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Solution structure of the N-terminal zinc binding domain of HIV-1 integrase

Nature Structural Biology volume 4, pages 567–577 (1997)Cite this article

An Erratum to this article was published on 01 October 1997

Abstract

The solution structure of the N-terminal zinc binding domain (residues 1–55; IN1–55) of HIV-1 integrase has been solved by NMR spectroscopy. IN1–55 is dimeric, and each monomer comprises four helices with the zinc tetrahedrally coordinated to His 12, His 16, Cys 40 and Cys 43. IN1–55 exists in two interconverting conformational states that differ with regard to the coordination of the two histidine side chains to zinc. The different histidine arrangements are associated with large conformational differences in the polypeptide backbone (residues 9–18) around the coordinating histidines. The dimer interface is predominantly hydrophobic and is formed by the packing of the N-terminal end of helix 1, and helices 3 and 4. The monomer fold is remarkably similar to that of a number of helical DMA binding proteins containing a helix-turn-helix (HTH) motif with helices 2 and 3 of IN1–55 corresponding to the HTH motif. In contrast to the DNA binding proteins where the second helix of the HTH motif is employed for DNA recognition, IN1–55 uses this helix for dimerization.

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References

  1. Whitcomb, J.M. & Hughes, S.H. Retroviral reverse transcription and integration: progress and problems. Annu. Rev. Cell Biol. 8, 275–306 (1992).

    Article  CAS  PubMed  Google Scholar 

  2. Goff, S.P. Genetics of retroviral integration. Annu. Rev. Genet. 26, 527–544 (1992).

    Article  CAS  PubMed  Google Scholar 

  3. Vink, C. & Plasterk, R.H.A. The human immunodeficiency virus integrase protein. Trends. Genet. 9, 433–438 (1993).

    Article  CAS  PubMed  Google Scholar 

  4. Katz, R.A. & Skalka, A.M. The retroviral enzymes. Annu. Rev. Biochem. 63, 133–173 (1994).

    Article  CAS  PubMed  Google Scholar 

  5. Engelman, A., Mizuuchi, K. & Craigie, R. HIV-1 DNA integration: mechanism of viral DNA cleavage and DNA strand transfer. Cell 67, 1211–1221 (1991).

    Article  CAS  PubMed  Google Scholar 

  6. Bushman, F.D., Engelman, A., Palmer, I., Wingfield, P.T. & Craigie, R. Domains of integrase protein of human immunodeficiency virus type-1 responsible for polynucleotidyl transfer and zinc binding. Proc. Natl. Acad. Sci. USA 90, 3428–3432 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Chow, S.A., Vincent, K.A., Ellison, V. & Brown, P.O. Reversal of integration and DNA splicing mediated by integrase of human immunodeficiency virus. Science 255, 723–726 (1992).

    Article  CAS  PubMed  Google Scholar 

  8. Vink, C., Oude Groeneger, A.M. & Plasterk, R.H.A. Identification of the catalytic and DNA-binding region of the human immunodeficiency virus type I integrase protein. Nucleic Acids Res. 21, 1419–1425 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Engelman, A., Hickman, A.B. & Craigie, R. The core and carboxyl-terminal domains of the integrase protein of human immunodeficiency virus type 1 each contribute to nonspecific DNA binding. J. Virol. 68, 5911–5917 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Woerner, A.M. & Marcus-Sekura, C.J. Characterization of a DNA binding domain in the C-terminus of HIV-1 integrase by deletion mutagenesis. Nucleic Acids Res. 21, 3507–3511 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Dyda, F., Hickman, A.B., Jenkins T.M., Engelman, A., Craigie, R. & Davies, D.R. Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transf erases. Science 266, 1981–1986 (1994).

    Article  CAS  PubMed  Google Scholar 

  12. Bujacz, G., Jaskolski, M., Alexandratos, J., Wlodawer, A., Merkel, G., Katz, R.A. & Skalka, A.M. High-resolution structure of the catalytic domain of avian sarcoma virus integrase. J. Mol. Biol. 253, 333–346 (1995).

    Article  CAS  PubMed  Google Scholar 

  13. Yang, W. & Steitz, T.A. Recombining the structures of HIV integrase, RuvC and RNase H. Structure 3, 131–134 (1995).

    Article  CAS  PubMed  Google Scholar 

  14. Rice, P., Craigie, R. & Davies, D.R. Retroviral integrases and their cousins. Curr. Opin. Struct. Biol. 6, 76–83 (1996).

