4ROV

The crystal structure of novel APOBEC3G CD2 head-to-tail dimer suggests the binding mode of full-length APOBEC3G to HIV-1 ssDNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of DNA cytidine deaminase ABOBEC3G catalytic deamination domain suggests a binding mode of full-length enzyme to single-stranded DNA

Lu, X.Zhang, T.Xu, Z.Liu, S.Zhao, B.Lan, W.Wang, C.Ding, J.Cao, C.

(2015) J.Biol.Chem. 290: 4010-4021

  • DOI: 10.1074/jbc.M114.624262
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • APOBEC3G (A3G) is a DNA cytidine deaminase (CD) that demonstrates antiviral activity against human immunodeficiency virus 1 (HIV-1) and other pathogenic virus. It has an inactive N-terminal CD1 virus infectivity factor (Vif) protein binding domain (A ...

    APOBEC3G (A3G) is a DNA cytidine deaminase (CD) that demonstrates antiviral activity against human immunodeficiency virus 1 (HIV-1) and other pathogenic virus. It has an inactive N-terminal CD1 virus infectivity factor (Vif) protein binding domain (A3G-CD1) and an actively catalytic C-terminal CD2 deamination domain (A3G-CD2). Although many studies on the structure of A3G-CD2 and enzymatic properties of full-length A3G have been reported, the mechanism of how A3G interacts with HIV-1 single-stranded DNA (ssDNA) is still not well characterized. Here, we reported a crystal structure of a novel A3G-CD2 head-to-tail dimer (in which the N terminus of the monomer H (head) interacts with the C terminus of monomer T (tail)), where a continuous DNA binding groove was observed. By constructing the A3G-CD1 structural model, we found that its overall fold was almost identical to that of A3G-CD2. We mutated the residues located in or along the groove in monomer H and the residues in A3G-CD1 that correspond to those seated in or along the groove in monomer T. Then, by performing enzymatic assays, we confirmed the reported key elements and the residues in A3G necessary to the catalytic deamination. Moreover, we identified more than 10 residues in A3G essential to DNA binding and deamination reaction. Therefore, this dimer structure may represent a structural model of full-length A3G, which indicates a possible binding mode of A3G to HIV-1 ssDNA.


    Organizational Affiliation

    From the State Key Laboratory of Bio-organic and Natural Product Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA dC->dU-editing enzyme APOBEC-3G
A, B
198Homo sapiensMutation(s): 0 
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 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.402α = 90.00
b = 76.535β = 90.00
c = 80.485γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data scaling
PHENIXmodel building
REFMACrefinement
PHENIXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-31
    Type: Initial release
  • Version 1.1: 2016-02-17
    Type: Database references