The structural basis for the phospholipid remodeling by lysophosphatidylcholine acyltransferase 3

Qing Zhang,Ming Lei,Yang Chen,An Qin,Deqiang Yao,Yafeng Shen,Ying Xia,Liyan Jian,Jie Zhao,Bing Rao,Lu Zhou,Kexin Hu,Yu Cao,Shaobai Li,Xian-Cheng Jiang

doi:10.1038/s41467-021-27244-1

Abstract

As the major component of cell membranes, phosphatidylcholine (PC) is synthesized de novo in the Kennedy pathway and then undergoes extensive deacylation-reacylation remodeling via Lands’ cycle. The re-acylation is catalyzed by lysophosphatidylcholine acyltransferase (LPCAT) and among the four LPCAT members in human, the LPCAT3 preferentially introduces polyunsaturated acyl onto the sn-2 position of lysophosphatidylcholine, thereby modulating the membrane fluidity and membrane protein functions therein. Combining the x-ray crystallography and the cryo-electron microscopy, we determined the structures of LPCAT3 in apo-, acyl donor-bound, and acyl receptor-bound states. A reaction chamber was revealed in the LPCAT3 structure where the lysophosphatidylcholine and arachidonoyl-CoA were positioned in two tunnels connected near to the catalytic center. A side pocket was found expanding the tunnel for the arachidonoyl CoA and holding the main body of arachidonoyl. The structural and functional analysis provides the basis for the re-acylation of lysophosphatidylcholine and the substrate preference during the reactions.

Highlights

As the major component of cell membranes, phosphatidylcholine (PC) is synthesized de novo in the Kennedy pathway and undergoes extensive deacylation-reacylation remodeling via Lands’ cycle
To probe the catalytic mechanism, extensive efforts in protein engineering and crystallization were conducted on human LPCAT3 (hLPCAT3) and chicken LPCAT3 (cLPCAT3), but most of them failed
When purified in undecyl maltoside (UM) and treated with trypsin digestion, cLPCAT3 was trimmed into a slightly smaller protein core with only two residues at C-terminal removed along with the affinity tag and yielded crystals with diffraction to about 3.4 Å resolution, allowing the structure determination of LPCAT3 by molecular replacement using a molecular model predicted by Tencent tFold server[38]

Summary

Introduction

As the major component of cell membranes, phosphatidylcholine (PC) is synthesized de novo in the Kennedy pathway and undergoes extensive deacylation-reacylation remodeling via Lands’ cycle. LPCAT3 is the main isoform in major metabolic tissues, including the liver, small intestine, skeletal muscle, macrophage, and adipocyte[12,14,15,16,17,18,19,20]. LPCAT3 deficiency increases insulin sensitivity in skeletal muscle, through modulating plasma membrane PC composition[27], and impairs preadipocyte adipogenesis through activating Wnt/beta-catenin pathway[20]. To probe the molecular mechanism underlying acyl transfer process in phospholipids remodeling and the unsaturation preference on the acyl to be transferred, we determined the crystal and cryo-EM structure for chicken LPCAT3 and explored the function of the critical residues implied by the structures

Methods

Results

Conclusion