    Article  CAS  PubMed  Google Scholar 

  15. Lodi, P.J., Ernst, J.A., Kuszewski, J., Hickman, A.B., Engelman, A., Craigie, R., Clore, G.M. & Gronenborn, A.M. Solution structure of the DNA binding domain of HIV-1 integrase. Biochemistry 34, 9826–9833 (1995).

    Article  CAS  PubMed  Google Scholar 

  16. Eijkelenboom, A.P., Lutzke, R.A., Boelens, R., Plasterk, R.H.A., Kaptein, R. & Hard, K. The DNA-binding domain of HIV-1 integrase has an SH3-like fold. Nature Struct. Biol. 2, 807–810 (1995).

    Article  CAS  PubMed  Google Scholar 

  17. Burke, C.J., Sanyal, G., Bruner, M.W., Ryan, J.A., LaFemina, R.L., Robbins, H.L., Zeft, A.S., Middaugh, C.R. & Cordingley, M.G. Structural implications of spectroscopic characterization of a putative zinc finger peptide from HIV-1 integrase. J. Biol. Chem. 267, 9639–9644 (1992).

    Article  CAS  PubMed  Google Scholar 

  18. Haugan, I.R., Nilsen, B.M., Worland, S., Olsen, L. & Helland, D.E. Characterization of the DNA-binding activity of HIV-1 integrase using a filter binding assay. Biochem. Biophys. Res. Commun. 217, 802–810 (1995).

    Article  CAS  PubMed  Google Scholar 

  19. Zheng, R., Jenkins, T.M. & Craigie, R. Zinc folds the N-terminal domain of HIV-1 integrase, promotes multimerization, and enhances catalytic activity. Proc. Natl. Acad. Sci. U.S.A. 93, 13659–13664 (1996)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Engelman, A., Bushman, F.D. & Craigie, R. Identification of discrete functional domains of HIV-1 integrase and their organization within an active multimeric complex. EMBO J. 12, 3269–3275 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. van Gent, D.C., Vink, C., Groeneger, A.A. & Plasterk, R.H.A. Complementation between HIV integrase proteins mutated in different domains. EMBO J. 12, 3261–3267 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Ellison, V., Gerton, J., Vincent, K.A. & Brown, P.O. An essential interaction between distinct domains of HIV-1 integrase mediates assembly of the active multimer. J. Biol. Chem. 270, 3320–3326 (1995).

    Article  CAS  PubMed  Google Scholar 

  23. Bizub-Bender, D., Kulkosky, J. & Skalka, A.M. Monoclonal antibodies against HIV type 1 integrase: clues to molecular structure. AIDS Research and Human Retroviruses 10, 1105–1115 (1994).

    Article  CAS  PubMed  Google Scholar 

  24. Clore, G.M., Driscoll, P.C., Wingfield, P.T. & Gronenborn, A.M. Analysis of backbone dynamics of interleukin-1β using two-dimensional inverse detected heteronuclear 15N-1H NMR spectroscopy. Biochemistry 29, 7387–7401 (1990).

    Article  CAS  PubMed  Google Scholar 

  25. Lide, D.R. Handbook of Chemistry and Physics, p. 6–10, CRC Press, Boca Raton (1993).

    Google Scholar 

  26. Pelton, J.G., Torchia, D.A., Meadow, M.D. & Roseman, S. Tautomeric states of the active-site histidines of phophorylated and unphophorylated IIIGlC, a signal transducing protein from Escherichia coli, using two-dimensional heteronuclear NMR techniques. Protein Sci. 2, 543–558 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Clore, G.M. & Gronenborn, A.M. Structures of larger proteins in solution: three- and four-dimensional heteronuclear NMR spectroscopy. Science 252, 1390–1399 (1991).

    Article  CAS  PubMed  Google Scholar 

  28. Bax, A. & Grzesiek, S. Methodological advances in protein NMR Acct. Chem. Res. 26, 131–138 (1993).

    Article  CAS  Google Scholar 

  29. Gronenborn, A.M. & Clore, G.M. Structures of protein complexes by multidimensional heteronuclear magnetic resonance spectroscopy. CRC Crit Rev. Biochem. Mol. Biol. 30, 351–385 (1995).

