6BWY

DNA substrate selection by APOBEC3G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Insights into DNA substrate selection by APOBEC3G from structural, biochemical, and functional studies.

Ziegler, S.J.Liu, C.Landau, M.Buzovetsky, O.Desimmie, B.A.Zhao, Q.Sasaki, T.Burdick, R.C.Pathak, V.K.Anderson, K.S.Xiong, Y.

(2018) PLoS ONE 13: e0195048-e0195048

  • DOI: 10.1371/journal.pone.0195048

  • PubMed Abstract: 
  • Human apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3 (A3) proteins are a family of cytidine deaminases that catalyze the conversion of deoxycytidine (dC) to deoxyuridine (dU) in single-stranded DNA (ssDNA). A3 proteins act in the i ...

    Human apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3 (A3) proteins are a family of cytidine deaminases that catalyze the conversion of deoxycytidine (dC) to deoxyuridine (dU) in single-stranded DNA (ssDNA). A3 proteins act in the innate immune response to viral infection by mutating the viral ssDNA. One of the most well-studied human A3 family members is A3G, which is a potent inhibitor of HIV-1. Each A3 protein prefers a specific substrate sequence for catalysis-for example, A3G deaminates the third dC in the CCCA sequence motif. However, the interaction between A3G and ssDNA is difficult to characterize due to poor solution behavior of the full-length protein and loss of DNA affinity of the truncated protein. Here, we present a novel DNA-anchoring fusion strategy using the protection of telomeres protein 1 (Pot1) which has nanomolar affinity for ssDNA, with which we captured an A3G-ssDNA interaction. We crystallized a non-preferred adenine in the -1 nucleotide-binding pocket of A3G. The structure reveals a unique conformation of the catalytic site loops that sheds light onto how the enzyme scans substrate in the -1 pocket. Furthermore, our biochemistry and virology studies provide evidence that the nucleotide-binding pockets on A3G influence each other in selecting the preferred DNA substrate. Together, the results provide insights into the mechanism by which A3G selects and deaminates its preferred substrates and help define how A3 proteins are tailored to recognize specific DNA sequences. This knowledge contributes to a better understanding of the mechanism of DNA substrate selection by A3G, as well as A3G antiviral activity against HIV-1.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protection of telomeres protein 1, DNA dC->dU-editing enzyme APOBEC-3G fusion
A, B, E, G
361Homo sapiensSchizosaccharomyces pombe (strain 972 / ATCC 24843)
This entity is chimeric
Mutations: A298C, A220C, K287F, A333C, K211L
Gene Names: APOBEC3G, pot1
EC: 3.5.4.-
Find proteins for Q9HC16 (Homo sapiens)
Go to Gene View: APOBEC3G
Go to UniProtKB:  Q9HC16
Find proteins for O13988 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O13988
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (30-MER)I,C,D,F30synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, I
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, E, G
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.234 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 79.072α = 90.00
b = 79.072β = 90.00
c = 266.411γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-04-18
    Type: Initial release