Abstract
The human APOBEC3G protein is a cytidine deaminase that generates cytidine to deoxy-uridine mutations in single-stranded DNA (ssDNA), and capable of restricting replication of HIV-1 by generating mutations in viral genome. The mechanism by which APOBEC3G specifically deaminates 5′-CC motifs has remained elusive since structural studies have been hampered due to apparently weak ssDNA binding of the catalytic domain of APOBEC3G. We overcame the problem by generating a highly active variant with higher ssDNA affinity. Here, we present the crystal structure of this variant complexed with a ssDNA substrate at 1.86 Å resolution. This structure reveals atomic-level interactions by which APOBEC3G recognizes a functionally-relevant 5′-TCCCA sequence. This complex also reveals a key role of W211 in substrate recognition, implicating a similar recognition in activation-induced cytidine deaminase (AID) with a conserved tryptophan.
Highlights
The human APOBEC3G protein is a cytidine deaminase that generates cytidine to deoxyuridine mutations in single-stranded DNA, and capable of restricting replication of human immunodeficiency virus type 1 (HIV-1) by generating mutations in viral genome
The sidechain of D317 is coordinated by a hydrogen bond formed between the carboxyl group and the mainchain amino proton of F289
Since we reported the first structure of the catalytic domain of A3G almost 10 years ago[23], structural studies of the A3GCTD–single-stranded DNA (ssDNA) complex have been hampered by apparently weak binding of A3G-C-terminal domain (CTD) to ssDNA23,31
Summary
The human APOBEC3G protein is a cytidine deaminase that generates cytidine to deoxyuridine mutations in single-stranded DNA (ssDNA), and capable of restricting replication of HIV-1 by generating mutations in viral genome. We present the crystal structure of this variant complexed with a ssDNA substrate at 1.86 Å resolution This structure reveals atomic-level interactions by which APOBEC3G recognizes a functionally-relevant 5′-TCCCA sequence. This complex reveals a key role of W211 in substrate recognition, implicating a similar recognition in activation-induced cytidine deaminase (AID) with a conserved tryptophan. Of the seven human APOBEC3 proteins, A3D, A3F, A3G, and A3H can restrict HIV-1, and hypermutation of the virus genomes by their deamination activity is the primary mechanism by which these A3 proteins restrict HIV-110–13.
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