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Structure paper

TitleStructural basis for catalysis and selectivity of phospholipid synthesis by eukaryotic choline-phosphotransferase.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 111, Year 2025
Publish dateJan 2, 2025
AuthorsJacquelyn R Roberts / Yasuhiro Horibata / Frank E Kwarcinski / Vinson Lam / Ashleigh M Raczkowski / Akane Hubbard / Betsy White / Hiroyuki Sugimoto / Gregory G Tall / Melanie D Ohi / Shoji Maeda /
PubMed AbstractPhospholipids are the most abundant component in lipid membranes and are essential for the structural and functional integrity of the cell. In eukaryotic cells, phospholipids are primarily ...Phospholipids are the most abundant component in lipid membranes and are essential for the structural and functional integrity of the cell. In eukaryotic cells, phospholipids are primarily synthesized de novo through the Kennedy pathway that involves multiple enzymatic processes. The terminal reaction is mediated by a group of cytidine-5'-diphosphate (CDP)-choline /CDP-ethanolamine-phosphotransferases (CPT/EPT) that use 1,2-diacylglycerol (DAG) and CDP-choline or CDP-ethanolamine to produce phosphatidylcholine (PC) or phosphatidylethanolamine (PE) that are the main phospholipids in eukaryotic cells. Here we present the structure of the yeast CPT1 in multiple substrate-bound states. Structural and functional analysis of these binding-sites reveal the critical residues for the DAG acyl-chain preference and the choline/ethanolamine selectivity. Additionally, we present the structure in complex with a potent inhibitor characterized in this study. The ensemble of structures allows us to propose the reaction mechanism for phospholipid biosynthesis by the family of CDP-alcohol phosphotransferases (CDP-APs).
External linksNat Commun / PubMed:39747155 / PubMed Central
MethodsEM (single particle)
Resolution2.9 - 3.71 Å
Structure data

42357

8ul9

EMDB-42357, PDB-8ul9:
Cholinephosphotransferase in complex with diacylglycerol
Method: EM (single particle) / Resolution: 3.2 Å

42496

8urp

EMDB-42496, PDB-8urp:
Cholinephosphotransferase in complex with CDP-choline and phosphatidylcholine
Method: EM (single particle) / Resolution: 2.9 Å

42500

8urt

EMDB-42500, PDB-8urt:
Cholinephosphotransferase in complex with selective inhibitor chelerythrine
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-46969: Cholinephosphotransferase in complex with diacylglycerol in nanodisc
Method: EM (single particle) / Resolution: 3.71 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

ChemComp-DGA:
DIACYL GLYCEROL

ChemComp-HOH:
WATER

ChemComp-CDC:
[2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM

ChemComp-PCF:
1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE

ChemComp-CTI:
1,2-dimethoxy-12-methyl[1,3]benzodioxolo[5,6-c]phenanthridin-12-ium

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • Lama glama (llama)
  • Saccharomyces cerevisiae S288C (yeast)
KeywordsMEMBRANE PROTEIN / lipid metabolism / phospholipid synthesis / membrane protein enzyme / choline metabolism

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