Crystal structure of GCN5 PCAF N-terminal domain reveals atypical ubiquitin ligase structure.

General control non-derepressible 5 (GCN5, also known as Kat2a) and p300/CBP-associated factor (PCAF, also known as Kat2b) are two homologous acetyltransferases. Both proteins share similar domain architecture consisting of a PCAF N-terminal (PCAF_N) domain, acetyltransferase domain and a bromodomain. PCAF also acts as a ubiquitin E3 ligase whose activity is attributable to PCAF_N domain, but its structural aspects are largely unknown. Here, we demonstrated that GCN5 exhibited ubiquitination activity in a similar manner to PCAF and its activity was supported by the ubiquitin-conjugating enzyme UbcH5. Moreover, we determined the crystal structure of PCAF_N domain at 1.8 A resolution and found PCAF_N domain folds into a helical structure with a characteristic binuclear Zn region, which was not predicted from sequence analyses. The Zn region is distinct from that of known E3 ligase structures, suggesting this region may form a new class of E3 ligase. Our biochemical and structural study provides new insight into not only the functional significance of GCN5 but also into ubiquitin biology.