PDBsum entry 2g3q

Endocytosis/signaling protein

PDB id: 2g3q

Contents

Protein chains

43 a.a. *

76 a.a. *

* Residue conservation analysis

PDB id:

2g3q

Name:

Endocytosis/signaling protein

Title:

Solution structure of ede1 uba-ubiquitin complex

Structure:

Protein ybl047c. Chain: a. Fragment: ede1 uba, residues 1339-1381. Engineered: yes. Ubiquitin. Chain: b. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: ede1. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

NMR struc:

20 models

Authors:

K.A.Swanson,L.Hicke,I.Radhakrishnan

Key ref:

K.A.Swanson et al. (2006). Structural basis for monoubiquitin recognition by the Ede1 UBA domain. J Mol Biol, 358, 713-724. PubMed id: 16563434 DOI: 10.1016/j.jmb.2006.02.059

Date:

20-Feb-06 Release date: 09-May-06

Protein chain

P34216  (EDE1_YEAST) -  EH domain-containing and endocytosis protein 1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1381 a.a.

Struc: 43 a.a.

Protein chain

P0CG63  (UBI4P_YEAST) -  Polyubiquitin from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 381 a.a.

Struc: 76 a.a.

DOI no: 10.1016/j.jmb.2006.02.059

J Mol Biol 358:713-724 (2006)

PubMed id: 16563434

Structural basis for monoubiquitin recognition by the Ede1 UBA domain.

K.A.Swanson, L.Hicke, I.Radhakrishnan.

ABSTRACT

Monoubiquitination is a general mechanism for downregulating the activity of cell surface receptors by consigning these proteins for lysosome-mediated degradation through the endocytic pathway. The yeast Ede1 protein functions at the internalization step of endocytosis and binds monoubiquitinated proteins through a ubiquitin associated (UBA) domain. UBA domains are found in a broad range of cellular proteins but previous studies have suggested that the mode of ubiquitin recognition might not be universally conserved. Here we present the solution structure of the Ede1 UBA domain in complex with monoubiquitin. The Ede1 UBA domain forms a three-helix bundle structure and binds ubiquitin through a largely hydrophobic surface in a manner reminiscent of the Dsk2 UBA and the remotely homologous Cue2 CUE domains, for which high-resolution structures have been described. However, the interaction is dissimilar to the molecular models proposed for the hHR23A UBA domains bound to either monoubiquitin or Lys48-linked diubiquitin. Our mutational analyses of the Ede1 UBA domain-ubiquitin interaction reveal several key affinity determinants and, unexpectedly, a negative affinity determinant in the wild-type Ede1 protein, implying that high-affinity interactions may not be the sole criterion for optimal function of monoubiquitin-binding endocytic proteins.

Selected figure(s)

Figure 2.
Figure 2. Solution structure of the Ede1 UBA domain–ubiquitin complex. (a) Stereo views of the C^α trace following a best fit superposition of the backbone atoms in well-ordered regions (1342–1378 of Ede1 and 1–70 of ubiquitin) in the ensemble of 20 NMR structures. The Ede1 UBA domain is colored light blue, whereas ubiquitin is shown in green. (b) Stereo views of the representative structure from the ensemble shown in a ribbon representation.

Figure 5.
Figure 5. Structural comparison of the monoubiquitin binding modes of the Ede1 UBA, Cue2 CUE^14 and Dsk2 UBA^13 domains. (a) A structure-guided multiple sequence alignment of the Ede1 UBA, Dsk2 UBA and Cue2 CUE domains. Residues in helical regions are shown in uppercase and in bold font for clarity. Residues constituting the hydrophobic cores of the respective domains are shaded in yellow, whereas those that interact with ubiquitin in the respective complexes are shaded in light blue. (b) Comparison of the Ede1 UBA domain–ubiquitin (light blue) and Dsk2 UBA domain–ubiquitin (purple) complexes following a best-fit superposition of the backbone atoms of residues 1–70 of ubiquitin. (c) Ribbon diagrams of the Ede1 UBA domain (light blue) and Cue2 CUE domain (magenta)–monoubiquitin complexes following a best-fit superposition of the polypeptide backbone encompassing residues 1–70 of ubiquitin.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 358, 713-724) copyright 2006.

Figures were selected by an automated process.