3KLF

Crystal structure of wild-type HIV-1 Reverse Transcriptase crosslinked to a DSDNA with a bound excision product, AZTPPPPA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.264 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

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: 1202-1209

  • DOI: 10.1038/nsmb.1908
  • Primary Citation of Related Structures:  
  • Also Cited By: 5TXP, 5TXO, 5TXN, 5TXM, 5TXL, 5I3U, 4R5P, 4Q0B, 4PWD, 4PUO, 4PQU, 3V81, 3V6D, 3V4I

  • PubMed Abstract: 

    • 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 ...

    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.

    Organizational Affiliation: 

    Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reverse transcriptase/ribonuclease H
A, E, I, M
557Human immunodeficiency virus type 1 group M subtype BMutation(s): 2 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
p51 RT
B, F, J, N
444Human immunodeficiency virus type 1 group M subtype BMutation(s): 1 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*T*GP*CP*AP*TP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3')C,G,K,O27N/A
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(2DA))-3')D,H,L,P21N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZP4
Query on ZP4
Download SDF File 
Download CCD File 
A, E, I, M
[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl] [(2S,3S,5R)-3-azido-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl hydrogen phosphate
C20 H28 N10 O19 P4
NHJROJSMKQZWCP-SLFMBYJQSA-N
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
B, F
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A, E, I, M
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
2DA
Query on 2DA
D, H, L, P
DNA LINKINGC10 H14 N5 O5 PDA
MRG
Query on MRG
D, H, L, P
DNA LINKINGC13 H20 N5 O7 P SDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.264 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 78.529α = 90.00
b = 274.806β = 90.11
c = 152.371γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
ADSCdata collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance