Supplementary Methods (PDF 4 kb)

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Cherepanov, P., Sun, ZY., Rahman, S. et al. Solution structure of the HIV-1 integrase-binding domain in LEDGF/p75. Nat Struct Mol Biol 12, 526–532 (2005). https://doi.org/10.1038/nsmb937

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