Crystal structure of rice APIP6 reveals a new dimerization mode of RING-type E3 ligases that facilities the construction of its working model

Ubiquitination is an important modification process in eukaryotic organisms, and ubiquitin ligase (E3) is the most diversified component of this system. APIP6 (AvrPiz-t interacting protein 6) is one of the E3s of rice, and is involved in the recognition of AvrPiz-t, one effector from the pathogen Magnaporthe oryzae, for the initiation of host defense against M. oryzae. However, the structural detail of how APIP6 performs its function remains elusive. Here, we present crystal structure of the RING domain (i.e., the E2-interaction domain) of APIP6 (APIP6-RING). APIP6-RING exists as a homodimer in crystal packing, in solution and in vivo. APIP6-RING consists of one β hairpin and one α helix, and β hairpins of two APIP6-RING molecules interact with each other in a novel ‘shoulder-to-shoulder’ mode to form a β sheet, and also rendering APIP6-RING to form a homodimer. Hydrogen bonds play a major role in the dimer formation of APIP6-RING, while hydrophobic-intermolecular interactions are inconspicuous. Due to the interaction mode between RING-type E3 and E2 is generally conserved, we constructed and verified a model of APIP6-RING/E2 complex, and proposed a working model of APIP6 with E2, ubiquitin, and the substrate AvrPiz-t. Taken together, our research presents the first structure of plant simple RING-type E3 ligase that exists in an unreported dimerization manner, as well as a working model of APIP6.