Crystal Structure of Arabidopsis Deg2 Protein Reveals an Internal PDZ Ligand Locking the Hexameric Resting State

Abstract

Background: The PDZ protease Deg2 is involved in chloroplast protein quality control through a yet unknown molecular mechanism.Results: A novel PDZ domain with an internal ligand mediates hexamer formation and locks Deg2 into the resting state.Conclusion: Formation of the resting hexamer may be a common strategy in a Deg protease subfamily.Significance: We provide structural insights into the PDZ domain-mediated regulation of Deg proteases.

AtDeg2 – a chloroplast protein with dual protease/chaperone activity

“…Apart from making AtDeg2 monomer and hexamer rigid, internal PDZ2 ligand may play a crucial role in conversion of the supposedly resting hexameric state into the enzymatically active 12-mers and 24-mers by dissociating from PDZ2 so that trimeric units may be rearranged into higher oligomeric states. The oligomerization of AtDeg2 in solution was demonstrated to be pH-independent and to increase with the incubation time with an artificial substrate (but the hexameric state existed predominantly all the time [14]). …”

“…3). In the AtDeg2 hexamer the assembly is stabilized through multiple interactions involving two interfaces formed for each monomer, consisting of the protease domain and PDZ2 (interface 1) and PDZ1 and PDZ2 (interface 2) [14]. While PDZ1 domain resembles conventional PDZ domains of bacterial Deg proteases, PDZ2 domain has a few unique features with respect to canonical PDZ domains of other Deg proteases.…”

“…A great progress has been made recently with regard to understanding structural organization of AtDeg2 since recombinant version of this protein (spanning 110-577 positions) has been crystallized and the crystal structure solved based on X-ray diffraction analysis [14]. When analyzed by size exclusion chromatography AtDeg2 in solution forms supposedly inactive hexamer (a dimer of trimers) of "sealed cage" type, consisting of two trimeric rings stacked upon each other in such a way that they form an inner, catalytic chamber the entrance to which is restricted to six pores.…”

“…According to HHPred platform (http://toolkit.tuebingen. mpg.de/hhpred/) [18] mature AtDeg2 molecule contains protease domain as well PDZ1 and PDZ2 domains (positions 110-313, 314-422 and 423-577, respectively [14]). The protease domain is preceded by and PDZ2 is followed by short regions, which are lacking any conserved domains (positions 70-109 and 578-607, respectively; Fig.…”

“…All AtDeg proteases were originally named as AtDegPX ones and then renamed just AtDegX [11]. It has been shown recently that AtDeg2 exhibits chaperone-like activity in vitro [14] yet no data exist with regard to how protease and chaperone activities are interlocked within a single AtDeg2 molecule.…”