1J5O

CRYSTAL STRUCTURE OF MET184ILE MUTANT OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH DOUBLE STRANDED DNA TEMPLATE-PRIMER


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.262 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Lamivudine (3TC) resistance in HIV-1 reverse transcriptase involves steric hindrance with beta-branched amino acids.

Sarafianos, S.G.Das, K.Clark Jr., A.D.Ding, J.Boyer, P.L.Hughes, S.H.Arnold, E.

(1999) Proc.Natl.Acad.Sci.USA 96: 10027-10032

  • Primary Citation of Related Structures:  1QE1

  • PubMed Abstract: 
  • An important component of triple-drug anti-AIDS therapy is 2', 3'-dideoxy-3'-thiacytidine (3TC, lamivudine). Single mutations at residue 184 of the reverse transcriptase (RT) in HIV cause high-level resistance to 3TC and contribute to the failure of ...

    An important component of triple-drug anti-AIDS therapy is 2', 3'-dideoxy-3'-thiacytidine (3TC, lamivudine). Single mutations at residue 184 of the reverse transcriptase (RT) in HIV cause high-level resistance to 3TC and contribute to the failure of anti-AIDS combination therapy. We have determined crystal structures of the 3TC-resistant mutant HIV-1 RT (M184I) in both the presence and absence of a DNA/DNA template-primer. In the absence of a DNA substrate, the wild-type and mutant structures are very similar. However, comparison of crystal structures of M184I mutant and wild-type HIV-1 RT with and without DNA reveals repositioning of the template-primer in the M184I/DNA binary complex and other smaller changes in residues in the dNTP-binding site. On the basis of these structural results, we developed a model that explains the ability of the 3TC-resistant mutant M184I to incorporate dNTPs but not the nucleotide analog 3TCTP. In this model, steric hindrance is expected for NRTIs with beta- or L- ring configurations, as with the enantiomer of 3TC that is used in therapy. Steric conflict between the oxathiolane ring of 3TCTP and the side chain of beta-branched amino acids (Val, Ile, Thr) at position 184 perturbs inhibitor binding, leading to a reduction in incorporation of the analog. The model can also explain the 3TC resistance of analogous hepatitis B polymerase mutants. Repositioning of the template-primer as observed in the binary complex (M184I/DNA) may also occur in the catalytic ternary complex (M184I/DNA/3TCTP) and contribute to 3TC resistance by interfering with the formation of a catalytically competent closed complex.


    Related Citations: 
    • Structure and Functional Implications of the Polymerase Active Site Region in a Complex of HIV-1 RT with a Double-Stranded DNA template-primer and an Antibody Fab Fragment at 2.8 Angstroms Resolution
      Ding, J.,Das, K.,Hsiou, Y.,Sarafianos, S.G.,Clark Jr., A.D.,Jacobo-Molina, A.,Tantillo, C.,Hughes, S.H.,Arnold, E.
      (1998) J.Mol.Biol. 284: 1095
    • Touching the Heart of HIV-1 Drug Resistance: The Fingers Close Down on the dNTP at the Polymerase Active Site
      Sarafianos, S.G.,Das, K.,Ding, J.,Boyer, P.L.,Hughes, S.H.,Arnold, E.
      (1999) Chem.Biol. 6: R137


    Organizational Affiliation

    Center for Advanced Biotechnology and Medicine (CABM) and Rutgers University Chemistry Department, 679 Hoes Lane, Piscataway, NJ 08854-5638, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Reverse transcriptase
A
558Human 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: 4
MoleculeChainsSequence LengthOrganismDetails
Reverse transcriptase
B
430Human 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: 5
MoleculeChainsSequence LengthOrganismDetails
ANTIBODY (LIGHT CHAIN)
L
214N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
ANTIBODY (HEAVY CHAIN)
H
220N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*TP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*C)-3'T19N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*A)-3'P18N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.262 
  • Space Group: P 32 1 2
Unit Cell:
Length (Å)Angle (°)
a = 169.180α = 90.00
b = 169.180β = 90.00
c = 221.910γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-14
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance