School of Life Sciences and Biotechnology, Korea University, Anam-Dong, Korea.
Nat Struct Mol Biol. 2010 Oct;17(10):1175-81. doi: 10.1038/nsmb.1907. Epub 2010 Sep 12.
The N-end rule pathway is a regulated proteolytic system that targets proteins containing destabilizing N-terminal residues (N-degrons) for ubiquitination and proteasomal degradation in eukaryotes. The N-degrons of type 1 substrates contain an N-terminal basic residue that is recognized by the UBR box domain of the E3 ubiquitin ligase UBR1. We describe structures of the UBR box of Saccharomyces cerevisiae UBR1 alone and in complex with N-degron peptides, including that of the cohesin subunit Scc1, which is cleaved and targeted for degradation at the metaphase-anaphase transition. The structures reveal a previously unknown protein fold that is stabilized by a novel binuclear zinc center. N-terminal arginine, lysine or histidine side chains of the N-degron are coordinated in a multispecific binding pocket. Unexpectedly, the structures together with our in vitro biochemical and in vivo pulse-chase analyses reveal a previously unknown modulation of binding specificity by the residue at position 2 of the N-degron.
N 端规则途径是一种受调控的蛋白水解系统，可靶向含有不稳定 N 端残基（N 降解基）的蛋白，使其在真核生物中发生泛素化和蛋白酶体降解。1 型底物的 N 降解基含有一个 N 端碱性残基，该残基被 E3 泛素连接酶 UBR1 的 UBR 盒结构域识别。我们描述了酿酒酵母 UBR1 的 UBR 盒结构，包括其结构与 N 降解肽的复合物结构，其中包括黏合蛋白亚基 Scc1，其在有丝分裂-后期转换时被切割并靶向降解。这些结构揭示了一个以前未知的蛋白折叠结构，由一个新的双核锌中心稳定。N 降解基的 N 端精氨酸、赖氨酸或组氨酸侧链在一个多特异性结合口袋中配位。出乎意料的是，这些结构以及我们的体外生化和体内脉冲追踪分析揭示了一个以前未知的 N 降解基第 2 位残基对结合特异性的调节作用。
