PDBsum entry 2mr9

Hydrolase

PDB id: 2mr9

Contents

Protein chain

44 a.a.

PDB id:

2mr9

Name:

Hydrolase

Title:

Nmr structure of uba domain of DNA-damage-inducible 1 protein (ddi1)

Structure:

DNA damage-inducible protein 1. Chain: a. Fragment: ubiquitin associated domain, unp residues 389-428. 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:

10 models

Authors:

D.Zhang,D.Fushman

Key ref:

U.Nowicka et al. (2015). DNA-damage-inducible 1 protein (Ddi1) contains an uncharacteristic ubiquitin-like domain that binds ubiquitin. Structure, 23, 542-557. PubMed id: 25703377 DOI: 10.1016/j.str.2015.01.010

Date:

02-Jul-14 Release date: 04-Feb-15

Protein chain

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

Seq: 428 a.a.

Struc: 44 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.4.23.- - ?????

DOI no: 10.1016/j.str.2015.01.010

Structure 23:542-557 (2015)

PubMed id: 25703377

DNA-damage-inducible 1 protein (Ddi1) contains an uncharacteristic ubiquitin-like domain that binds ubiquitin.

U.Nowicka, D.Zhang, O.Walker, D.Krutauz, C.A.Castañeda, A.Chaturvedi, T.Y.Chen, N.Reis, M.H.Glickman, D.Fushman.

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.