Structure-Guided Analysis of the Human APOBEC3-HIV Restrictome

Abstract

Human APOBEC3 (A3) proteins are host-encoded intrinsic restriction factors that inhibit the replication of many retroviral pathogens. Restriction is believed to occur as a result of the DNA cytosine deaminase activity of the A3 proteins; this activity converts cytosines into uracils in single-stranded DNA retroviral replication intermediates. A3 proteins are also equipped with deamination-independent means to restrict retroviruses that work cooperatively with deamination-dependent restriction pathways. A3 proteins substantially bolster the intrinsic immune system by providing a powerful block to the transmission of retroviral pathogens; however, most retroviruses are able to subvert this replicative restriction in their natural host. HIV-1, for instance, evades A3 proteins through the activity of its accessory protein Vif. Here, we summarize data from recent A3 structural and functional studies to provide perspectives into the interactions between cellular A3 proteins and HIV-1 macromolecules throughout the viral replication cycle.

Determinants of Efficient Degradation of APOBEC3 Restriction Factors by HIV-1 Vif

“…Within this E3 ligase complex, Rbx2 recruits an E2 ubiquitin-conjugating enzyme to induce 48 Klinked poly-Ub of A3 enzymes, which is concomitant with their proteasomal degradation (8,(17)(18)(19)(20) (21)(22)(23)(24)(25)(26)(27)(28). The positively charged surfaces of Vif interact with negatively charged amino acids on the A3 enzyme, with some contribution from hydrophobic amino acid interactions, depending on the interface (23). There are three distinct structural motifs on the A3 enzymes that interact with a corresponding Vif region.…”

“…There are three distinct structural motifs on the A3 enzymes that interact with a corresponding Vif region. These can be categorized into three classes: A3G-, A3H-, or A3C/A3F/A3D-like (23).…”

Identification of a Novel HIV-1 Inhibitor Targeting Vif-dependent Degradation of Human APOBEC3G Protein

“…These residues were shown to be part of a negatively charged interface that is directly involved in Vif binding. These residues were not important for A3C-Vif binding (68,69), so the Vif binding sites in A3F and A3C may be different. N.41 may target the Vif-binding site in A3F, similar to its target site in A3G.…”

Determinants of Substrate Specificity in APOBEC3B

“…19,20 All A3 domains share a minimum sequence identity of 30%, which corresponds to a high degree of overall structure similarity. 21,22 Only single A3 domain structures have been elucidated through X ray crystallography. Among the A3 members, A3Bctd proved to be one of the most challenging proteins to crystallize, unlike its closest homolog A3A (85% sequence identity).…”

“…24,[31][32][33][34][35] Initial crystal structures of A3 deaminase domains show these loops being adjacent to the binding site. 22 Subsequent crystallization of A3 proteins in complex with substrates showed residues on loops 1 and 7 binding to oligonucleotide substrates. 24,26,[36][37][38] Previous experimental studies have explored the binding of A3s and other cytidine deaminases to chemically modified oligonucleotides, such as those with a ribose cytidine (rC) base at the target site, as well as other modifications to the oligonucleotide backbone and base.…”