7YMR

Complex structure of lysoplasmalogen specific phopholipase D, F211L mutant with LPC

Summary for 7YMR

• Entry DOI: 10.2210/pdb7ymr/pdb
• Descriptor: Lysoplasmalogenase, [(2~{R})-2-oxidanyl-3-[oxidanyl-[2-(trimethyl-$l^{5}-azanyl)ethoxy]phosphoryl]oxy-propyl] hexadecanoate (3 entities in total)
• Functional Keywords: phospholipase d, lysoplasalogen, lysopaf, lpc, hydrolase
• Biological source: Thermocrispum sp. RD004668
• Total number of polymer chains: 4
• Total formula weight: 139658.79

Authors

Murayama, K.,Kato-Murayama, M.,Sugimori, D.,Shirouzu, M.,Hamana, H. (deposition date: 2022-07-29, release date: 2023-02-08, Last modification date: 2023-11-29)

Primary citation

Hamana, H.,Yasutake, Y.,Kato-Murayama, M.,Hosaka, T.,Shirouzu, M.,Sakasegawa, S.I.,Sugimori, D.,Murayama, K.
Structural basis for the substrate specificity switching of lysoplasmalogen-specific phospholipase D from Thermocrispum sp. RD004668.
Biosci.Biotechnol.Biochem., 87:74-81, 2022

PubMed Abstract: Lysoplasmalogen-specific phospholipase D (LyPls-PLD) hydrolyzes choline lysoplasmalogen to choline and 1-(1-alkenyl)-sn-glycero-3-phosphate. Mutation of F211 to leucine altered its substrate specificity from lysoplasmalogen to 1-O-hexadecyl-2-hydroxy-sn-glycero-3-phosphocholine (lysoPAF). Enzymes specific to lysoPAF have good potential for clinical application, and understanding the mechanism of their activity is important. The crystal structure of LyPls-PLD exhibited a TIM barrel fold assigned to glycerophosphocholine phosphodiesterase, a member of glycerophosphodiester phosphodiesterase. LyPls-PLD possesses a hydrophobic cleft for the binding of the aliphatic chain of the substrate. In the structure of the F211L mutant, Met232 and Tyr258 form a "small lid" structure that stabilizes the binding of the aliphatic chain of the substrate. In contrast, F211 may inhibit small lid formation in the wild-type structure. LysoPAF possesses a flexible aliphatic chain; therefore, a small lid is effective for stabilizing the substrate during catalytic reactions.

PubMed: 36307380
DOI: 10.1093/bbb/zbac169

Experimental method

X-RAY DIFFRACTION (2.69 Å)