Abstract
We describe the crystal structures of the RNA dimerization initiation sites (DIS) of HIV-1 subtypes A and B. Both molecules adopt a hairpin conformation, with loop sequences consisting of 272-AGGUGCACA-280 and 272-AAGCGCGCA-280, respectively. This includes a six-base self-complementary stretch (underlined) that allows homodimerization through the formation of a loop–loop, or 'kissing-loop', complex. The DISs for the two sequences have identical conformations, and the two interacting hairpins show a perfect coaxial alignment. The conserved purines, A272 and R273, are stacked in a bulged-out conformation and symmetrically join the upward and downward strands of each hairpin by crossing the helix major groove. There is good agreement between these structures and previous results from chemical probing in solution, as well as with differences in magnesium dependence for dimerization. The overall shape of the kissing-loop complex is very similar to that of the previously determined subtype A DIS duplex form. Unexpectedly, the purine R273 is the only base seen at a different position and is responsible for the difference in topology between the two forms. We propose that the transition from kissing-loop duplex could occur by a recombination mechanism based on symmetrical chain cleavage at R273 of each hairpin and subsequent cross-religation, rather than by base-pair melting and subsequent reannealing.
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References
Bender, W. & Davidson, N. Cell 7, 595–607 (1976).
Panganiban, A. & Fiore, D. Science 241, 1064–1069 (1988).
Hu, W.S. & Temin, H.M. Proc. Natl Acad. Sci. USA 87, 1556–1560 (1990).
Skripkin, E., Paillart, J.C., Marquet, R., Ehresmann, B. & Ehresmann, C. Proc. Natl Acad. Sci. USA 91, 4945–4949 (1994).
Paillart, J.C., Marquet, R., Skripkin, E., Ehresmann, B. & Ehresmann, C. J. Biol. Chem. 269, 27486–27493 (1994).
Laughrea, M. & Jetté, L. Biochemistry 33, 13464–13474 (1994).
Paillart, J.-C., Marquet, R., Skripkin, E., Ehresmann, C. & Ehresmann, B. Biochimie 78, 639–653 (1996).
Muriaux, D., Fossé, P. & Paoletti, J. Biochemistry 35, 5075–5082 (1996).
Laughrea, M. & Jetté, L. Biochemistry 35, 1589–1598 (1996).
Feng, Y.-X., Fu, W., Winter, A.J., Levin, J.G. & Rein, A. J. Virol. 69, 2486–2490 (1995).
Polge, E., Darlix, J., Paoletti, J. & Fossé, P. J. Mol. Biol. 300, 41–56 (2000).
Fu, W., Gorelick, R.J. & Rein, A. J. Virol. 68, 5013–5018 (1994).
Fu, W. & Rein, A. J. Virol 67, 5443–5449 (1993).
Muriaux, D., Rocquigny, H.D., Roques, B.P. & Paoletti, J. J. Biol. Chem. 271, 33686–33692 (1996).
Ennifar, E. et al. Structure 7, 1439–1449 (1999).
Westhof, E., Dumas, P. & Moras, D. J. Mol. Biol. 184, 119–145 (1985).
Ban, N., Nissen, P., Hansen, J., Moore, P.B. & Steitz, T.A. Science 289, 905–919 (2000).
Lee, A.J. & Crothers, D.M. Structure 6, 993–1005. (1998).
Mujeeb, A., Clever, J.L., Billeci, T.M., James, T.L. & Parslow, T.G. Nat. Struct. Biol. 5, 432–436 (1998).
Paillart, J.C., Westhof, E., Ehresmann, C., Ehresmann, B. & Marquet, R. J. Mol. Biol. 270, 36–49 (1997).
Jossinet, F. et al. RNA 5, 1222–1234 (1999).
Lodmell, J.S. et al. Antisense Nucleic Acid Drug Dev 8, 517–529 (1998).
Korber, B. et al. in Human retroviruses and AIDS (ed. Los Alamos National Laboratory) 1–199 (Theoretical Biology and Biophysics Group T-10, Los Alamos, New Mexico; 1997).
Lodmell, J.S., Ehresmann, C., Ehresmann, B. & Marquet, R. RNA 6, 1267–1276 (2000).
Zeiler, B.N. & Simons, R.W. in RNA Structure and function (eds. Simons, R.W. & Grunberg-Manago, M.) 437–464 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York; 1998).
Lund, A.H., Mikkelsen, J.G., Schmidt, J., Duch, M. & Pedersen, F.S. J. Virol. 73, 9614–9618 (1999).
Balakrishnan, M., Fay, P.J. & Bambara, R.A. J. Biol. Chem. 276, 36482–36492 (2001).
Chetverina, H.V., Demidenko, A.A., Ugarov, V.I. & Chetverin, A.B. FEBS Lett. 450, 89–94 (1999).
Yusupov, M. et al. Acta Crystallogr. D 54, 281–284 (1998).
Navaza, J. Acta Crystallogr. A 50, 157–163 (1994).
Brünger, A.T. et al. Acta Crystallogr. D 54, 905–921 (1998).
Scott, W.G., Murray, J.B., Arnold, J.R.P., Stoddard, B.L. & Klug, A. Science 274, 2065–2069 (1996).
Rupert, P.B. & Ferre-D'Amare, A.R. Nature 410, 780–786. (2001).
Read, R. Acta Crystallogr. A 42, 140–149 (1986).
Acknowledgements
This work was supported by funds from the French ANRS. We are indebted to the staff of beam line BM30 (FIP) at ESRF for their excellent and friendly support, to N. Potier for mass spectrometry analysis, and to G. Bec, F. Jossinet, R. Marquet, J.C. Paillart, P. Romby and E. Westhof for fruitful discussions.
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Ennifar, E., Walter, P., Ehresmann, B. et al. Crystal structures of coaxially stacked kissing complexes of the HIV-1 RNA dimerization initiation site. Nat Struct Mol Biol 8, 1064–1068 (2001). https://doi.org/10.1038/nsb727
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DOI: https://doi.org/10.1038/nsb727
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