4R5P: Crystal Structure Of Hiv-1 Reverse Transcriptase (rt) With Dna And A Nucleoside Triphosphate Mimic Alpha-carboxy Nucleoside Phosphonate Inhibitor

Citation:
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, alpha-carboxy nucleoside phosphonate (alpha-CNP), was designed that is recognized by a variety of polymerases. Kinetic, biochemical, and crystallographic studies with HIV-1 reverse transcriptase revealed that alpha-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 alpha-CNP acts as the potential equivalent of the alpha-phosphate oxygen of dNTPs and two oxygens of the phosphonate group of the alpha-CNP chelate Mg(2+), mimicking the chelation by the beta- and gamma-phosphate oxygens of dNTPs. alpha-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, alpha-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. alpha-CNPs represent an entirely novel and broad technological platform for the development of specific substrate active- or regulatory-site inhibitors with therapeutic potential.
PDB ID: 4R5PDownload
MMDB ID: 127657
PDB Deposition Date: 2014/8/21
Updated in MMDB: 2015/04
Experimental Method:
x-ray diffraction
Resolution: 2.89  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 4R5P: tetrameric; determined by author and by software (PISA)
Molecular Components in 4R5P
Label Count Molecule
Proteins (2 molecules)
1
Hiv-1 Reverse Transcriptase, P66 Subunit
Molecule annotation
1
Hiv-1 Reverse Transcriptase, P51 Subunit
Molecule annotation
Nucleotides(2 molecules)
1
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'
Molecule annotation
1
5'-d(*cp*ap*gp*tp*cp*cp*cp*tp*gp*tp*tp*cp*gp*gp*(mrg) P*cp*gp*cp*cp*g)-3'
Molecule annotation
Chemicals (5 molecules)
1
3
2
1
3
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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