PDBsum entry 1zc1

Protein turnover

PDB id: 1zc1

Contents

Protein chain

208 a.a. *

* Residue conservation analysis

PDB id:

1zc1

Name:

Protein turnover

Title:

Ufd1 exhibits the aaa-atpase fold with two distinct ubiquitin interaction sites

Structure:

Ubiquitin fusion degradation protein 1. Chain: a. Fragment: n domain, residues 1-208. Synonym: ub fusion protein 1, polymerase-interacting protein 3. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: ufd1, pip3. Expressed in: escherichia coli. Expression_system_taxid: 562

NMR struc:

15 models

Authors:

S.Park,R.Isaacson,H.T.Kim,P.A.Silver,G.Wagner

Key ref:

S.Park et al. (2005). Ufd1 exhibits the AAA-ATPase fold with two distinct ubiquitin interaction sites. Structure, 13, 995. PubMed id: 16004872 DOI: 10.1016/j.str.2005.04.013

Date:

10-Apr-05 Release date: 26-Jul-05

Protein chain

P53044  (UFD1_YEAST) -  Ubiquitin fusion degradation protein 1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 361 a.a.

Struc: 208 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/j.str.2005.04.013

Structure 13:995 (2005)

PubMed id: 16004872

Ufd1 exhibits the AAA-ATPase fold with two distinct ubiquitin interaction sites.

S.Park, R.Isaacson, H.T.Kim, P.A.Silver, G.Wagner.

ABSTRACT

Ufd1 mediates ubiquitin fusion degradation by association with Npl4 and Cdc48/p97. The Ufd1-ubiquitin interaction is essential for transfer of substrates to the proteasome. However, the mechanism and specificity of ubiquitin recognition by Ufd1 are poorly understood due to the lack of detailed structural information. Here, we present the solution structure of yeast Ufd1 N domain and show that it has two distinct binding sites for mono- and polyubiquitin. The structure exhibits striking similarities to the Cdc48/p97 N domain. It contains the double-psi beta barrel motif, which is thus identified as a ubiquitin binding domain. Significantly, Ufd1 shows higher affinity toward polyubiquitin than monoubiquitin, attributable to the utilization of separate binding sites with different affinities. Further studies revealed that the Ufd1-ubiquitin interaction involves hydrophobic contacts similar to those in well-characterized ubiquitin binding proteins. Our results provide a structural basis for a previously proposed synergistic binding of polyubiquitin by Cdc48/p97 and Ufd1.

Selected figure(s)

Figure 1.
Figure 1. Structure, Sequence Alignment, and p97 Association of Ufd1
(A) Schematic model of the Ufd1-Npl4-p97 complex based on the 6-fold symmetry of the p97 AAA-ATPase. See text for the domain names.
(B) Ensemble of backbone traces of the 15 lowest-energy conformers of Ufd1. Regular secondary structured regions are aligned and overlaid to generate the ensemble.
(C) Ribbon diagram of the lowest-energy conformer of the ensemble showing the presence of the two separate domains. The Nn subdomain is in red, and the Nc subdomain is in blue. Secondary structural elements are numbered. The two psi loops (psi1 and psi2) in the double-psi b barrel are also labeled. The position of the V94 found in ufd1-1 is shown.
(D) Structure-based sequence alignment of Ufd1, its orthologs, and the p97 N domain. The alignments within the Ufd1 orthologs were generated with the ClustalX program. The alignment of p97 to the rest of the sequences is based on the experimental structure of S. cerevisiae Ufd1 reported here and the mouse p97 N domain structure reported previously (Dreveny et al., 2004) and differs from a previously proposed alignment (Golbik et al., 1999). The conserved residues are in red and boxed in blue, with the strictly conserved residues in all of the sequences in inverse shading in red. The secondary structure cartoon (red) above the alignment is for the yeast Ufd1, and the one below (blue) is for p97. The residue numbering above the alignment is for the S. cerevisiae sequence used in this study. The gene bank accession numbers of the sequences used are: S. ser, gi1717964; H. sap, gi12053683; M. mus, gi2501439; C. ele, gi2501440; A. tha, gi42573225; S. pom, gi3123677; p97, gi14488635.

The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 995-0) copyright 2005.

Figure was selected by the author.