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

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 binding(1-4). 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 beta- 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 structure(6). 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.