PDBsum entry 3m63

Ligase/protein binding

PDB id: 3m63

Contents

Protein chains

953 a.a. *

72 a.a. *

Ligands

1PE

Metals

__K

Waters ×183

* Residue conservation analysis

PDB id:

3m63

Name:

Ligase/protein binding

Title:

Crystal structure of ufd2 in complex with the ubiquitin-like (ubl) domain of dsk2

Structure:

Ubiquitin conjugation factor e4. Chain: a. Synonym: ubiquitin fusion degradation protein 2, ub fusion protein 2. Engineered: yes. Mutation: yes. Ubiquitin domain-containing protein dsk2. Chain: b. Fragment: unp residues 1-75, ubiquitin-like domain. Engineered: yes

Source:

Saccharomyces cerevisiae. Yeast. Organism_taxid: 4932. Gene: d1255, ufd2, ydl190c. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: dsk2, she4, ym8021.02, ymr276w.

Resolution:

2.40Å R-factor: 0.210 R-free: 0.270

Authors:

P.Haenzelmann,H.Schindelin

Key ref:

P.Hänzelmann et al. (2010). The yeast E4 ubiquitin ligase Ufd2 interacts with the ubiquitin-like domains of Rad23 and Dsk2 via a novel and distinct ubiquitin-like binding domain. J Biol Chem, 285, 20390-20398. PubMed id: 20427284

Date:

15-Mar-10 Release date: 28-Apr-10

Protein chain

P54860  (UFD2_YEAST) -  E4 ubiquitin-protein ligase UFD2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 961 a.a.

Struc: 953 a.a.

Protein chain

P48510  (DSK2_YEAST) -  Ubiquitin domain-containing protein DSK2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 373 a.a.

Struc: 72 a.a.

Enzyme reactions

• Enzyme class: Chain A: E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.
• Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N₆- ubiquitinyl-[acceptor protein]-L-lysine

J Biol Chem 285:20390-20398 (2010)

PubMed id: 20427284

The yeast E4 ubiquitin ligase Ufd2 interacts with the ubiquitin-like domains of Rad23 and Dsk2 via a novel and distinct ubiquitin-like binding domain.

P.Hänzelmann, J.Stingele, K.Hofmann, H.Schindelin, S.Raasi.

ABSTRACT

Proteins containing ubiquitin-like (UBL) and ubiquitin-associated (UBA) domains interact with various binding partners and function as hubs during ubiquitin-mediated protein degradation. A common interaction of the budding yeast UBL-UBA proteins Rad23 and Dsk2 with the E4 ubiquitin ligase Ufd2 has been described in endoplasmic reticulum-associated degradation among other pathways. The UBL domains of Rad23 and Dsk2 play a prominent role in this process by interacting with Ufd2 and different subunits of the 26 S proteasome. Here, we report crystal structures of Ufd2 in complex with the UBL domains of Rad23 and Dsk2. The N-terminal UBL-interacting region of Ufd2 exhibits a unique sequence pattern, which is distinct from any known ubiquitin- or UBL-binding domain identified so far. Residue-specific differences exist in the interactions of these UBL domains with Ufd2, which are coupled to subtle differences in their binding affinities. The molecular details of their differential interactions point to a role for adaptive evolution in shaping these interfaces.