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Docking SspB-ClpX

Goal

To generate an interaction model for the SspB-ClpX system used in our V sublab.

Background

In the ClpXP proteolysis model reported by McGinness et al (McGinnes et al, 2006 - FALTA LINK) SspB acts as an adaptor protein which helps in the target protein degradation (general information of SspB is presented in table 1). This SspB protein interacts with the protease subunit ClpX. ClpX (information of this protein available in table 2) forms a protease complex with ClpP in which the target protein is degraded.

[Table 1]. Relevant information of SspB protein from Uniprot protein database entry B1XHK1 (http://www.uniprot.org/uniprot/B1XHK1) and the corresponding SspB Pfam database entry. (http://pfam.sanger.ac.uk/protein/B1XHK1)

[Table 2]. Relevant information of ClpX protein from Uniprot protein database entry P0A6H1 and the corresponding ClpX Pfam database entry.

The complete structure of ClpX was published by Glynn (Glynn et al, 2009) and it is displayed in figure 1. This molecule acquires a homohexameric ring-like structure which allows the peptidic degradation process when interacting with ClpP, the other protease subunit.

[Figure 1]. ClpX protein complex (from PDB entry 3hte). A. Structure coloured by chain. B. Same structure displaying the AAA 2 protein domain (red) and the ClpB D2-small domain (blue). More information of these domains is available in the ClpX protein Pfam entry.