title: APOBEC4, a new member of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases predicted by computational analysis.
abstract: Using iterative database searches, we identified a new subfamily of the AID/APOBEC family of RNA/DNA editing cytidine deaminases. The new subfamily, which is represented by readily identifiable orthologs in mammals, chicken, and frog, but not fishes, was designated APOBEC4. The zinc-coordinating motifs involved in catalysis and the secondary structure of the APOBEC4 deaminase domain are evolutionarily conserved, suggesting that APOBEC4 proteins are active polynucleotide (deoxy)cytidine deaminases. In reconstructed maximum likelihood phylogenetic trees, APOBEC4 forms a distinct clade with a high statistical support. APOBEC4 and APOBEC1 are joined in a moderately supported cluster clearly separated from AID, APOBEC2 and APOBEC3 subfamilies. In mammals, APOBEC4 is expressed primarily in testis which suggests the possibility that it is an editing enzyme for mRNAs involved in spermatogenesis.
authors.affiliation: National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, Maryland 20894, USA.
authors.forename: Igor B
authors.initials: IB
authors.lastname: Rogozin
authors.forename: Malay K
authors.initials: MK
authors.lastname: Basu
authors.forename: I King
authors.initials: IK
authors.lastname: Jordan
authors.forename: Youri I
authors.initials: YI
authors.lastname: Pavlov
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Koonin
mesh_terms: D000071478:APOBEC Deaminases; D000071479:APOBEC-1 Deaminase; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D003564:Cytidine Deaminase / Q000737:chemistry / Q000378:metabolism / Q000502:physiology*; D043525:Cytosine Deaminase / Q000378:metabolism; D004926:Escherichia coli / Q000378:metabolism; D019143:Evolution, Molecular; D006801:Humans; D016013:Likelihood Functions; D008297:Male; D051379:Mice; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009700:Nucleoside Deaminases / Q000737:chemistry*; D010802:Phylogeny; D011487:Protein Conformation; D017393:RNA Editing; D012333:RNA, Messenger / Q000378:metabolism; D012984:Software; D014018:Tissue Distribution; D014981:Xenopus; D015032:Zinc / Q000737:chemistry
chemical_list: D012333:RNA, Messenger; D009700:Nucleoside Deaminases; D043525:Cytosine Deaminase; D000071479:APOBEC-1 Deaminase; C000605089:APOBEC1 protein, human; C000605090:Apobec1 protein, mouse; D000071478:APOBEC Deaminases; C502889:APOBEC3 proteins, human; C510823:APOBEC4 protein, human; C510824:Apobec4 protein, mouse; D003564:Cytidine Deaminase; C011530:deoxycytidine deaminase; D015032:Zinc