title: Nuclear Magnetic Resonance Structure of the APOBEC3B Catalytic Domain: Structural Basis for Substrate Binding and DNA Deaminase Activity.
abstract: Human APOBEC3B (A3B) is a member of the APOBEC3 (A3) family of cytidine deaminases, which function as DNA mutators and restrict viral pathogens and endogenous retrotransposons. Recently, A3B was identified as a major source of genetic heterogeneity in several human cancers. Here, we determined the solution nuclear magnetic resonance structure of the catalytically active C-terminal domain (CTD) of A3B and performed detailed analyses of its deaminase activity. The core of the structure comprises a central five-stranded β-sheet with six surrounding helices, common to all A3 proteins. The structural fold is most similar to that of A3A and A3G-CTD, with the most prominent difference being found in loop 1. The catalytic activity of A3B-CTD is ∼15-fold lower than that of A3A, although both exhibit a similar pH dependence. Interestingly, A3B-CTD with an A3A loop 1 substitution had significantly increased deaminase activity, while a single-residue change (H29R) in A3A loop 1 reduced A3A activity to the level seen with A3B-CTD. This establishes that loop 1 plays an important role in A3-catalyzed deamination by precisely positioning the deamination-targeted C into the active site. Overall, our data provide important insights into the determinants of the activities of individual A3 proteins and facilitate understanding of their biological function.
authors.forename: In-Ja L
authors.initials: IJ
authors.lastname: Byeon
authors.forename: Chang-Hyeock
authors.initials: CH
authors.lastname: Byeon
authors.affiliation: Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States.
authors.forename: Tiyun
authors.initials: T
authors.lastname: Wu
authors.affiliation: Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States.
authors.forename: Mithun
authors.initials: M
authors.lastname: Mitra
authors.affiliation: Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States.
authors.forename: Dustin
authors.initials: D
authors.lastname: Singer
authors.affiliation: Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States.
authors.forename: Judith G
authors.initials: JG
authors.lastname: Levin
authors.forename: Angela M
authors.initials: AM
authors.lastname: Gronenborn
mesh_terms: D020134:Catalytic Domain; D003564:Cytidine Deaminase / Q000737:chemistry / Q000378:metabolism*; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D015778:Minor Histocompatibility Antigens / Q000737:chemistry* / Q000378:metabolism*; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D013379:Substrate Specificity
chemical_list: D015778:Minor Histocompatibility Antigens; D004247:DNA; C495794:APOBEC3B protein, human; D003564:Cytidine Deaminase