Structural studies of the yeast DNA damage-inducible protein Ddi1 reveal domain architecture of this eukaryotic protein family

0464345 - ÚOCHB 2017 RIV GB eng J - Journal Article
Trempe, J. F. - Grantz Šašková, Klára - Sivá, Monika - Ratcliffe, C. D. H. - Veverka, Václav - Hoegl, A. - Ménade, M. - Feng, X. - Shenker, S. - Svoboda, Michal - Kožíšek, Milan - Konvalinka, Jan - Gehring, K.
Structural studies of the yeast DNA damage-inducible protein Ddi1 reveal domain architecture of this eukaryotic protein family.
Scientific Reports. Roč. 6, Sep 20 (2016), č. článku 33671. ISSN 2045-2322. E-ISSN 2045-2322
R&D Projects: GA MŠMT(CZ) LK11205; GA MŠMT(CZ) LO1304
Institutional support: RVO:61388963
Keywords : ubiquitin-associated domains * ray solution scattering * torsion angle dynamics
Subject RIV: CE - Biochemistry
Impact factor: 4.259, year: 2016
http://www.nature.com/articles/srep33671

The eukaryotic Ddi1 family is defined by a conserved retroviral aspartyl protease-like (RVP) domain found in association with a ubiquitin-like (UBL) domain. Ddi1 from Saccharomyces cerevisiae additionally contains a ubiquitin-associated (UBA) domain. The substrate specificity and role of the protease domain in the biological functions of the Ddi family remain unclear. Yeast Ddi1 has been implicated in the regulation of cell cycle progression, DNA-damage repair, and exocytosis. Here, we investigated the multi-domain structure of yeast Ddi1 using X-ray crystallography, nuclear magnetic resonance, and small-angle X-ray scattering. The crystal structure of the RVP domain sheds light on a putative substrate recognition site involving a conserved loop. Isothermal titration calorimetry confirms that both UBL and UBA domains bind ubiquitin, and that Ddi1 binds K48-linked diubiquitin with enhanced affinity. The solution NMR structure of a helical domain that precedes the protease displays tertiary structure similarity to DNA-binding domains from transcription regulators. Our structural studies suggest that the helical domain could serve as a landing platform for substrates in conjunction with attached ubiquitin chains binding to the UBL and UBA domains.
Permanent Link: http://hdl.handle.net/11104/0263262