5J2Q

HIV-1 reverse transcriptase in complex with DNA that has incorporated a mismatched EFdA-MP at the N-(pre-translocation) site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.789 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis of HIV inhibition by translocation-defective RT inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA).

Salie, Z.L.Kirby, K.A.Michailidis, E.Marchand, B.Singh, K.Rohan, L.C.Kodama, E.N.Mitsuya, H.Parniak, M.A.Sarafianos, S.G.

(2016) Proc.Natl.Acad.Sci.USA 113: 9274-9279

  • DOI: 10.1073/pnas.1605223113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 4'-Ethynyl-2-fluoro-2'-deoxyadenosine (EFdA) is the most potent nucleoside analog inhibitor of HIV reverse transcriptase (RT). It retains a 3'-OH yet acts as a chain-terminating agent by diminishing translocation from the pretranslocation nucleotide- ...

    4'-Ethynyl-2-fluoro-2'-deoxyadenosine (EFdA) is the most potent nucleoside analog inhibitor of HIV reverse transcriptase (RT). It retains a 3'-OH yet acts as a chain-terminating agent by diminishing translocation from the pretranslocation nucleotide-binding site (N site) to the posttranslocation primer-binding site (P site). Also, facile misincorporation of EFdA-monophosphate (MP) results in difficult-to-extend mismatched primers. To understand the high potency and unusual inhibition mechanism of EFdA, we solved RT crystal structures (resolutions from 2.4 to 2.9 Å) that include inhibition intermediates (i) before inhibitor incorporation (catalytic complex, RT/DNA/EFdA-triphosphate), (ii) after incorporation of EFdA-MP followed by dT-MP (RT/DNAEFdA-MP(P)• dT-MP(N) ), or (iii) after incorporation of two EFdA-MPs (RT/DNAEFdA-MP(P)• EFdA-MP(N) ); (iv) the latter was also solved with EFdA-MP mismatched at the N site (RT/DNAEFdA-MP(P)• EFdA-MP(*N) ). We report that the inhibition mechanism and potency of EFdA stem from interactions of its 4'-ethynyl at a previously unexploited conserved hydrophobic pocket in the polymerase active site. The high resolution of the catalytic complex structure revealed a network of ordered water molecules at the polymerase active site that stabilize enzyme interactions with nucleotide and DNA substrates. Finally, decreased translocation results from favorable interactions of primer-terminating EFdA-MP at the pretranslocation site and unfavorable posttranslocation interactions that lead to observed localized primer distortions.


    Organizational Affiliation

    Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219.,Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261; Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA 15213;,Division of Infectious Diseases, Tohoku University and Tohoku Medical Megabank Organization, Sendai 980-8575, Japan;,Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; Department of Infectious Diseases, Kumamoto University Graduate School of Medical Sciences, Kumamoto 860-8556, Japan; Department of Hematology, Kumamoto University Graduate School of Medical Sciences, Kumamoto 860-8556, Japan; Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan; Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo 162-8655, Japan;,C. S. Bond Life Sciences Center, Department of Biochemistry, University of Missouri, Columbia, MO 65211;,C. S. Bond Life Sciences Center, Department of Biochemistry, University of Missouri, Columbia, MO 65211; C. S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO 65211; sarafianoss@missouri.edu.,C. S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO 65211;




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 reverse transcriptase p66 subunit
A
560Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)Mutation(s): 2 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04585
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HIV-1 reverse transcriptase p51 domain
B
440Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)Mutation(s): 1 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04585
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(6FM)P*(6FM))-3')P22Human immunodeficiency virus 1
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (27-MER)T27Human immunodeficiency virus 1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6FM
Query on 6FM

Download SDF File 
Download CCD File 
P, T
2'-deoxy-4'-ethynyl-2-fluoroadenosine 5'-(dihydrogen phosphate)
C12 H13 F N5 O6 P
MAIQRKKYFLNZMS-QRPMWFLTSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
6FM
Query on 6FM
P
DNA linkingC12 H13 F N5 O6 P

--

MRG
Query on MRG
P
DNA LINKINGC13 H20 N5 O7 P SDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.789 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.212 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 165.557α = 90.00
b = 170.512β = 90.00
c = 102.235γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI076119
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI099284
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI100890
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI112417
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI120860
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM103368
University of MissouriUnited StatesMizzou Advantage

Revision History 

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-08-17
    Type: Database references
  • Version 1.2: 2016-08-31
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Advisory, Author supporting evidence, Database references, Derived calculations