Molecular Playground/Hexameric ClpX

From Proteopedia

Revision as of 07:04, 11 December 2010

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."

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 monomers 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 a monomeric crystal structure of ClpX from Helicobacter pylori, therefore information about the mechanistic abilities of hexameric ClpX was limited.

The repetitive motion of hexameric ClpX due to ATP hydrolysis can be visualized [2] through the use of the above mentioned crystal structures ().

Hexameric Structure of ClpX

Hexameric ClpX has a highly and .

The central pore contains along the pore channel known as the RKH loops (not shown), pore-1 (GYVG) loops, and pore-2 loops [3], [4]. Loops at the top of the hexamer help recognize specific protein motifs. The other loops coordinate to denature and 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.

Hexameric ClpX contain that interface to form a near 2-fold rotational symmetry ([5]). 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" which have binding sites for ADP (or ATP), and "Type-2 subunits" which cannot bind ADP (or ATP) [6]. 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[7]. Therefore, in sum, there are only four sites for ATP/ADP nucleotide binding, instead of six sites typical of AAA+ hexameric ATPases [8]. This is not surprising because of previous experimental findings that ClpX hexamer bind a maximum number of four ATP only [9].

The positioning of Leucine 317 in the linker region is responsible for the availability of an ADP (or ATP) binding site. contacts the adenine base of the nucleotide ADP within the loop of the linker, while faces the opposite direction, causing conformation changes that prevents ADP binding.

The large AAA+ domains of the two types of subunits are structurally similar. However, when these large AAA+ domains are lined in the same orientation, it is obvious that the structure of the small AAA+ domains show significant variability ( | ).

Summarily, all the above described structural characteristics of hexameric ClpX contribute to the mechanistic motion of hexameric ClpX ().

My research interest

Currently, ClpX is best known for its proteolytic ability in the ClpXP complex because of its roles in the control of bacterial cell cycle [10].

My overall research goal at the Chien Lab at the University of Massachusetts Amherst is to determine the specificity of ClpX and study its influence beyond cell cycle regulation.

Main References for this Proteopedia page

Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine. Glynn et al. Cell (2009) 139 (4): 744-56 [11].

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 [12].

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[13].

Acknowledgement

Professor Emeritus Eric Martz, for his kind help with advanced tools for building this page.