Fig. 2: Complex structure of PRT1ZZ with N-degron.
a A. thaliana BB has a proteolytic site cleaved by DA1 protease. As a result, cleaved BB (Tyr61-BB) has an exposed tyrosine residue at the N-terminus, which is an N-degron. To mimic this N-degron, the YKFG amino acid sequence was added between LC3B and PRT1ZZ by mutagenesis. The N-degron residues (Tyr, Phe, and Trp) are exposed by cleaving LC3B using ATG4B protease. b Complex structure of PRT1ZZ with the N-degron of Tyr61-BB. Tyr317 at site 1 (red dotted box) and Ile333 and Phe352 at site 2 (blue dotted box) are key residues interacting with N-degron. c Close-up view of N-degron-binding region with a transparent electrostatic surface. d Structural superposition of N-degron-bound PRT1ZZ (cyan) and apo-form (orange). L2 and L3 loops are very flexible without bound N-degron. e Close-up view of the superposition of the N-degron-binding region. Compared with the apo-form ZZ domain, the flexible loops underwent a large conformational change upon complex formation. The movements of the residues upon complex formation are as follows: Phe352 − 9.5 Å and Ile333 − 2.9 Å.
