6WMB

Crystal structure of a soluble variant of full-length human APOBEC3G (pH 8.0)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.253 

wwPDB Validation   3D Report Full Report



Literature

Crystal Structure of a Soluble APOBEC3G Variant Suggests ssDNA to Bind in a Channel that Extends between the Two Domains.

Maiti, A.Myint, W.Delviks-Frankenberry, K.A.Hou, S.Kanai, T.Balachandran, V.Sierra Rodriguez, C.Tripathi, R.Kurt Yilmaz, N.Pathak, V.K.Schiffer, C.A.Matsuo, H.

(2020) J Mol Biol 432: 6042-6060

  • DOI: 10.1016/j.jmb.2020.10.020
  • Primary Citation of Related Structures:  
    6WMA, 6WMC, 6WMB

  • PubMed Abstract: 
  • APOBEC3G (A3G) is a single-stranded DNA (ssDNA) cytosine deaminase that can restrict HIV-1 infection by mutating the viral genome. A3G consists of a non-catalytic N-terminal domain (NTD) and a catalytic C-terminal domain (CTD) connected by a short linker ...

    APOBEC3G (A3G) is a single-stranded DNA (ssDNA) cytosine deaminase that can restrict HIV-1 infection by mutating the viral genome. A3G consists of a non-catalytic N-terminal domain (NTD) and a catalytic C-terminal domain (CTD) connected by a short linker. While the CTD catalyzes cytosine deamination, the NTD is believed to provide additional affinity for ssDNA. Structures of both A3G domains have been solved individually; however, a full-length A3G structure has been challenging. Recently, crystal structures of full-length rhesus macaque A3G variants were solved which suggested dimerization mechanisms and RNA binding surfaces, whereas the dimerization appeared to compromise catalytic activity. We determined the crystal structure of a soluble variant of human A3G (sA3G) at 2.5 Å and from these data generated a model structure of wild-type A3G. This model demonstrated that the NTD was rotated 90° relative to the CTD along the major axis of the molecule, an orientation that forms a positively charged channel connected to the CTD catalytic site, consisting of NTD loop-1 and CTD loop-3. Structure-based mutations, in vitro deamination and DNA binding assays, and HIV-1 restriction assays identify R24, located in the NTD loop-1, as essential to a critical interaction with ssDNA. Furthermore, sA3G was shown to bind a deoxy-cytidine dinucleotide near the catalytic Zn 2+ , yet not in the catalytic position, where the interactions between deoxy-cytidines and CTD loop-1 and loop-7 residues were different from those formed with substrate. These new interactions suggest a mechanism explaining why A3G exhibits a 3' to 5' directional preference in processive deamination.


    Organizational Affiliation

    Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA. Electronic address: hiroshi.matsuo@nih.gov.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
APOLIPOPROTEIN B MRNA EDITING ENZYME, CATALYTIC PEPTIDE- LIKE 3GA367Homo sapiensMutation(s): 0 
Gene Names: APOBEC3G
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*CP*C)-3')B2Escherichia coli
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    A
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.02 Å
    • R-Value Free: 0.305 
    • R-Value Work: 0.247 
    • R-Value Observed: 0.253 
    • Space Group: I 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 60.238α = 90
    b = 42.081β = 95.759
    c = 194.21γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-2000data reduction
    HKL-2000data scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data

    • Deposited Date: 2020-04-21 
    • Released Date: 2020-12-23 
    • Deposition Author(s): Maiti, A., Matsuo, H.

    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesRO1AI150478

    Revision History 

    • Version 1.0: 2020-12-23
      Type: Initial release