Structural basis of HIV-1 resistance to AZT by excision

Nat Struct Mol Biol. 2010 Oct;17(10):1202-9. doi: 10.1038/nsmb.1908. Epub 2010 Sep 19.


Human immunodeficiency virus (HIV-1) develops resistance to 3'-azido-2',3'-deoxythymidine (AZT, zidovudine) by acquiring mutations in reverse transcriptase that enhance the ATP-mediated excision of AZT monophosphate from the 3' end of the primer. The excision reaction occurs at the dNTP-binding site, uses ATP as a pyrophosphate donor, unblocks the primer terminus and allows reverse transcriptase to continue viral DNA synthesis. The excision product is AZT adenosine dinucleoside tetraphosphate (AZTppppA). We determined five crystal structures: wild-type reverse transcriptase-double-stranded DNA (RT-dsDNA)-AZTppppA; AZT-resistant (AZTr; M41L D67N K70R T215Y K219Q) RT-dsDNA-AZTppppA; AZTr RT-dsDNA terminated with AZT at dNTP- and primer-binding sites; and AZTr apo reverse transcriptase. The AMP part of AZTppppA bound differently to wild-type and AZTr reverse transcriptases, whereas the AZT triphosphate part bound the two enzymes similarly. Thus, the resistance mutations create a high-affinity ATP-binding site. The structure of the site provides an opportunity to design inhibitors of AZT-monophosphate excision.

MeSH terms

  • Adenosine Triphosphate / metabolism
  • Amino Acid Substitution
  • Binding Sites / drug effects
  • Crystallography, X-Ray
  • DNA, Viral / biosynthesis
  • Deoxyribonucleotides / metabolism
  • Dideoxynucleotides / metabolism
  • Drug Design
  • Drug Resistance, Viral / genetics
  • Drug Resistance, Viral / physiology*
  • Genes, rev
  • HIV Reverse Transcriptase / chemistry*
  • HIV Reverse Transcriptase / genetics
  • HIV-1 / drug effects*
  • HIV-1 / enzymology
  • HIV-1 / genetics
  • Models, Molecular
  • Mutation, Missense
  • Point Mutation
  • Protein Conformation
  • Reverse Transcriptase Inhibitors / pharmacology*
  • Structure-Activity Relationship
  • Thymine Nucleotides / metabolism
  • Zidovudine / analogs & derivatives
  • Zidovudine / metabolism
  • Zidovudine / pharmacology*


  • AZTp4A
  • DNA, Viral
  • Deoxyribonucleotides
  • Dideoxynucleotides
  • Reverse Transcriptase Inhibitors
  • Thymine Nucleotides
  • Zidovudine
  • zidovudine triphosphate
  • Adenosine Triphosphate
  • reverse transcriptase, Human immunodeficiency virus 1
  • HIV Reverse Transcriptase

Associated data

  • PDB/3KLE
  • PDB/3KLF
  • PDB/3KLG
  • PDB/3KLH
  • PDB/3KLI