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: 42.35). 02/2007; 445(7126):447-51. 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.

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    • "Structural studies of the C-terminal CDA of A3G (Chen et al., 2008; Furukawa et al., 2009; Harjes et al., 2009; Holden et al., 2008; Zhang et al., 2007) and the single domain APOBEC2 protein (Prochnow et al., 2007) revealed that, the CDA consists of five β strands flanked by an α-helix on each side plus appropriate connecting loops. "
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    ABSTRACT: The Vif protein of HIV is essential for the effective propagation of this pathogenic retrovirus in vivo. Vif acts by preventing virion encapsidation of two potent antiviral factors, the APOBEC3G and APOBEC3F cytidine deaminases. Decreased encapsidation in part involves Vif-mediated recruitment of a ubiquitin E3 ligase complex that promotes polyubiquitylation and proteasome-mediated degradation of APOBEC3G/F. The resultant decline in intracellular levels of these enzymes leads to decreased encapsidation of APOBECG/F into budding virions. This review discusses recent advances in our understanding of the dynamic interplay of Vif with the antiviral APOBEC3 enzymes.
    Molecular Aspects of Medicine 10/2010; 31(5):383-97. DOI:10.1016/j.mam.2010.06.001 · 10.30 Impact Factor
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    • ").Inthesemice,theproportionofmutations thatsegregatedwithRGYW/WRCYwasmorethan 44%higherthaninC57BL/6mice:41.2vs.28.6% (p,0.002).RGYW/WRCYcontainstheWRCmotif anditscomplementGYW,whicharepreferentially targetedbyAIDinvitro,indicatingthattheintrinsic SHMhotspotowesmuchtotheinherentsequence specificityofAIDitself[52].SinceAIDcanform dimers[71] [72],partiallyoverlappingWRConopposite strandswouldfacilitatebindingbytwosubunits ofanAIDdimer. "
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    ABSTRACT: Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by the production of an array of pathogenic autoantibodies, including high-affinity anti-dsDNA IgG antibodies. These autoantibodies are mutated and class-switched, mainly to IgG, indicating that immunoglobulin (Ig) gene somatic hypermutation (SHM) and class switch DNA recombination (CSR) are important in their generation. Lupus-prone MRL/fas(lpr/lpr) mice develop a systemic autoimmune syndrome that shares many features with human SLE. We found that Ig genes were heavily mutated in MRL/fas(lpr/lpr) mice and contained long stretches of DNA deletions and insertions. The spectrum of mutations in MRL/fas(lpr/lpr) B cells was significantly altered, including increased dG/dC transitions, increased targeting of the RGYW/WRCY mutational hotspot and the WGCW AID-targeting hotspot. We also showed that MRL/fas(lpr/lpr) greatly upregulated CSR, particularly to IgG2a and IgA in B cells of the spleen, lymph nodes and Peyer's patches. In MRL/fas(lpr/lpr) mice, the significant upregulation of SHM and CSR was associated with increased expression of activation-induced cytidine deaminase (AID), which mediates DNA lesion, the first step in SHM and CSR, and translesion DNA synthesis (TLS) polymerase (pol) theta, pol eta and pol zeta, which are involved in DNA synthesis/repair process associated with SHM and, possibly, CSR. Thus, in lupus-prone MRL/fas(lpr/lpr) mice, SHM and CSR are upregulated, as a result of enhanced AID expression and, therefore, DNA lesions, and dysregulated DNA repair factors, including TLS polymerases, which are involved in the repair process of AID-mediated DNA lesions.
    Autoimmunity 03/2009; 42(2):89-103. DOI:10.1080/08916930802629554 · 2.75 Impact Factor
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    • "In spite of the great attention to the APOBEC/AID protein family, the structural knowledge on this family is quite limited. The structure of APOBEC2 was reported last year (Prochnow et al, 2007), but APOBEC2 does not possess enzymatic activity. APOBEC3G is composed of 384 residues and possesses two consensus cytidine deaminase motifs of the zinc-finger type, His-X-Glu-X 27-28 -Pro-Cys-X 2 -Cys, in its N-and C-terminal domains (Harris and Liddament, 2004). "
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    ABSTRACT: Human APOBEC3G exhibits anti-human immunodeficiency virus-1 (HIV-1) activity by deaminating cytidines of the minus strand of HIV-1. Here, we report a solution structure of the C-terminal deaminase domain of wild-type APOBEC3G. The interaction with DNA was examined. Many differences in the interaction were found between the wild type and recently studied mutant APOBEC3Gs. The position of the substrate cytidine, together with that of a DNA chain, in the complex, was deduced. Interestingly, the deamination reaction of APOBEC3G was successfully monitored using NMR signals in real time. Real-time monitoring has revealed that the third cytidine of the d(CCCA) segment is deaminated at an early stage and that then the second one is deaminated at a late stage, the first one not being deaminated at all. This indicates that the deamination is carried out in a strict 3' --> 5' order. Virus infectivity factor (Vif) of HIV-1 counteracts the anti-HIV-1 activity of APOBEC3G. The structure of the N-terminal domain of APOBEC3G, with which Vif interacts, was constructed with homology modelling. The structure implies the mechanism of species-specific sensitivity of APOBEC3G to Vif action.
    The EMBO Journal 01/2009; 28(4):440-51. DOI:10.1038/emboj.2008.290 · 10.75 Impact Factor
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