PDBsum entry 2n7e

Unknown function

PDB id: 2n7e

Contents

Protein chain

86 a.a.

PDB id:

2n7e

Name:

Unknown function

Title:

Solution structure of the ubl domain of yeast ddi1

Structure:

DNA damage-inducible protein 1. Chain: a. Fragment: ubl domain (unp residues 1-80). Synonym: v-snare-master 1. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Gene: ddi1, vsm1, yer143w. Expressed in: escherichia coli. Expression_system_taxid: 562

NMR struc:

43 models

Authors:

M.Siva,K.Grantz Saskova,V.Veverka

Key ref:

J.F.Trempe et al. (2016). Structural studies of the yeast DNA damage-inducible protein Ddi1 reveal domain architecture of this eukaryotic protein family. Sci Rep, 6, 33671. PubMed id: 27646017 DOI: 10.1038/srep33671

Date:

09-Sep-15 Release date: 20-Jul-16

Protein chain

P40087  (DDI1_YEAST) -  DNA damage-inducible protein 1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 428 a.a.

Struc: 86 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.23.- - ?????

DOI no: 10.1038/srep33671

Sci Rep 6:33671 (2016)

PubMed id: 27646017

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

J.F.Trempe, K.G.Šašková, M.Sivá, C.D.Ratcliffe, V.Veverka, A.Hoegl, M.Ménade, X.Feng, S.Shenker, M.Svoboda, M.Kožíšek, J.Konvalinka, K.Gehring.

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.