2MRP

NMR solution structure of the Ubiquitin like domain (UBL) of DNA-damage-inducible 1 protein (Ddi1)

2MRP の概要

• エントリーDOI: 10.2210/pdb2mrp/pdb
• 分子名称: DNA damage-inducible protein 1 (1 entity in total)
• 機能のキーワード: dna-damage-inducible 1 protein, ddi1, ubiquitin like domain, ubl, ubiquitin binding, ubiquitin-binding protein
• 由来する生物種: Saccharomyces cerevisiae (Baker's yeast)
• 細胞内の位置: Cytoplasm : P40087
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 10589.90

構造登録者

Nowicka, U.,Fushman, D.,Chen, T. (登録日: 2014-07-14, 公開日: 2015-03-11, 最終更新日: 2024-05-01)

主引用文献

Nowicka, U.,Zhang, D.,Walker, O.,Krutauz, D.,Castaneda, C.A.,Chaturvedi, A.,Chen, T.Y.,Reis, N.,Glickman, M.H.,Fushman, D.
DNA-Damage-Inducible 1 Protein (Ddi1) Contains an Uncharacteristic Ubiquitin-like Domain that Binds Ubiquitin.
Structure, 23:542-557, 2015

PubMed Abstract: 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.

PubMed: 25703377
DOI: 10.1016/j.str.2015.01.010

実験手法

SOLUTION NMR