SNAP output for PDB entry 5k83 [SNAP web server]

PDB-id

5k83; SNAP-derived features in text and JSON formats; DNAproDB

Class

hydrolase

Method

X-ray (2.39 Å)

Summary

Crystal structure of a primate apobec3g n-domain, in complex with ssDNA

Reference

Xiao X, Li SX, Yang H, Chen XS (2016): "Crystal structures of APOBEC3G N-domain alone and its complex with DNA." Nat Commun, 7, 12193. doi: 10.1038/ncomms12193.

Abstract

APOBEC3G (A3G) is a potent restriction factor of HIV-1. The N-terminal domain of A3G (A3G-CD1) is responsible for oligomerization and nucleic acid binding, both of which are essential for anti-HIV activity. As a countermeasure, HIV-1 viral infectivity factor (Vif) binds A3G-CD1 to mediate A3G degradation. The structural basis for the functions of A3G-CD1 remains elusive. Here, we report the crystal structures of a primate A3G-CD1 (rA3G-CD1) alone and in complex with single-stranded DNA (ssDNA). rA3G-CD1 shares a conserved core structure with the previously determined catalytic APOBECs, but displays unique features for surface charge, dimerization and nucleic acid binding. Its co-crystal structure with ssDNA reveals how the conformations of loops and residues surrounding the Zn-coordinated centre (Zn-centre) change upon DNA binding. The dimerization interface of rA3G-CD1 is important for oligomerization, nucleic acid binding and Vif-mediated degradation. These findings elucidate the molecular basis of antiviral mechanism and HIV-Vif targeting of A3G.