Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications

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Abstract
This paper describes a high-resolution crystal structure of the catalytic deaminase CD2 domain of APOBEC3G, a human antiviral defence protein that restricts replication of HIV and hepatitis B virus. This structure will provide a basis to pursue further functional studies of proteins of the APOBEC superfamily that will facilitate our understanding of their important biological functions, such as how they interact with nucleic acid substrates for deamination, how their activity is regulated, and how they restrict HIV and other viral pathogens. The APOBEC family members are involved in diverse biological functions. APOBEC3G restricts the replication of human immunodeficiency virus (HIV), hepatitis B virus and retroelements by cytidine deamination on single-stranded DNA or by RNA binding1,2,3,4. Here we report the high-resolution crystal structure of the carboxy-terminal deaminase domain of APOBEC3G (APOBEC3G-CD2) purified from Escherichia coli. The APOBEC3G-CD2 structure has a five-stranded β-sheet core that is common to all known deaminase structures and closely resembles the structure of another APOBEC protein, APOBEC2 (ref. 5). A comparison of APOBEC3G-CD2 with other deaminase structures shows a structural conservation of the active-site loops that are directly involved in substrate binding. In the X-ray structure, these APOBEC3G active-site loops form a continuous ‘substrate groove’ around the active centre. The orientation of this putative substrate groove differs markedly (by 90 degrees) from the groove predicted by the NMR structure6. We have introduced mutations around the groove, and have identified residues involved in substrate specificity, single-stranded DNA binding and deaminase activity. These results provide a basis for understanding the underlying mechanisms of substrate specificity for the APOBEC family.