6ASW

STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE (RT) TERNARY COMPLEX WITH A DOUBLE STRANDED DNA AND AN INCOMING D4TTP AT PH 9.0

Summary for 6ASW

• Entry DOI: 10.2210/pdb6asw/pdb
• Descriptor: HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT, HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT, DNA (27-MER), ... (8 entities in total)
• Functional Keywords: ternary n site complex, d4t (stavudine), dna template/primer, crosslink, viral protein, viral protein-dna complex, transferase-dna complex, transferase/dna
• Biological source: Human immunodeficiency virus type 1 group M subtype B (isolate BH10) (HIV-1); More
• Total number of polymer chains: 8
• Total formula weight: 263617.69

Authors

Martinez, S.E.,Das, K.,Arnold, E. (deposition date: 2017-08-25, release date: 2018-08-15, Last modification date: 2023-10-04)

Primary citation

Martinez, S.E.,Bauman, J.D.,Das, K.,Arnold, E.
Structure of HIV-1 reverse transcriptase/d4TTP complex: Novel DNA cross-linking site and pH-dependent conformational changes.
Protein Sci., 28:587-597, 2019

PubMed Abstract: Stavudine (d4T, 2',3'-didehydro-2',3'-dideoxythymidine) was one of the first chain-terminating nucleoside analogs used to treat HIV infection. We present the first structure of the active, triphosphate form of d4T (d4TTP) bound to a catalytic complex of HIV-1 RT/dsDNA template-primer. We also present a new strategy for disulfide (S-S) chemical cross-linking between N of a modified adenine at the second overhang base to I63C in the fingers subdomain of RT. The cross-link site is upstream of the duplex-binding region of RT, however, the structure is very similar to published RT structures with cross-linking to Q258C in the thumb, which suggests that cross-linking at either site does not appreciably perturb the RT/DNA structures. RT has a catalytic maximum at pH 7.5. We determined the X-ray structures of the I63C-RT/dsDNA/d4TTP cross-linked complexes at pH 7, 7.5, 8, 8.5, 9, and 9.5. We found small (~0.5 Å), pH-dependent motions of the fingers subdomain that folds in to form the dNTP-binding pocket. We propose that the pH-activity profile of RT relates to this motion of the fingers. Due to side effects of neuropathy and lipodystrophy, use of d4T has been stopped in most countries, however, chemical modification of d4T might lead to the development of a new class of nucleoside analogs targeting RNA and DNA polymerases.

PubMed: 30499174
DOI: 10.1002/pro.3559

Experimental method

X-RAY DIFFRACTION (2.605 Å)