4R5P

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.894 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Alpha-carboxy nucleoside phosphonates as universal nucleoside triphosphate mimics.

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.

(2015) Proc.Natl.Acad.Sci.USA 112: 3475-3480

  • DOI: 10.1073/pnas.1420233112
  • Also Cited By: 5I3U

  • 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 ...

    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.


    Related Citations: 
    • HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism.
      Das, K.,Martinez, S.E.,Bauman, J.D.,Arnold, E.
      (2012) Nat.Struct.Mol.Biol. 19: 253
    • Structures of HIV-1 RT-RNA/DNA ternary complexes with dATP and nevirapine reveal conformational flexibility of RNA/DNA: insights into requirements for RNase H cleavage.
      Das, K.,Martinez, S.E.,Bandwar, R.P.,Arnold, E.
      (2014) Nucleic Acids Res. 42: 8125
    • High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: strategic flexibility explains potency against resistance mutations.
      Das, K.,Bauman, J.D.,Clark, A.D.,Frenkel, Y.V.,Lewi, P.J.,Shatkin, A.J.,Hughes, S.H.,Arnold, E.
      (2008) Proc.Natl.Acad.Sci.USA 105: 1466
    • Structural basis for the role of the K65R mutation in HIV-1 reverse transcriptase polymerization, excision antagonism, and tenofovir resistance.
      Das, K.,Bandwar, R.P.,White, K.L.,Feng, J.Y.,Sarafianos, S.G.,Tuske, S.,Tu, X.,Clark, A.D.,Boyer, P.L.,Hou, X.,Gaffney, B.L.,Jones, R.A.,Miller, M.D.,Hughes, S.H.,Arnold, E.
      (2009) J.Biol.Chem. 284: 35092
    • Structural basis of HIV-1 resistance to AZT by excision.
      Tu, X.,Das, K.,Han, Q.,Bauman, J.D.,Clark, A.D.,Hou, X.,Frenkel, Y.V.,Gaffney, B.L.,Jones, R.A.,Boyer, P.L.,Hughes, S.H.,Sarafianos, S.G.,Arnold, E.
      (2010) Nat.Struct.Mol.Biol. 17: 1202


    Organizational Affiliation

    Rega Institute for Medical Research and jan.balzarini@rega.kuleuven.be.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 reverse transcriptase, p66 subunit
A, C
556Human immunodeficiency virus type 1 group M subtype B (isolate BH10)Mutation(s): 3 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03366
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HIV-1 reverse transcriptase, p51 subunit
B, D
428Human immunodeficiency virus type 1 group M subtype B (isolate BH10)Mutation(s): 1 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03366
Entity ID: 3
MoleculeChainsLengthOrganism
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'T,E27synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
5'-D(*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*G)-3'P,F21synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC

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Download CCD File 
B, D
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
3JY
Query on 3JY

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Download CCD File 
A, C
[(1R)-2-methoxy-1-{[(1S,3R)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclopentyl]oxy}-2-oxoethyl]phosphonic acid
C13 H19 N2 O8 P
VZWKSNLNIFIGPO-VDDIYKPWSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MRG
Query on MRG
F, P
DNA LINKINGC13 H20 N5 O7 P SDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.894 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 89.905α = 90.00
b = 133.529β = 97.81
c = 139.218γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
MOLREPphasing
HKL-2000data scaling
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-04-01
    Type: Database references