Basis for Metabolite-dependent Cullin-RING Ligase Deneddylation by the COP9 Signalosome

The Cullin-RING ligases (CRLs) are the largest family of ubiquitin E3s activated by neddylation and regulated by the deneddylase COP9 signalosome (CSN). The inositol polyphosphate metabolites promote the formation of CRL-CSN complexes, but with unclear mechanism of action. Here, we provide structural and genetic evidence supporting inositol hexakisphosphate (IP) as a general CSN cofactor recruiting CRLs. We determined the crystal structure of IP in complex with CSN subunit 2 (CSN2), based on which we identified the IP-corresponding electron density in the cryoelectron microscopy map of a CRL4A-CSN complex. IP binds to a cognate pocket formed by conserved lysine residues from CSN2 and Rbx1/Roc1, thereby strengthening CRL-CSN interactions to dislodge the E2 CDC34/UBE2R from CRL and to promote CRL deneddylation. IP binding-deficient knockin mice are embryonic lethal. The same mutation disabled Csn2 from rescuing UV-hypersensitivity of -null yeast. These data suggest that CRL transition from the E2-bound active state to the CSN-bound sequestered state is critically assisted by an interfacial IP small molecule, whose metabolism may be coupled to CRL-CSN complex dynamics.