Albany 2001

category image Biomolecular
SUNY at Albany
June 19-23, 2001

HIV-1 Polypurine Tract RNA/DNA Decamer Crystal Structure With an Unusual Sugar Conformation

The 15-base pair polypurine tract (PPT) of HIV-1 serves as the initiation site for synthesis of the second or (+) strand, which with the first or (-) strand will be incorporated into the host. During reverse transcription in vivo the PPT exists as an RNA/DNA hybrid. It is believed that this hybrid sequence has some unusual structure that causes the RNase H domain of reverse transcriptase to stop degrading the first (-) strand and to initiate second strand synthesis. The 1.15 Å atomic resolution crystal structure of a RNA/DNA decamer sequence, encompassing the 5' end of the PPT, provides a closeup view of this end of the tract. The sequence r-(c-a-a-a-g-a-a-a-a-g)/ d-(C-T-T-T-T-G-T-T-T-G) crystallized in two space groups as well as with two cations, Mg and Ca. These varying crystal environments, along with high resolution data, allowed us to solve this structure using two different crystallographic techniques molecular replacement and ab initio direct methods. An unusual intercalation between decamers in one space group will be discussed, as well as a sugar switch at sugar 2 on the RNA strand.

Mary L. Kopka, Gye Won Han, Laurence Lavelle, Ho Leung Ng and Richard E. Dickerson

Molecular Biology Institute, University of California, Los Angeles, CA 90095
e-mail: kopka@mbi.ucla.edu, fax: (310) 267-1957, ph.: (310) 206-8278