The APOBEC-2 crystal structure and functional implications for the deaminase AID

Molecular and Computational Biology, University of Southern California Los Angeles, California 90089, USA.
Nature (Impact Factor: 41.46). 02/2007; 445(7126):447-51. DOI: 10.1038/nature05492
Source: PubMed


APOBEC-2 (APO2) belongs to the family of apolipoprotein B messenger RNA-editing enzyme catalytic (APOBEC) polypeptides, which deaminates mRNA and single-stranded DNA. Different APOBEC members use the same deamination activity to achieve diverse human biological functions. Deamination by an APOBEC protein called activation-induced cytidine deaminase (AID) is critical for generating high-affinity antibodies, and deamination by APOBEC-3 proteins can inhibit retrotransposons and the replication of retroviruses such as human immunodeficiency virus and hepatitis B virus. Here we report the crystal structure of APO2. APO2 forms a rod-shaped tetramer that differs markedly from the square-shaped tetramer of the free nucleotide cytidine deaminase, with which APOBEC proteins share considerable sequence homology. In APO2, two long alpha-helices of a monomer structure prevent the formation of a square-shaped tetramer and facilitate formation of the rod-shaped tetramer via head-to-head interactions of two APO2 dimers. Extensive sequence homology among APOBEC family members allows us to test APO2 structure-based predictions using AID. We show that AID deamination activity is impaired by mutations predicted to interfere with oligomerization and substrate access. The structure suggests how mutations in patients with hyper-IgM-2 syndrome inactivate AID, resulting in defective antibody maturation.

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    • "Several X-ray crystallographic or NMR-based structures of the catalytic domain of A3G are available [18] [19] [20] [21] [22]. NMR-based structures of A3A [23] and X-ray crystal structures of A3F [24] and APOBEC2 [25] provide insights into the structure– function relationships in this family of proteins. "
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    ABSTRACT: Human APOBEC3B deaminates cytosines in DNA and belongs to the AID/APOBEC family of enzymes. These proteins are involved in innate and adaptive immunity, and may cause mutations in a variety of cancers. To characterize its ability to convert cytosines to uracils, we tested several derivatives of APOBEC3B gene for their ability to cause mutations in Escherichia coli. Through this analysis, a methionine residue at the junction of amino- and carboxy-terminal domains was found to be essential for high mutagenicity. Properties of mutants with substitutions at this position, examination of existing molecular structures of APOBEC3 family members and molecular modeling suggest that this residue is essential for the structural stability of this family of proteins. The APOBEC3B carboxy-terminal domain (CTD) with the highest mutational activity was purified to homogeneity and its kinetic parameters were determined. Size exclusion chromatography of the CTD monomer showed that it is in equilibrium with its dimeric form and MALDI-TOF analysis of the protein suggested that the dimer may be quite stable. The partially purified amino-terminal domain did not show intrinsic deamination activity and did not enhance the activity of the CTD in biochemical assays. Finally, APOBEC3B was at least 10-fold less efficient at mutating 5-methylcytosine (5mC) to thymine than APOBEC3A in a genetic assay, and was at least 10-fold less efficient at deaminating 5mC compared to C in biochemical assays. These results shed light on the structural organization of APOBEC3B catalytic domain, its substrate specificity and its possible role in causing genome-wide mutations. Copyright © 2015. Published by Elsevier Ltd.
    Journal of Molecular Biology 08/2015; DOI:10.1016/j.jmb.2015.08.006 · 4.33 Impact Factor
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    • "Previously, the crystal structure of human A2 has been used as a model for oligomerization of A3G and other APOBEC family proteins. The structure of A2 displayed an atypical butterfly-shaped tetramer formed by head-to-head interactions of two A2 dimers (Prochnow et al., 2007). However, this tetrameric model has been controversial, as other studies using nuclear magnetic resonance (NMR) and fluorescence fluctuation spectroscopy have demonstrated that A2 exists as a monomer in solution (Krzysiak et al., 2012) and inside the cytoplasm of the living cell (Li et al., 2014). "
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    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.
    Structure 03/2014; 22(5). DOI:10.1016/j.str.2014.02.011 · 5.62 Impact Factor
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    • "Head-to-head dimer models of hA3G N-terminal domain were obtained by homology modelling using either the crystal structure of human APOBEC2 (hA2) at a resolution of 2.50 Å or the NMR structure of the C-terminal domain of hA3G (PDB code: 2NYT chain A [56] or 2JYW [57], respectively) as a template, as previously performed [34,58-60]. To minimize misalignments between the hA3G N-terminal domain as a target sequence and either hA2 or the C-terminal domain of hA3G as a template sequence, we used the multiple sequence alignment method with the sequences of hA3A (GenBank accession number: NM_145699), hA3C (GenBank accession number: NM_014508), and hA3F (GenBank accession number: NM_145298). "
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    ABSTRACT: Alu and LINE-1 (L1), which constitute ~11% and ~17% of the human genome, respectively, are transposable non-LTR retroelements. They transpose not only in germ cells but also in somatic cells, occasionally causing cancer. We have previously demonstrated that antiretroviral restriction factors, human APOBEC3 (hA3) proteins (A-H), differentially inhibit L1 retrotransposition. In this present study, we found that hA3 members also restrict Alu retrotransposition at differential levels that correlate with those observed previously for L1 inhibition. Through deletion analyses based on the best-characterized hA3 member human APOBEC3G (hA3G), its N-terminal 30 amino acids were required for its inhibitory activity against Alu retrotransposition. The inhibitory effect of hA3G on Alu retrotransposition was associated with its oligomerization that was affected by the deletion of its N-terminal 30 amino acids. Through structural modeling, the amino acids 24 to 28 of hA3G were predicted to be located at the interface of the dimer. The mutation of these residues resulted in abrogated hA3G oligomerization, and consistently abolished the inhibitory activity of hA3G against Alu retrotransposition. Importantly, the anti-L1 activity of hA3G was also associated with hA3G oligomerization. These results suggest that the inhibitory activities of hA3G against Alu and L1 retrotransposition might involve a common mechanism.
    PLoS ONE 12/2013; 8(12):e84228. DOI:10.1371/journal.pone.0084228 · 3.23 Impact Factor
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