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TitleTransport mechanism of P4 ATPase phosphatidylcholine flippases.
Journal, issue, pagesElife, Vol. 9, Year 2020
Publish dateDec 15, 2020
AuthorsLin Bai / Qinglong You / Bhawik K Jain / H Diessel Duan / Amanda Kovach / Todd R Graham / Huilin Li /
PubMed AbstractThe P4 ATPases use ATP hydrolysis to transport large lipid substrates across lipid bilayers. The structures of the endosome- and Golgi-localized phosphatidylserine flippases-such as the yeast Drs2 ...The P4 ATPases use ATP hydrolysis to transport large lipid substrates across lipid bilayers. The structures of the endosome- and Golgi-localized phosphatidylserine flippases-such as the yeast Drs2 and human ATP8A1-have recently been reported. However, a substrate-binding site on the cytosolic side has not been found, and the transport mechanisms of P4 ATPases with other substrates are unknown. Here, we report structures of the Dnf1-Lem3 and Dnf2-Lem3 complexes. We captured substrate phosphatidylcholine molecules on both the exoplasmic and cytosolic sides and found that they have similar structures. Unexpectedly, Lem3 contributes to substrate binding. The conformational transitions of these phosphatidylcholine transporters match those of the phosphatidylserine transporters, suggesting a conserved mechanism among P4 ATPases. Dnf1/Dnf2 have a unique P domain helix-turn-helix insertion that is important for function. Therefore, P4 ATPases may have retained an overall transport mechanism while evolving distinct features for different lipid substrates.
External linksElife / PubMed:33320091 / PubMed Central
MethodsEM (single particle)
Resolution2.8 - 4.05 Å
Structure data

23068

7ky5

EMDB-23068, PDB-7ky5:
Structure of the S. cerevisiae phosphatidylcholine flippase Dnf2-Lem3 complex in the E2P transition state
Method: EM (single particle) / Resolution: 3.98 Å

23069

7ky6

EMDB-23069, PDB-7ky6:
Structure of the S. cerevisiae phosphatidylcholine flippase Dnf1-Lem3 complex in the apo E1 state
Method: EM (single particle) / Resolution: 3.1 Å

23070

7ky7

EMDB-23070, PDB-7ky7:
Structure of the S. cerevisiae phosphatidylcholine flippase Dnf2-Lem3 complex in the apo E1 state
Method: EM (single particle) / Resolution: 3.08 Å

23071

7ky8

EMDB-23071, PDB-7ky8:
Structure of the S. cerevisiae phosphatidylcholine flippase Dnf2-Lem3 complex in the E1-ATP state
Method: EM (single particle) / Resolution: 3.85 Å

23072

7ky9

EMDB-23072, PDB-7ky9:
Structure of the S. cerevisiae phosphatidylcholine flippase Dnf2-Lem3 complex in the E1-ADP state
Method: EM (single particle) / Resolution: 4.05 Å

23073

7kya

EMDB-23073, PDB-7kya:
Structure of the S. cerevisiae phosphatidylcholine flippase Dnf2-Lem3 complex in the E2P state
Method: EM (single particle) / Resolution: 3.5 Å

23074

7kyb

EMDB-23074, PDB-7kyb:
Structure of the S. cerevisiae phosphatidylcholine flippase Dnf1-Lem3 complex in the E1-ADP state
Method: EM (single particle) / Resolution: 3.2 Å

23075

7kyc

EMDB-23075, PDB-7kyc:
Structure of the S. cerevisiae phosphatidylcholine flippase Dnf1-Lem3 complex in the E2P state
Method: EM (single particle) / Resolution: 2.8 Å

Chemicals

ChemComp-CLR:
CHOLESTEROL / Cholesterol

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

ChemComp-MG:
Unknown entry

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

ChemComp-ACP:
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / AMP-PCP, energy-carrying molecule analogue*YM

ChemComp-MAN:
alpha-D-mannopyranose / Mannose

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM / POPC

Source
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
KeywordsTRANSLOCASE / P4 ATPase / