Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Mechanistic insights into intramembrane proteolysis by site-2 protease homolog RseP.
Journal, issue, pages	Sci Adv, Vol. 8, Issue 34, Page eabp9011, Year 2022
Publish date	Aug 26, 2022
Authors	Yuki Imaizumi / Kazunori Takanuki / Takuya Miyake / Mizuki Takemoto / Kunio Hirata / Mika Hirose / Rika Oi / Tatsuya Kobayashi / Kenichi Miyoshi / Rie Aruga / Tatsuhiko Yokoyama / Shizuka Katagiri / Hiroaki Matsuura / Kenji Iwasaki / Takayuki Kato / Mika K Kaneko / Yukinari Kato / Michiko Tajiri / Satoko Akashi / Osamu Nureki / Yohei Hizukuri / Yoshinori Akiyama / Terukazu Nogi /
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 ...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.
External links	Sci Adv / PubMed:36001659 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	1.15 - 19.2 Å
Structure data	EMDB-33409: Detergent-solubilized E. coli RseP in complex with Fab Method: EM (single particle) / Resolution: 19.2 Å EMDB-33410: Deterget-solubilized E. coli RseP(L358C) mutant in complex with Fab Method: EM (single particle) / Resolution: 14.0 Å PDB-7w6x: Crystal structure of E. coli RseP in complex with batimastat Method: X-RAY DIFFRACTION / Resolution: 3.2 Å PDB-7w6y: Crystal structure of Kangiella koreensis RseP orthologue in complex with batimastat in space group P1 Method: X-RAY DIFFRACTION / Resolution: 3.1 Å PDB-7w6z: Crystal structure of Kangiella koreensis RseP orthologue in complex with batimastat in space group P21 Method: X-RAY DIFFRACTION / Resolution: 3.15 Å PDB-7w70: Crystal structure of the PDZ-C domain fragment of Kangiella koreensis RseP orthologue Method: X-RAY DIFFRACTION / Resolution: 1.15 Å PDB-7w71: Crystal structure of the PDZ-C domain of E. coli RseP in complex with 12C7 Fab Method: X-RAY DIFFRACTION / Resolution: 3.2 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-BAT: 4-(N-HYDROXYAMINO)-2R-ISOBUTYL-2S-(2-THIENYLTHIOMETHYL)SUCCINYL-L-PHENYLALANINE-N-METHYLAMIDE / inhibitorYM / Batimastat ChemComp-HOH*: WATER / Water
Source	escherichia coli (E. coli) mus musculus (house mouse) kangiella koreensis dsm 16069 (bacteria)
Keywords	HYDROLASE / Intramembrane protease / HYDROLASE/IMMUNE SYSTEM / HYDROLASE-IMMUNE SYSTEM complex