Crystal Structure of the DNA Cytosine Deaminase APOBEC3F: The Catalytically Active and HIV-1 Vif-Binding Domain

Bohn, Markus-Frederik; Shandilya, Shivender M.D.; Albin, John S.; Kouno, Takahide; Anderson, Brett D.; McDougle, Rebecca M.; Carpenter, Michael A.; Rathore, Anurag S.; Evans, Leah; Davis, Ahkillah N.; Zhang, Jing Ying; Lu, Yang; Somasundaran, Mohan; Matsuo, Hiroshi; Harris, Reuben S.; Schiffer, Celia A.

doi:10.1016/j.str.2013.04.010

Cited by 86 publications

(133 citation statements)

References 64 publications

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“…A crystal structure of the rhesus A3G N-terminal domain (NTD) shows that A3G (NTD) dimerizes using helix 6 and loop 7, where F126/W127 are located, confirming previous mutational studies (48,70,71). Further, this dimerization of rhesus A3G NTD is distinct from any of the existing A3F dimer models that have resulted from A3F C-terminal domain structures (72)(73)(74)(75). It remains to be determined how full-length A3F oligomerizes in solution.…”

Section: Discussionsupporting

confidence: 61%

Mechanism of Enhanced HIV Restriction by Virion Coencapsidated Cytidine Deaminases APOBEC3F and APOBEC3G

Ara

Love

Follack

et al. 2017

J Virol

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The APOBEC3 (A3) enzymes, A3G and A3F, are coordinately expressed in CD4 ϩ T cells and can become coencapsidated into HIV-1 virions, primarily in the absence of the viral infectivity factor (Vif). A3F and A3G are deoxycytidine deaminases that inhibit HIV-1 replication by inducing guanine-to-adenine hypermutation through deamination of cytosine to form uracil in minus-strand DNA. The effect of the simultaneous presence of both A3G and A3F on HIV-1 restriction ability is not clear. Here, we used a single-cycle infectivity assay and biochemical analyses to determine if coencapsidated A3G and A3F differ in their restriction capacity from A3G or A3F alone. Proviral DNA sequencing demonstrated that compared to each A3 enzyme alone, A3G and A3F, when combined, had a coordinate effect on hypermutation. Using size exclusion chromatography, rotational anisotropy, and in vitro deamination assays, we demonstrate that A3F promotes A3G deamination activity by forming an A3F/G hetero-oligomer in the absence of RNA which is more efficient at deaminating cytosines. Further, A3F caused the accumulation of shorter reverse transcripts due to decreasing reverse transcriptase efficiency, which would leave singlestranded minus-strand DNA exposed for longer periods of time, enabling more deamination events to occur. Although A3G and A3F are known to function alongside each other, these data provide evidence for an A3F/G hetero-oligomeric A3 with unique properties compared to each individual counterpart.IMPORTANCE The APOBEC3 enzymes APOBEC3F and APOBEC3G act as a barrier to HIV-1 replication in the absence of the HIV-1 Vif protein. After APOBEC3 enzymes are encapsidated into virions, they deaminate cytosines in minus-strand DNA, which forms promutagenic uracils that induce transition mutations or proviral DNA degradation. Even in the presence of Vif, footprints of APOBEC3-catalyzed deaminations are found, demonstrating that APOBEC3s still have discernible activity against HIV-1 in infected individuals. We undertook a study to better understand the activity of coexpressed APOBEC3F and APOBEC3G. The data demonstrate that an APOBEC3F/ APOBEC3G hetero-oligomer can form that has unique properties compared to each APOBEC3 alone. This hetero-oligomer has increased efficiency of virus hypermutation, raising the idea that we still may not fully realize the antiviral mechanisms of endogenous APOBEC3 enzymes. Hetero-oligomerization may be a mechanism to increase their antiviral activity in the presence of Vif.

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Section: Discussionsupporting

confidence: 61%

Mechanism of Enhanced HIV Restriction by Virion Coencapsidated Cytidine Deaminases APOBEC3F and APOBEC3G

Ara

Love

Follack

et al. 2017

J Virol

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“…In contrast to A3C, A3F has another key residue (E324) that is required for interaction with Vif (33). Bohn et al reported that an additional 13 residues in the vicinity of the Vif interaction interface are presumably involved in the Vif-A3F interaction, according to predictions based on electrostatic calculations of the A3F CTD surface (58). To assess whether these additional A3F residues are actually involved in the Vif interaction, we tested the effects of a mutation at each residue on changes in susceptibility to Vif-mediated degradation.…”

Section: Resultsmentioning

confidence: 99%

“…Two crystal structures of the A3F CTD are currently available, although they are both modified from WT A3F sequences: one, called A3F 185-373 -11X (PDB ID no. 4IOU), has 11 amino acid substitutions (58), whereas the other (PDB ID no. 4J4J) has a 23-amino-acid replacement that included swapping of the whole ␣1 helix architecture of the A3F CTD with A3G residues 197 to 221 (59).…”

