Phosphorylation by PINK1 Releases the UBL Domain and Initializes the Conformational Opening of the E3 Ubiquitin Ligase Parkin
Figure 5
Phosphorylation of Ser65 releases the safety belts of Parkin.
A) Zoom into safety belt 1: The UBL blocks RING1 and IBR domains. Key cysteine residues of the E2 binding site in RING1 are indicated. The E2 binding site was defined as follows: Ile236, Thr237, Cys238, Ile239, Thr240, Cys241, Thr242, Asp243, Val244, Arg245, Ile259, Cys260, Leu261, Asp262, Cys263, Phe264, His265, Leu266, and Tyr267 B) The distance between UBL domain (Leu26) and RING1 (Cys238) significantly increased over time MDS. C) Similarly, the distance between UBL (Leu26) and IBR (Phe364) domains significantly increased over time MDS. D) Zoom into safety belt 2: The REP region blocks the E2 binding site in RING1 (as defined in A). E) Dynamic change in REP-RING1 interaction during Parkin opening motion. Graph shows the release of the REP region from the E2-binding site in RING1 as measured by RMSD. The RING1 is released from the REP region by MdMD time of 20 ns, exposing the E2 binding site. F) Loosened interaction between the center Tyr391 in REP region and Cys238 in RING1. The distance increases from 10 to 20 Å. During longer simulations, the distance eventually collapses as the UBL domain moves away and E2 binding has transiently occurred. Across many replicates, we find that the availability of adequate space for an E2 enzyme to approach the binding site in RING1 begins somewhere between 5–22 ns. G) Zoom into safety belt 3: Cys431 is buried by RING0. H) Release of the active site (Cys431) from RING0 (Arg163 C-alpha atom) as measured by RMSD for center-of-mass. RMSD increases moderately over time indicative of a less compacted area. I) SASA for Cys431 entire residue. During MDS, more water is available to Cys431, indicating its enhanced exposure.