5TXP

STRUCTURE OF Q151M complex (A62V, V75I, F77L, F116Y, Q151M) mutant HIV-1 REVERSE TRANSCRIPTASE (RT) TERNARY COMPLEX WITH A DOUBLE STRANDED DNA AND AN INCOMING DDATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Insights into HIV Reverse Transcriptase Mutations Q151M and Q151M Complex That Confer Multinucleoside Drug Resistance.

Das, K.Martinez, S.E.Arnold, E.

(2017) Antimicrob. Agents Chemother. 61: --

  • DOI: 10.1128/AAC.00224-17
  • Primary Citation of Related Structures:  5TXL, 5TXM, 5TXN, 5TXO

  • PubMed Abstract: 
  • HIV-1 reverse transcriptase (RT) is targeted by multiple drugs. RT mutations that confer resistance to nucleoside RT inhibitors (NRTIs) emerge during clinical use. Q151M and four associated mutations, A62V, V75I, F77L, and F116Y, were detected in pat ...

    HIV-1 reverse transcriptase (RT) is targeted by multiple drugs. RT mutations that confer resistance to nucleoside RT inhibitors (NRTIs) emerge during clinical use. Q151M and four associated mutations, A62V, V75I, F77L, and F116Y, were detected in patients failing therapies with dideoxynucleosides (didanosine [ddI], zalcitabine [ddC]) and/or zidovudine (AZT). The cluster of the five mutations is referred to as the Q151M complex (Q151Mc), and an RT or virus containing Q151Mc exhibits resistance to multiple NRTIs. To understand the structural basis for Q151M and Q151Mc resistance, we systematically determined the crystal structures of the wild-type RT/double-stranded DNA (dsDNA)/dATP (complex I), wild-type RT/dsDNA/ddATP (complex II), Q151M RT/dsDNA/dATP (complex III), Q151Mc RT/dsDNA/dATP (complex IV), and Q151Mc RT/dsDNA/ddATP (complex V) ternary complexes. The structures revealed that the deoxyribose rings of dATP and ddATP have 3'-endo and 3'-exo conformations, respectively. The single mutation Q151M introduces conformational perturbation at the deoxynucleoside triphosphate (dNTP)-binding pocket, and the mutated pocket may exist in multiple conformations. The compensatory set of mutations in Q151Mc, particularly F116Y, restricts the side chain flexibility of M151 and helps restore the DNA polymerization efficiency of the enzyme. The altered dNTP-binding pocket in Q151Mc RT has the Q151-R72 hydrogen bond removed and has a switched conformation for the key conserved residue R72 compared to that in wild-type RT. On the basis of a modeled structure of hepatitis B virus (HBV) polymerase, the residues R72, Y116, M151, and M184 in Q151Mc HIV-1 RT are conserved in wild-type HBV polymerase as residues R41, Y89, M171, and M204, respectively; functionally, both Q151Mc HIV-1 and wild-type HBV are resistant to dideoxynucleoside analogs.


    Related Citations: 
    • 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
    • Roles Of Conformational And Positional Adaptability In Structure-Based Design Of Tmc125-R165335 (Etravirine) And Related Non-Nucleoside Reverse Transcriptase Inhibitors That Are Highly Potent And Effective Against Wild-Type And Drug-Resistant Hiv-1 Variants.
      Das, K.,Clark, A.D.,Lewi, P.J.,Heeres, J.,De Jonge, M.R.,Koymans, L.M.,Vinkers, H.M.,Daeyaert, F.,Ludovici, D.W.,Kukla, M.J.,De Corte, B.,Kavash, R.W.,Ho, C.Y.,Ye, H.,Lichtenstein, M.A.,Andries, K.,Pauwels, R.,De Bethune, M.P.,Boyer, P.L.,Clark, P.,Hughes, S.H.,Janssen, P.A.,Arnold, E.
      (2004) J.Med.Chem. 47: 2550


    Organizational Affiliation

    Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT
A, C
556Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HIV-1 REVERSE TRANSCRIPTASE P61 SUBUNIT
B, D
428Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*GP*TP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*G)-3')T,E27Human immunodeficiency virus 1
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (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,F21Human immunodeficiency virus 1
Small Molecules
Ligands 5 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 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
B, D, T
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
DDS
Query on DDS

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Download CCD File 
A, C
2',3'-dideoxyadenosine triphosphate
C10 H16 N5 O11 P3
OAKPWEUQDVLTCN-NKWVEPMBSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-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: 2.7 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 89.945α = 90.00
b = 133.273β = 97.59
c = 139.062γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXphasing
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI027690

Revision History 

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-04-26
    Type: Database references
  • Version 1.2: 2017-06-07
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence