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

ArticleinNature 445(7126):447-51 · February 2007with16 Reads
DOI: 10.1038/nature05492 · Source: PubMed
Abstract
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.
    • "The structure of the deaminase domain of hADAR2 has been solved by X-ray crystallography [41]. This C-terminal 45 kDa domain comprises of 400 residues which form a globular structure similar to the deaminase domain found in other CDA family members42434445. This core deaminase motif consists of two α-helices (α2 and α5) and four β-strands (β1, β2, β5, and β8) [41]. "
    [Show abstract] [Hide abstract] ABSTRACT: The ADAR proteins deaminate adenosine to inosine in double-stranded RNA which is one of the most abundant modifications present in mammalian RNA. Inosine can have a profound effect on the RNAs that are edited, not only changing the base-pairing properties, but can also result in recoding, as inosine behaves as if it were guanosine. In mammals there are three ADAR proteins and two ADAR-related proteins (ADAD) expressed. All have a very similar modular structure; however, both their expression and biological function differ significantly. Only two of the ADAR proteins have enzymatic activity. However, both ADAR and ADAD proteins possess the ability to bind double-strand RNA. Mutations in ADARs have been associated with many diseases ranging from cancer, innate immunity to neurological disorders. Here, we will discuss in detail the domain structure of mammalian ADARs, the effects of RNA editing, and the role of ADARs in human diseases.
    Full-text · Article · Sep 2015
    • "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. "
    [Show abstract] [Hide abstract] 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.
    Full-text · Article · Aug 2015
    • "Co-immunoprecipitation and cross-linking studies indicated that the Y124 and W127 residues were important for A3G's ability to bind to RNA and to form oligomers in an RNA-dependent manner. Consistent with the models of dimer interaction [42,45,218], it has been shown that A3G, A3F, and A3DE form homodimers and heterodimers in cells [166,196]. We used a bimolecular fluorescence complementation system to investigate A3G oligomerization and RNA binding in situ and found that wild-type A3G molecules oligomerized and reconstituted fluorescence, while RNA-binding defective mutants of A3G were monomeric and failed to reconstitute fluorescence [221]. "
    Full-text · Dataset · Jul 2014 · Journal of Molecular Biology
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