1R0A

Crystal structure of HIV-1 reverse transcriptase covalently tethered to DNA template-primer solved to 2.8 angstroms

Summary for 1R0A

• Entry DOI: 10.2210/pdb1r0a/pdb
• Related: 1HYS 1N5Y 1N6Q
• Descriptor: 5'-D(*A*TP*GP*CP*AP*TP*CP*GP*GP*CP*GP*CP*TP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*GP*GP*T)-3', 5'-D(*C*CP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*AP*GP*CP*GP*CP*CP*GP*(2DA))-3', Reverse transcriptase, ... (10 entities in total)
• Functional Keywords: hiv-1, transferase, immune system, dna, transferase-immune system-dna complex, transferase/immune system/dna
• Biological source: Human immunodeficiency virus 1; More
• Cellular location: Matrix protein p17: Virion (Potential). Capsid protein p24: Virion (Potential). Nucleocapsid protein p7: Virion (Potential). Reverse transcriptase/ribonuclease H: Virion (Potential). Integrase: Virion (Potential): P03366 P03366
• Total number of polymer chains: 6
• Total formula weight: 176881.90

Authors

Tuske, S.,Ding, J.,Arnold, E. (deposition date: 2003-09-19, release date: 2004-08-03, Last modification date: 2021-10-27)

Primary citation

Peletskaya, E.N.,Kogon, A.A.,Tuske, S.,Arnold, E.,Hughes, S.H.
Nonnucleoside inhibitor binding affects the interactions of the fingers subdomain of human immunodeficiency virus type 1 reverse transcriptase with DNA.
J.Virol., 78:3387-3397, 2004

PubMed Abstract: Site-directed photoaffinity cross-linking experiments were performed by using human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) mutants with unique cysteine residues at several positions (i.e., positions 65, 67, 70, and 74) in the fingers subdomain of the p66 subunit. Since neither the introduction of the unique cysteine residues into the fingers nor the modification of the SH groups of these residues with photoaffinity cross-linking reagents caused a significant decrease in the enzymatic activities of RT, we were able to use this system to measure distances between specific positions in the fingers domain of RT and double-stranded DNA. HIV-1 RT is quite flexible. There are conformational changes associated with binding of the normal substrates and nonnucleoside RT inhibitors (NNRTIs). Cross-linking was used to monitor intramolecular movements associated with binding of an NNRTI either in the presence or in the absence of an incoming deoxynucleoside triphosphate (dNTP). Binding an incoming dNTP at the polymerase active site decreased the efficiency of cross-linking but caused only modest changes in the preferred positions of cross-linking. This finding suggests that the fingers of p66 are closer to an extended template in the "open" configuration of the enzyme with the fingers away from the active site than in the closed configuration with the fingers in direct contact with the incoming dNTP. NNRTI binding caused increased cross-linking in experiments with diazirine reagents (especially with a diazirine reagent with a longer linker) and a moderate shift in the preferred sites of interaction with the template. Cross-linking occurred closer to the polymerase active site for RTs modified at positions 70 and 74. The effects of NNRTI binding were more pronounced in the absence of a bound dNTP; pretreatment of HIV-1 RT with an NNRTI reduced the effect of dNTP binding. These observations can be explained if the binding of NNRTI causes a decrease in the flexibility in the fingers subdomain of RT-NNRTI complex and a decrease in the distance from the fingers to the template extension.

PubMed: 15016861
DOI: 10.1128/JVI.78.7.3387-3397.2004

Experimental method

X-RAY DIFFRACTION (2.8 Å)