Download citation
Acta Cryst. (2014). A70, C1497
Download citation

link to html
Regulated intramembrane proteolysis (RIP), wherein a target membrane protein is specifically cleaved within the transmembrane region, is now accepted as a form of cellular signaling. As a result of proteolysis, a soluble portion of the target membrane protein is liberated to act as a signaling molecule. RIP is catalyzed by intramembrane-cleaving proteases, which are now classified into site-2 protease, rhomboid and γ-secretase/SPP families based on the mechanism of catalysis. E. coli possesses a site-2 protease homolog RseP, which is implicated in the extracytoplasmic stress response. RseP cleaves a membrane-spanning anti-σE protein RseA to release σE from the membrane, where truncation of the C-terminal periplasmic part of RseA by a membrane-anchored protease DegS triggers the action of RseP. Hence, there must be some mechanism by which RseP senses the DegS-cleavage of RseA. RseP possesses two tandemly-arranged PDZ domains (PDZ tandem) in the periplasmic region, which have been suggested to be involved in the regulation of cleavage. Although PDZ domains generally recognize the C-terminal sequence of a ligand, most of the previous works suggested that the RseP PDZ domains are involved in the suppression of the intramembrane cleavage of RseA. In this study, we determined the 3D structure of the PDZ tandem by X-ray crystallography and SAXS and showed that the two PDZ domains are arranged in an overall "clam-like" configuration to constitute a "pocket-like" structure. Sequence analysis suggested that the PDZ tandem would lie just above the active center sequestrated within the membrane. Furthermore, chemical modification demonstrated that the interior of the pocket is inaccessible to a bulky reagent in the full-length RseP. Taken together, we have made a proposal that RseP accommodates the truncated RseA into the active center by a steric size-exclusion mechanism through the PDZ tandem, rather than by recognition of a specific sequence/motif of RseA.

Download citation
Acta Cryst. (2014). A70, C1626
Download citation

link to html
Crystal structure prediction is one of the useful theoretical tools for designing and synthesizing new materials in pharmaceutical therapeutics and industrial electronics. Furthermore, the prediction can provide immense valuable scientific knowledge on a crystal growth, polymorphism and many properties of organic molecular crystals. Therefore, we have started the development of high-speed and high-accurate prediction method for organic molecular crystal structures [1,2]. In this work, we demonstrate the theoretical predictions of crystal structures of fourteen target molecules that were used in the international competitions known as CSP blind tests hosted by CCDC [3]. All strategies required for crystal lattice construction expanded to a given effective crystal radius, crystal energy calculation with the reliable molecular force field (MMFF94s) and exhaustive geometry search included a variety of crystal polymorphism are implemented into CONFLEX program [1]. As the results of the applications, we confirmed in all cases of target molecules that, at least, one calculated crystal structure in agreement with the corresponding observed ones can be found. Essential ability required for the prediction method to survive the CSP competitions is that the experimental crystal structure can computationally reproduce within top 3 of most stable structures in crystal energy evaluation. In these tests, only three applications to the target I (Orth. polymorph), II and VIII can successfully satisfy the demand. Details will be discussed in this conference.
Follow Acta Cryst. A
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds