7YM0

Lysoplasmalogen-specific phospholipase D (LyPls-PLD) with Ca2+

Summary for 7YM0

• Entry DOI: 10.2210/pdb7ym0/pdb
• Descriptor: Lysoplasmalogenase, CALCIUM ION (2 entities in total)
• Functional Keywords: phospholipase d, lisoplasmalogen, thermocrispum, lysopaf, hydrolase
• Biological source: Thermocrispum sp. RD004668
• Total number of polymer chains: 2
• Total formula weight: 67326.56

Authors

Yasutake, Y.,Sakasegawa, S.,Sugimori, D.,Murayama, K. (deposition date: 2022-07-27, release date: 2023-01-04, Last modification date: 2024-10-16)

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 (2.91 Å)