Molecular Playground/Hexameric ClpX
From Proteopedia
ClpX is a CBI Molecules that is being studied in the Chemistry-Biology Interface Program at the University of Massachusetts Amherst. This is the banner for its display at Molecular Playground: "ClpX ‘spring cleans’ by dumping some proteins and refolding others."
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Introduction
ClpX is known to function as a molecular chaperone that unfolds native proteins, and as a protein degradation machinery when it forms a complex with the protease ClpP. Six ClpX form a homo-hexamer that almost resembles a (electron micrographs). The top of the ring contain regions that assist in recognizing specific protein motifs. These proteins are unfolded through the central pore, and sent out of the bottom of the ring.
ClpX belongs to the AAA+ (ATPases Associated with diverse cellular Activities) family of proteins which require chemical energy from ATP hydrolysis for mechanical activity. The crystal structure of hexameric ClpX without ATP and with ATP from Escherichia coli was solved in 2009 ([1]). Before that, there was only the crystal structure of monomeric ClpX from Helicobacter pylori, therefore information about the mechanistic abilities of hexameric ClpX was limited.
The repetitive structural changes for hexameric ClpX can be visualized here: Motion representation of hexameric ClpX.
Hexameric Structure of ClpX
Hexameric ClpX has a highly and .
The central pore contain along the pore channel known as the RKH loops, pore-1 (GYVG) loops, and pore-2 loops [2], [3]. Loops at the top of the hexamer interacts help recognize specific protein motifs. The other loops coordinate to transport proteins through the pore channel. Loops at the bottom of the hexamer interact with the ClpX-partner protease, ClpP, and passes on the denatured proteins for degradation into short peptides.
The hexamer contain that interface to form a near 2-fold rotational symmetry [4]. Each consist of a large AAA+ domain, small AAA+ domain, and a linker that joins the two domain.
Even though the structure is literally a homo-hexamer, the subunits are structurally heterogenous. Two have been distinguished as "Type-1 subunits" where ADP nucleotides were found, and "Type-2 subunits" which do not contain ADP nucleotides [5]. There are altogether four Type-1 subunits and two Type-2 subunits in a hexameric ClpX, fashioned in a cyclic 1-1-2-1-1 manner[6]. Therefore, in sum, there are only four sites for ATP/ADP nucleotide binding, instead of six sites given that there are six ClpX monomers units, and this is not surprising because of previous experimental findings that ClpX hexamer bind a maximum number of four ATP only.
The positioning of Leucine 317 in the linker region is responsible for ADP (or ATP) binding. The contacts the adenine base of the nucleotide ADP within the loop of the linker, while the faces the opposite direction, causing conformation changes that prevents ADP binding .
Interestingly, the large domain in the two types of subunits are structurally similar, however structural variability is obvious in the small domain ( | )
Taken together, these structure characteristics attribute to the mechanistic motion of hexameric ClpX ().
My research interest
To further define the specificity of ClpX function and determine its influences beyond cell cycle regulation.
References
Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine. Glynn et al. Cell (2009) 139 (4): 744-56 [7].
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Ashkenazy H., Erez E., Martz E., Pupko T. and Ben-Tal N. (2010) Nucleic Acids Res; DOI: 10.1093/nar/gkq399; PMID: 20478830 [8].
The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework. WG Krebs, M Gerstein (2000) Nucleic Acids Res 28: 1665-75[9].
Acknowledgment
Emeritus Professor Eric Martz, for his kind consultation.
