PDBsum entry 1yx6

Hydrolase

PDB id: 1yx6

Contents

Protein chains

112 a.a.

76 a.a.

References listed in PDB file

Key reference

Title

Structure of s5a bound to monoubiquitin provides a model for polyubiquitin recognition.

Authors

Q.Wang, P.Young, K.J.Walters.

Ref.

J Mol Biol, 2005, 348, 727-739. [DOI no: 10.1016/j.jmb.2005.03.007]

PubMed id

15826667

Abstract

Ubiquitin is a key regulatory molecule in diverse cellular events. How cells determine the outcome of ubiquitylation remains unclear; however, a likely determinant is the specificity of ubiquitin receptor proteins for polyubiquitin chains of certain length and linkage. Proteasome subunit S5a contains two ubiquitin-interacting motifs (UIMs) through which it recruits ubiquitylated substrates to the proteasome for their degradation. Here, we report the structure of S5a (196-306) alone and complexed with two monoubiquitin molecules. This construct contains the two UIMs of S5a and we reveal their different ubiquitin-binding mechanisms and provide a rationale for their unique specificities for different ubiquitin-like domains. Furthermore, we provide direct evidence that S5a (196-306) binds either K63-linked or K48-linked polyubiquitin, and in both cases prefers longer chains. On the basis of these results we present a model for how S5a and other ubiquitin-binding proteins recognize polyubiquitin.

Figure 4.
Figure 4. S5a (196-306) binds both K48-linked and K63-linked polyubiquitin chains. His-S5a (196-306) on Ni-NTA resin was incubated for two hours with 5 µg of either K48-linked or K63-linked polyubiquitin with a chain length ranging from one to seven (BostonBiochem Inc.). Proteins were fractionated on gels, transferred to a membrane and then probed with a-ubiquitin. Samples of the input polyubiquitin chains used in these experiments are provided on the left.

Figure 5.
Figure 5. S5a flexible regions allow adaptable binding to tetraubiquitin. In (a) K48-linked tetraubiquitin from a crystal structure (PDB code 1TBE)39 binds each of the UIMs of S5a via its two distal ubiquitin moieties. A snapshot of the two UIMs contacting either (b) neighboring or (c) terminal ubiquitin moieties is provided for K48-linked tetraubiquitin, in which the ubiquitin subunits are not forced to contact each other. The ubiquitin moieties are numbered sequentially according to the position of a hypothetical protein substrate: Ub1 (colored red) would be attached to a protein substrate via its G76. This Figure was generated by using MOLSCRIPT.50

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 348, 727-739) copyright 2005.