title: DNA cytosine and methylcytosine deamination by APOBEC3B: enhancing methylcytosine deamination by engineering APOBEC3B.
abstract: APOBEC (apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like) is a family of enzymes that deaminates cytosine (C) to uracil (U) on nucleic acid. APOBEC3B (A3B) functions in innate immunity against intrinsic and invading retroelements and viruses. A3B can also induce genomic DNA mutations to cause cancer. A3B contains two cytosine deaminase domains (CD1, CD2), and there are conflicting reports about whether both domains are active. Here we demonstrate that only CD2 of A3B (A3BCD2) has C deamination activity. We also reveal that both A3B and A3BCD2 can deaminate methylcytosine (mC). Guided by structural and functional analysis, we successfully engineered A3BCD2 to gain over two orders of magnitude higher activity for mC deamination. Important determinants that contribute to the activity and selectivity for mC deamination have been identified, which reveals that multiple elements, rather than single ones, contribute to the mC deamination activity and selectivity in A3BCD2 and possibly other APOBECs.
authors.affiliation: Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, U.S.A.
authors.forename: Yang
authors.initials: Y
authors.lastname: Fu
authors.affiliation: Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, U.S.A.
authors.forename: Fumiaki
authors.initials: F
authors.lastname: Ito
authors.affiliation: Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, U.S.A.
authors.forename: Gewen
authors.initials: G
authors.lastname: Zhang
authors.affiliation: Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, U.S.A.
authors.forename: Braulio
authors.initials: B
authors.lastname: Fernandez
authors.affiliation: Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, U.S.A.
authors.forename: Hanjing
authors.initials: H
authors.lastname: Yang
authors.affiliation: Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, U.S.A. Department of Chemistry, Center of Excellence in NanoBiophysics, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, U.S.A.
authors.forename: Xiaojiang S
authors.initials: XS
authors.lastname: Chen
mesh_terms: D003564:Cytidine Deaminase / Q000737:chemistry* / Q000235:genetics; D003596:Cytosine / Q000737:chemistry*; D006801:Humans; D015778:Minor Histocompatibility Antigens; D015202:Protein Engineering; D017434:Protein Structure, Tertiary
chemical_list: D015778:Minor Histocompatibility Antigens; D003596:Cytosine; C495794:APOBEC3B protein, human; D003564:Cytidine Deaminase
keywords: cytosine/methylcytosine (C/mC) selectivity; enzyme engineering; multiple determinants for mC specificity; substrate specificity alteration; zinc (Zn) deaminase