4R5P

Crystal structure of HIV-1 reverse transcriptase (RT) with DNA and a nucleoside triphosphate mimic alpha-carboxy nucleoside phosphonate inhibitor

Summary for 4R5P

• Entry DOI: 10.2210/pdb4r5p/pdb
• Related: 3V4I
• Related PRD ID: PRD_900003
• Descriptor: HIV-1 reverse transcriptase, p66 subunit, HIV-1 reverse transcriptase, p51 subunit, 5'-D(*TP*GP*GP*AP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*G)-3', ... (9 entities in total)
• Functional Keywords: zidovudine, rt-dna complex, aids, dna-directed dna polymerase, rn lipoprotein, hiv, metal-binding, alpha-cnp, ribonuclease h, rnase h, a-cnp, multifunctional enzyme, nucleotidyltransferase, rna-directed polymerase, transferase, hydrolase-dna-inhibitor complex, hydrolase/dna/inhibitor
• Biological source: Human immunodeficiency virus type 1 (HIV-1); More
• Cellular location: Gag-Pol polyprotein: Host cell membrane; Lipid-anchor. Matrix protein p17: Virion membrane; Lipid- anchor . Capsid protein p24: Virion . Nucleocapsid protein p7: Virion . Reverse transcriptase/ribonuclease H: Virion . Integrase: Virion : P03366 P03366
• Total number of polymer chains: 8
• Total formula weight: 259540.17

Authors

Das, K.,Martinez, S.E.,Arnold, E. (deposition date: 2014-08-21, release date: 2015-03-11, Last modification date: 2024-10-30)

Primary citation

Balzarini, J.,Das, K.,Bernatchez, J.A.,Martinez, S.E.,Ngure, M.,Keane, S.,Ford, A.,Maguire, N.,Mullins, N.,John, J.,Kim, Y.,Dehaen, W.,Vande Voorde, J.,Liekens, S.,Naesens, L.,Gotte, M.,Maguire, A.R.,Arnold, E.
Alpha-carboxy nucleoside phosphonates as universal nucleoside triphosphate mimics.
Proc.Natl.Acad.Sci.USA, 112:3475-3480, 2015

PubMed Abstract: Polymerases have a structurally highly conserved negatively charged amino acid motif that is strictly required for Mg(2+) cation-dependent catalytic incorporation of (d)NTP nucleotides into nucleic acids. Based on these characteristics, a nucleoside monophosphonate scaffold, α-carboxy nucleoside phosphonate (α-CNP), was designed that is recognized by a variety of polymerases. Kinetic, biochemical, and crystallographic studies with HIV-1 reverse transcriptase revealed that α-CNPs mimic the dNTP binding through a carboxylate oxygen, two phosphonate oxygens, and base-pairing with the template. In particular, the carboxyl oxygen of the α-CNP acts as the potential equivalent of the α-phosphate oxygen of dNTPs and two oxygens of the phosphonate group of the α-CNP chelate Mg(2+), mimicking the chelation by the β- and γ-phosphate oxygens of dNTPs. α-CNPs (i) do not require metabolic activation (phosphorylation), (ii) bind directly to the substrate-binding site, (iii) chelate one of the two active site Mg(2+) ions, and (iv) reversibly inhibit the polymerase catalytic activity without being incorporated into nucleic acids. In addition, α-CNPs were also found to selectively interact with regulatory (i.e., allosteric) Mg(2+)-dNTP-binding sites of nucleos(t)ide-metabolizing enzymes susceptible to metabolic regulation. α-CNPs represent an entirely novel and broad technological platform for the development of specific substrate active- or regulatory-site inhibitors with therapeutic potential.

PubMed: 25733891
DOI: 10.1073/pnas.1420233112

Experimental method

X-RAY DIFFRACTION (2.894 Å)