5I42

Structure of HIV-1 Reverse Transcriptase in complex with a DNA aptamer, AZTTP, and CA(2+) ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Conformational States of HIV-1 Reverse Transcriptase for Nucleotide Incorporation vs Pyrophosphorolysis-Binding of Foscarnet.

Das, K.Balzarini, J.Miller, M.T.Maguire, A.R.DeStefano, J.J.Arnold, E.

(2016) Acs Chem.Biol. 11: 2158-2164

  • DOI: 10.1021/acschembio.6b00187
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • HIV-1 reverse transcriptase (RT) catalytically incorporates individual nucleotides into a viral DNA strand complementing an RNA or DNA template strand; the polymerase active site of RT adopts multiple conformational and structural states while perfor ...

    HIV-1 reverse transcriptase (RT) catalytically incorporates individual nucleotides into a viral DNA strand complementing an RNA or DNA template strand; the polymerase active site of RT adopts multiple conformational and structural states while performing this task. The states associated are dNTP binding at the N site, catalytic incorporation of a nucleotide, release of a pyrophosphate, and translocation of the primer 3'-end to the P site. Structural characterization of each of these states may help in understanding the molecular mechanisms of drug activity and resistance and in developing new RT inhibitors. Using a 38-mer DNA template-primer aptamer as the substrate mimic, we crystallized an RT/dsDNA complex that is catalytically active, yet translocation-incompetent in crystals. The ability of RT to perform dNTP binding and incorporation in crystals permitted obtaining a series of structures: (I) RT/DNA (P-site), (II) RT/DNA/AZTTP ternary, (III) RT/AZT-terminated DNA (N-site), and (IV) RT/AZT-terminated DNA (N-site)/foscarnet complexes. The stable N-site complex permitted the binding of foscarnet as a pyrophosphate mimic. The Mg(2+) ions dissociated after catalytic addition of AZTMP in the pretranslocated structure III, whereas ions A and B had re-entered the active site to bind foscarnet in structure IV. The binding of foscarnet involves chelation with the Mg(2+) (B) ion and interactions with K65 and R72. The analysis of interactions of foscarnet and the recently discovered nucleotide-competing RT inhibitor (NcRTI) α-T-CNP in two different conformational states of the enzyme provides insights for developing new classes of polymerase active site RT inhibitors.


    Organizational Affiliation

    Center for Advanced Biotechnology and Medicine (CABM), Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT
A, C
555Human 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: 2
MoleculeChainsSequence LengthOrganismDetails
HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT
B, D
444Human 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
DNA (38-MER)E,F38synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
AZT
Query on AZT

Download SDF File 
Download CCD File 
A, C
3'-AZIDO-3'-DEOXYTHYMIDINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
GLWHPRRGGYLLRV-XLPZGREQSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OMC
Query on OMC
E, F
RNA LINKINGC10 H16 N3 O8 PC
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AZTKi: 91 nM (98) BINDINGDB
AZTIC50: 3 - 2100 nM (98) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 90.151α = 90.00
b = 132.192β = 97.15
c = 139.658γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-02-11 
  • Released Date: 2016-06-01 
  • Deposition Author(s): Das, K., Arnold, E.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR37 AI027690

Revision History 

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2016-06-15
    Type: Database references
  • Version 1.2: 2016-08-31
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Derived calculations