Nowicka Urszula, Zhang Daoning, Walker Olivier, Krutauz Daria, Castañeda Carlos A, Chaturvedi Apurva, Chen Tony Y, Reis Noa, Glickman Michael H, Fushman David
Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA.
Institut des Sciences Analytiques, UMR5280-Université de Lyon, 69100 Villeurbanne, France.
Structure. 2015 Mar 3;23(3):542-557. doi: 10.1016/j.str.2015.01.010. Epub 2015 Feb 19.
Ddi1 belongs to a family of shuttle proteins targeting polyubiquitinated substrates for proteasomal degradation. Unlike the other proteasomal shuttles, Rad23 and Dsk2, Ddi1 remains an enigma: its function is not fully understood and structural properties are poorly characterized. We determined the structure and binding properties of the ubiquitin-like (UBL) and ubiquitin-associated (UBA) domains of Ddi1 from Saccharomyces cerevisiae. We found that while Ddi1UBA forms a characteristic UBA:ubiquitin complex, Ddi1UBL has entirely uncharacteristic binding preferences. Despite having a ubiquitin-like fold, Ddi1UBL does not interact with typical UBL receptors but unexpectedly binds ubiquitin, forming a unique interface mediated by hydrophobic contacts and by salt bridges between oppositely charged residues of Ddi1UBL and ubiquitin. In stark contrast to ubiquitin and other UBLs, the β-sheet surface of Ddi1UBL is negatively charged and therefore is recognized in a completely different way. The dual functionality of Ddi1UBL, capable of binding both ubiquitin and proteasome, suggests an intriguing mechanism for Ddi1 as a proteasomal shuttle.
Ddi1属于一类穿梭蛋白家族，该家族将多聚泛素化底物靶向蛋白酶体进行降解。与其他蛋白酶体穿梭蛋白Rad23和Dsk2不同，Ddi1仍是一个谜：其功能尚未完全了解，结构特性也鲜有描述。我们确定了酿酒酵母中Ddi1的类泛素（UBL）和泛素相关（UBA）结构域的结构及结合特性。我们发现，虽然Ddi1UBA形成了典型的UBA：泛素复合物，但Ddi1UBL具有完全非典型的结合偏好。尽管具有类泛素折叠结构，但Ddi1UBL并不与典型的UBL受体相互作用，而是意外地结合泛素，形成了一个由疏水接触以及Ddi1UBL和泛素带相反电荷残基之间的盐桥介导的独特界面。与泛素和其他UBL形成鲜明对比的是，Ddi1UBL的β折叠表面带负电荷，因此其识别方式完全不同。Ddi1UBL能够结合泛素和蛋白酶体的双重功能，为Ddi1作为蛋白酶体穿梭蛋白提供了一种有趣的机制。
