Structure-function analyses point to a polynucleotide-accommodating groove essential for APOBEC3A restriction activities.
Members of the human APOBEC3 family of editing enzymes can inhibit various mobile genetic elements. APOBEC3A (A3A) can block the retrotransposon LINE-1 and the parvovirus adeno-associated virus type 2 (AAV-2) but does not inhibit retroviruses. In contrast, APOBEC3G (A3G) can block retroviruses but has only limited effects on AAV-2 or LINE-1. What dictates this differential target specificity remains largely undefined. Here, we modeled the structure of A3A based on its homology with the C-terminal domain of A3G and further compared the sequence of human A3A to those of 11 nonhuman primate orthologues. We then used these data to perform a mutational analysis of A3A, examining its ability to restrict LINE-1, AAV-2, and foreign plasmid DNA and to edit a single-stranded DNA substrate. The results revealed an essential functional role for the predicted single-stranded DNA-docking groove located around the A3A catalytic site. Within this region, amino acid differences between A3A and A3G are predicted to affect the shape of the polynucleotide-binding groove. Correspondingly, transferring some of these A3A residues to A3G endows the latter protein with the ability to block LINE-1 and AAV-2. These results suggest that the target specificity of APOBEC3 family members is partly defined by structural features influencing their interaction with polynucleotide substrates.
School of Life Sciences and Frontiers-in-Genetics National Program, Ecole Polytechnique Fe´de´rale de Lausanne,1015 Lausanne, Switzerland.
Yannick
Y
Bulliard
Iñigo
I
Narvaiza
Alessandro
A
Bertero
Shyam
S
Peddi
Ute F
UF
Röhrig
Millán
M
Ortiz
Vincent
V
Zoete
Nataly
N
Castro-Díaz
Priscilla
P
Turelli
Amalio
A
Telenti
Olivier
O
Michielin
Matthew D
MD
Weitzman
Didier
D
Trono
D000071480:APOBEC-3G Deaminase; D000818:Animals; D001483:Base Sequence; D003564:Cytidine Deaminase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D004277:DNA, Single-Stranded / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D000229:Dependovirus / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D057809:HEK293 Cells; D000882:Haplorhini; D006367:HeLa Cells; D006801:Humans; D020084:Long Interspersed Nucleotide Elements / Q000235:genetics / Q000502:physiology*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D010957:Plasmids; D011119:Polynucleotides / Q000737:chemistry / Q000378:metabolism*; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D018626:Retroelements / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D013329:Structure-Activity Relationship; D013379:Substrate Specificity
D004277:DNA, Single-Stranded; D011119:Polynucleotides; D011506:Proteins; D018626:Retroelements; D000071480:APOBEC-3G Deaminase; C121399:APOBEC3A protein, human; C464924:APOBEC3G protein, human; D003564:Cytidine Deaminase