5J2P

HIV-1 reverse transcriptase in complex with DNA that has incorporated EFdA-MP at the P-(post-translocation) site and a second EFdA-MP at the N-(pre-translocation) site

5J2P の概要

• エントリーDOI: 10.2210/pdb5j2p/pdb
• 関連するPDBエントリー: 5J2M 5J2N 5J2Q
• 分子名称: reverse transcriptase, p66 domain, reverse transcriptase, p51 domain, DNA (5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(6FM)P*(6FM))-3'), ... (7 entities in total)
• 機能のキーワード: hiv-1, reverse transcriptase, rt, dna, double stranded dna, dsdna, efda, 4'-ethynyl-2-fluoro-2'-deoxyadenosine, efda-monophosphate, efda-mp, inhibitors, nrti, tdrti, translocation defective, p site, n site, pre-translocation, post-translocation, transferase-dna complex, transferase/dna
• 由来する生物種: Human immunodeficiency virus type 1 group M subtype B (isolate HXB2) (HIV-1); 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 131945.55

構造登録者

Salie, Z.L.,Kirby, K.A.,Sarafianos, S.G. (登録日: 2016-03-29, 公開日: 2016-08-03, 最終更新日: 2025-07-02)

主引用文献

Salie, Z.L.,Kirby, K.A.,Michailidis, E.,Marchand, B.,Singh, K.,Rohan, L.C.,Kodama, E.N.,Mitsuya, H.,Parniak, M.A.,Sarafianos, S.G.
Structural basis of HIV inhibition by translocation-defective RT inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA).
Proc.Natl.Acad.Sci.USA, 113:9274-9279, 2016

PubMed Abstract: 4'-Ethynyl-2-fluoro-2'-deoxyadenosine (EFdA) is the most potent nucleoside analog inhibitor of HIV reverse transcriptase (RT). It retains a 3'-OH yet acts as a chain-terminating agent by diminishing translocation from the pretranslocation nucleotide-binding site (N site) to the posttranslocation primer-binding site (P site). Also, facile misincorporation of EFdA-monophosphate (MP) results in difficult-to-extend mismatched primers. To understand the high potency and unusual inhibition mechanism of EFdA, we solved RT crystal structures (resolutions from 2.4 to 2.9 Å) that include inhibition intermediates (i) before inhibitor incorporation (catalytic complex, RT/DNA/EFdA-triphosphate), (ii) after incorporation of EFdA-MP followed by dT-MP (RT/DNAEFdA-MP(P)• dT-MP(N) ), or (iii) after incorporation of two EFdA-MPs (RT/DNAEFdA-MP(P)• EFdA-MP(N) ); (iv) the latter was also solved with EFdA-MP mismatched at the N site (RT/DNAEFdA-MP(P)• EFdA-MP(*N) ). We report that the inhibition mechanism and potency of EFdA stem from interactions of its 4'-ethynyl at a previously unexploited conserved hydrophobic pocket in the polymerase active site. The high resolution of the catalytic complex structure revealed a network of ordered water molecules at the polymerase active site that stabilize enzyme interactions with nucleotide and DNA substrates. Finally, decreased translocation results from favorable interactions of primer-terminating EFdA-MP at the pretranslocation site and unfavorable posttranslocation interactions that lead to observed localized primer distortions.

PubMed: 27489345
DOI: 10.1073/pnas.1605223113

実験手法

X-RAY DIFFRACTION (2.53 Å)