7W6Z

Crystal structure of Kangiella koreensis RseP orthologue in complex with batimastat in space group P21

Summary for 7W6Z

• Entry DOI: 10.2210/pdb7w6z/pdb
• Descriptor: Zinc metalloprotease, ZINC ION, 4-(N-HYDROXYAMINO)-2R-ISOBUTYL-2S-(2-THIENYLTHIOMETHYL)SUCCINYL-L-PHENYLALANINE-N-METHYLAMIDE (3 entities in total)
• Functional Keywords: intramembrane protease, hydrolase
• Biological source: Kangiella koreensis DSM 16069 (RseP)
• Total number of polymer chains: 1
• Total formula weight: 50986.32

Authors

Imaizumi, Y.,Takanuki, K.,Nogi, T. (deposition date: 2021-12-02, release date: 2022-09-07, Last modification date: 2024-11-06)

Primary citation

Imaizumi, Y.,Takanuki, K.,Miyake, T.,Takemoto, M.,Hirata, K.,Hirose, M.,Oi, R.,Kobayashi, T.,Miyoshi, K.,Aruga, R.,Yokoyama, T.,Katagiri, S.,Matsuura, H.,Iwasaki, K.,Kato, T.,Kaneko, M.K.,Kato, Y.,Tajiri, M.,Akashi, S.,Nureki, O.,Hizukuri, Y.,Akiyama, Y.,Nogi, T.
Mechanistic insights into intramembrane proteolysis by E. coli site-2 protease homolog RseP.
Sci Adv, 8:eabp9011-eabp9011, 2022

PubMed Abstract: Site-2 proteases are a conserved family of intramembrane proteases that cleave transmembrane substrates to regulate signal transduction and maintain proteostasis. Here, we elucidated crystal structures of inhibitor-bound forms of bacterial site-2 proteases including RseP. Structure-based chemical modification and cross-linking experiments indicated that the RseP domains surrounding the active center undergo conformational changes to expose the substrate-binding site, suggesting that RseP has a gating mechanism to regulate substrate entry. Furthermore, mutational analysis suggests that a conserved electrostatic linkage between the transmembrane and peripheral membrane-associated domains mediates the conformational changes. In vivo cleavage assays also support that the substrate transmembrane helix is unwound by strand addition to the intramembrane β sheet of RseP and is clamped by a conserved asparagine residue at the active center for efficient cleavage. This mechanism underlying the substrate binding, i.e., unwinding and clamping, appears common across distinct families of intramembrane proteases that cleave transmembrane segments.

PubMed: 36001659
DOI: 10.1126/sciadv.abp9011

Experimental method

X-RAY DIFFRACTION (3.15 Å)