3V4J

First-In-Class Small Molecule Inhibitors of the Single-strand DNA Cytosine Deaminase APOBEC3G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

First-In-Class Small Molecule Inhibitors of the Single-Strand DNA Cytosine Deaminase APOBEC3G.

Li, M.Shandilya, S.M.Carpenter, M.A.Rathore, A.Brown, W.L.Perkins, A.L.Harki, D.A.Solberg, J.Hook, D.J.Pandey, K.K.Parniak, M.A.Johnson, J.R.Krogan, N.J.Somasundaran, M.Ali, A.Schiffer, C.A.Harris, R.S.

(2012) Acs Chem.Biol. 7: 506-517

  • DOI: 10.1021/cb200440y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • APOBEC3G is a single-stranded DNA cytosine deaminase that comprises part of the innate immune response to viruses and transposons. Although APOBEC3G is the prototype for understanding the larger mammalian polynucleotide deaminase family, no specific ...

    APOBEC3G is a single-stranded DNA cytosine deaminase that comprises part of the innate immune response to viruses and transposons. Although APOBEC3G is the prototype for understanding the larger mammalian polynucleotide deaminase family, no specific chemical inhibitors exist to modulate its activity. High-throughput screening identified 34 compounds that inhibit APOBEC3G catalytic activity. Twenty of 34 small molecules contained catechol moieties, which are known to be sulfhydryl reactive following oxidation to the orthoquinone. Located proximal to the active site, C321 was identified as the binding site for the inhibitors by a combination of mutational screening, structural analysis, and mass spectrometry. Bulkier substitutions C321-to-L, F, Y, or W mimicked chemical inhibition. A strong specificity for APOBEC3G was evident, as most compounds failed to inhibit the related APOBEC3A enzyme or the unrelated enzymes E. coli uracil DNA glycosylase, HIV-1 RNase H, or HIV-1 integrase. Partial, but not complete, sensitivity could be conferred to APOBEC3A by introducing the entire C321 loop from APOBEC3G. Thus, a structural model is presented in which the mechanism of inhibition is both specific and competitive, by binding a pocket adjacent to the APOBEC3G active site, reacting with C321, and blocking access to substrate DNA cytosines.


    Organizational Affiliation

    Department of Biochemistry, Molecular Biology & Biophysics, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA dC->dU-editing enzyme APOBEC-3G
A, B
207Homo sapiensMutation(s): 5 
Gene Names: APOBEC3G
EC: 3.5.4.-
Find proteins for Q9HC16 (Homo sapiens)
Go to Gene View: APOBEC3G
Go to UniProtKB:  Q9HC16
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
PQR
Query on PQR

Download SDF File 
Download CCD File 
A, B
4-[methyl(nitroso)amino]benzene-1,2-diol
Methyl-3,4-dephostatin
C7 H8 N2 O3
XAKAQCMEMMZUEO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PQRIC50: 9100 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 53.080α = 90.00
b = 67.764β = 107.38
c = 64.472γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-01
    Type: Initial release
  • Version 1.1: 2012-03-28
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description