4Z2Z

New crystal structure of yeast Ddi1 aspartyl protease reveals substrate engagement mode

Summary for 4Z2Z

• Entry DOI: 10.2210/pdb4z2z/pdb
• Descriptor: DNA damage-inducible protein 1 (2 entities in total)
• Functional Keywords: protease, ddi1, hydrolase
• Biological source: Saccharomyces cerevisiae (Baker's yeast)
• Total number of polymer chains: 2
• Total formula weight: 32663.94

Authors

Trempe, J.-F.,Feng, X.,Gehring, K. (deposition date: 2015-03-30, release date: 2016-04-13, Last modification date: 2023-09-27)

Primary citation

Trempe, J.F.,Saskova, K.G.,Siva, M.,Ratcliffe, C.D.,Veverka, V.,Hoegl, A.,Menade, M.,Feng, X.,Shenker, S.,Svoboda, M.,Kozisek, M.,Konvalinka, J.,Gehring, K.
Structural studies of the yeast DNA damage-inducible protein Ddi1 reveal domain architecture of this eukaryotic protein family.
Sci Rep, 6:33671-33671, 2016

PubMed Abstract: 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.

PubMed: 27646017
DOI: 10.1038/srep33671

Experimental method

X-RAY DIFFRACTION (1.8 Å)