    Article  CAS  Google Scholar 

  30. Bax, A. et al. Measurement of homo- and hetero-nuclear J couplings from quantitative J correlation. Meth. Enzymol. 239, 79–106 (1994).

    Article  CAS  Google Scholar 

  31. Eisenberg, D. & McLaghlan, D. Solvation energy in protein folding and binding. Nature 319, 199–203 (1986).

    Article  CAS  PubMed  Google Scholar 

  32. Junius, F.K., MacKay, J.P., Bubb, W.A., Jensen, S.A., Weiss, M.A.S. & King, G.F. Nuclear magnetic resonance characterization of the Jun Leucine zipper domain: unusual properties of coiled-coil interfacial polar residues. Biochemistry 34, 6164–6174.

    Article  CAS  PubMed  Google Scholar 

  33. Khan, E., Mack, J.P.G., Katz, R.A., Kulkosky, J. & Skalka, A.M. Retroviral integrase domains: DNA binding and the recognition of LTR sequences. Nucl. Acids Res. 19, 851–860 (1991).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Otwinowski, Z. et al. Crystal structure of the trp repressor/operator complex at atomic resoution. Nature 335, 3321–329 (1988).

    Google Scholar 

  35. Xu, W., Rould, M.A., Jun, S., Desplan, C. & Pabo, C.O. Crystal structure of a paired domain-DNA complex at 2.5 Å resolution reveals structural basis for Pax developmental mutations. Cell 80, 639–650 (1995).

    Article  CAS  PubMed  Google Scholar 

  36. Yang, W. & Steitz, T.A. Crystal structure of the site-specific recombinase γδ resolvase complexed with a 34 bp cleavage site. Cell 82, 193–207 (1995).

    Article  CAS  PubMed  Google Scholar 

  37. Baikalov, I. et al. Structure of the Escherichia coli response regulator NarL. Biochemistry 35, 11053–11061 (1996).

    Article  CAS  PubMed  Google Scholar 

  38. Kissinger, C., Liu, B., Martin-Blanco, E., Kornberg, T. & Pabo, C.O. Crystal structure of the engrailed homeodomain-DNA complex at 2.8 Å resolution: a framework for understanding homeodomain-DNA interactions. Cell 63, 579–590 (1990).

    Article  CAS  PubMed  Google Scholar 

  39. 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 

  40. Jenkins, T.M., Hickman, A.B., Dyda, F., Ghirlando, R., Davies, D.R. & Craigie, R. Catalytic domain of human immunodeficiency virus type 1 integrase: identification of a soluble mutant by systematic replacement of hydrophobic residues. Proc. Natl. Acad. Sci. USA 92, 6057–6061.

    Article  CAS  Google Scholar 

  41. Hickman, A.B., Dyda, F. & Craigie, R. Heterogeneity in recombinant HIV-1 integrase corrected by site-directed mutagenesis: the identification and elimination of a protease cleavage site. Prot. Engng. 10, in the press.

    Article  CAS  Google Scholar 

  42. Vink, C. et al. Analysis of the junctions between human immunodeficiency virus type 1 proviral DNA and human DNA. J. Virol. 64, 5626–5627 (1990).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Adachi, A. et al. Production of acquired immunodeficiency syndrome-associated retrovirus in human and non-human cells transfected with an infectious molecular clone. J. Virol. 59, 284–291 (1986).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Delaglio, F. et al. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomolec. NMR 6, 277–293 (1995).

    Article  CAS  Google Scholar 

  45. Garrett, D.S., Powers, R., Gronenborn, A.M. & Clore, G.M. A common sense approach to peak picking in two-, three- and four-dimensional spectra using automatic computer analysis of contour diagrams. J. Magn. Reson. 95, 214–220 (1991).

    CAS  Google Scholar 

  46. Hu, J.-S., Grzesiek, S. & Bax, A. Two-dimensional NMR methods for determining χ1 angles of aromatic residues in proteins from thee-bond JC′Cγ and JNCγ couplings. J. Am. Chem. Soc. 119, 1803–1804 (1997).

    Article  CAS  Google Scholar 

  47. Hu, J.-S. & Bax, A. Determination of Φ and χ1 angles in proteins from 13C-13C three-bond J couplings measured by three-dimensional heteronuclear NMR. How planar is the peptide bond. J. Am. Chem. Soc. in the press.