Section: Resultsmentioning

confidence: 99%

Structural Insights into HIV-1 Vif-APOBEC3F Interaction

Nakashima

Ode

Kawamura

et al. 2016

J Virol

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The HIV-1 Vif protein inactivates the cellular antiviral cytidine deaminase APOBEC3F (A3F) in virus-infected cells by specifically targeting it for proteasomal degradation. Several studies identified Vif sequence motifs involved in A3F interaction, whereas a Vif-binding A3F interface was proposed based on our analysis of highly similar APOBEC3C (A3C). However, the structural mechanism of specific Vif-A3F recognition is still poorly understood. Here we report structural features of interaction interfaces for both HIV-1 Vif and A3F molecules. Alanine-scanning analysis of Vif revealed that six residues located within the conserved Vif F1-, F2-, and F3-box motifs are essential for both A3C and A3F degradation, and an additional four residues are uniquely required for A3F degradation. Modeling of the Vif structure on an HIV-1 Vif crystal structure revealed that three discontinuous flexible loops of Vif F1-, F2-, and F3-box motifs sterically cluster to form a flexible A3F interaction interface, which represents hydrophobic and positively charged surfaces. We found that the basic Vif interface patch (R17, E171, and R173) involved in the interactions with A3C and A3F differs. Furthermore, our crystal structure determination and extensive mutational analysis of the A3F C-terminal domain demonstrated that the A3F interface includes a unique acidic stretch (L291, A292, R293, and E324) crucial for Vif interaction, suggesting additional electrostatic complementarity to the Vif interface compared with the A3C interface. Taken together, these findings provide structural insights into the A3F-Vif interaction mechanism, which will provide an important basis for development of novel anti-HIV-1 drugs using cellular cytidine deaminases. IMPORTANCEHIV-1 Vif targets cellular antiviral APOBEC3F (A3F) enzyme for degradation. However, the details on the structural mechanism for specific A3F recognition remain unclear. This study reports structural features of interaction interfaces for both HIV-1 Vif and A3F molecules. Three discontinuous sequence motifs of Vif, F1, F2, and F3 boxes, assemble to form an A3F interaction interface. In addition, we determined a crystal structure of the wild-type A3F C-terminal domain responsible for the Vif interaction. These results demonstrated that both electrostatic and hydrophobic interactions are the key force driving Vif-A3F binding and that the Vif-A3F interfaces are larger than the Vif-A3C interfaces. These findings will allow us to determine the configurations of the Vif-A3F complex and to construct a structural model of the complex, which will provide an important basis for inhibitor development. Human cells have evolved intrinsic defense systems against retroviruses, which include the APOBEC3 (A3) family of polynucleotide cytidine deaminases (reviewed in references 1, 2, 3, and 4]). The A3 family comprises seven members that contain either one (A3A, A3C, and A3H) or two (A3B, A3D, A3F, and A3G) Zn 2ϩ coordination domains (Z domains) with conserved HXE(X) 23-28 CXXC motifs (5, 6). Based ...

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“…An important difference between A3G and A3F is the relative positions of the Vif-binding site and the single-strand DNA (ssDNA)-binding site; in A3G, the Vif-binding site maps to residues 126 -132, and the ssDNA-binding site maps to the C-terminal domain. In contrast, in A3F, the Vif-binding site and ssDNA-binding site are in much closer proximity (68,70). Thus, potential effects of N.41 on the Vif-binding site in A3F might also impede its interaction with ssDNA, which is required for A3F antiviral activity.…”

Section: Discussionmentioning

confidence: 99%

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

Pery

Sheehy

Nebane

et al. 2015

Journal of Biological Chemistry

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Background:The interaction between HIV Vif protein and innate antiviral factor APOBEC3G represents a potential therapeutic target. Results: Screening for inhibitors of Vif-APOBEC3G interaction identified a small molecule, N.41, that protects APOBEC3G from Vif-mediated degradation and exhibits antiviral activity. Conclusion: N.41 is a lead for further development as an antiviral. Significance: These findings suggest new strategies for developing anti-HIV therapeutics.

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Crystal Structure of the DNA Cytosine Deaminase APOBEC3F: The Catalytically Active and HIV-1 Vif-Binding Domain

Cited by 86 publications

References 64 publications

Mechanism of Enhanced HIV Restriction by Virion Coencapsidated Cytidine Deaminases APOBEC3F and APOBEC3G

Mechanism of Enhanced HIV Restriction by Virion Coencapsidated Cytidine Deaminases APOBEC3F and APOBEC3G

Structural Insights into HIV-1 Vif-APOBEC3F Interaction

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

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