  48. Hu, J.-S. & Bax, A. x, A. χ1 angle information from a simple two-dimensional NMR experiment which identifies trans 3JNCγ couplings in isotopically enriched proteins. J. Biomol. NMR in press (1997).

    Google Scholar 

  49. Tjandra, N., Kuboniwa, H., Ren, H. & Bax, A. Rotational dynamics of calcium-free calmodulin studied by 15N-NMR relaxation measurements Eur. J. Biochem. 230, 1014–1024 (1995).

    Article  CAS  PubMed  Google Scholar 

  50. Nilges, M. A calculational strategy for the structure determination of symmetric dimers by 1H NMR. Proteins Struct. Funct. Genet. 17, 297–309 (1993).

    Article  CAS  PubMed  Google Scholar 

  51. Nilges, M., Clore, G.M. & Gronenborn, A.M. 1H-NMR stereospecific assignments by conformational database searches. Biopolymers 29, 813–822 (1990).

    Article  CAS  PubMed  Google Scholar 

  52. Nilges, M., Clore, G.M. & Gronenborn, A.M. Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations. FEBS Lett. 229, 317–324 (1988).

    Article  CAS  PubMed  Google Scholar 

  53. Brünger, A.T. X-PLOR Version 3.1: A system for X-ray crystallography and NMR. (Yale University Press, New Haven, Connecticut; 1993).

  54. Garrett, D.S. et al. The impact of direct refinement against three-bond HN-CαH coupling constants on protein structure determination by NMR. J. Magn. Reson. Series B 104, 99–103 (1994).

    Article  CAS  Google Scholar 

  55. Kuszewski, J., Qin, J., Gronenborn, A.M. & Clore, G.M. The impact of direct refinement against 13Cα and 13Cβ chemical shifts on protein structure determination by NMR. J. Magn. Reson. Series B 106, 92–96 (1995).

    Article  CAS  Google Scholar 

  56. Kuszewski, J., Gronenborn, A.M. & Clore, G.M. Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases. Prot. Sci. 5, 1067–1080 (1996).

    Article  CAS  Google Scholar 

  57. Kuszewski, J., Gronenborn, A.M. & Clore, G.M. Improvements and extensions in the conformational database potential for the refinement of NMR and X-ray structures of proteins and nucleic acids. J. Magn. Reson. 125, 171–177 (1997).

    Article  CAS  PubMed  Google Scholar 

  58. Stein, E.G., Rice, L.M. & Brünger, A.T. Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation. J. Magn. Reson. 124, 154–164 (1997).

    Article  CAS  PubMed  Google Scholar 

  59. Nilges, M., Gronenborn, A.M., Brünger, A.T. & Clore, G.M. Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints: application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. Prot. Engng. 2, 27–38 (1988).

    Article  CAS  Google Scholar 

  60. Omichinski, J., Clore, G.M., Appella, E., Sakaguchi, K. & Gronenborn, A.M. High resolution three-dimensional solution structure of a single zinc finger from a human enhancer binding protein in solution. Biochemistry 29, 9324–9334. (1990).

    Article  CAS  PubMed  Google Scholar 

  61. Koradi, R., Billeter, M. & Wüthrich, K. MOLMOL a program for display and analysis of macromolecular structures. J. Mol. Graphics 14, 52–55 (1996).

    Article  Google Scholar 

  62. Nicholls, A., Sharp, K.A. & Honig, B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281–296 (1991).

    Article  CAS  PubMed  Google Scholar 

  63. Jones, T.A. & O - The Manual. Version 5.8.1, University of Uppsala, Sweden (1992).

    Google Scholar 

  64. Brooks, B.R. et al. CHARMM: a program for macromolecular energy minimization and dynamics calculations. J. Comput. Chem. 4, 187–217 (1993).

    Article  Google Scholar 

  65. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: a program to check stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283–291 (1993).

    Article  CAS  Google Scholar 

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  1. Laboratories of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892-0520, USA

    Mengli Cai, Michael Caffrey, G. Marius Clore & Angela M. Gronenborn

  2. Molecular Biology, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892-0520, USA

    Ronglan Zheng & Robert Craigie

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Cai, M., Zheng, R., Caffrey, M. et al. Solution structure of the N-terminal zinc binding domain of HIV-1 integrase. Nat Struct Mol Biol 4, 567–577 (1997). https://doi.org/10.1038/nsb0797-567

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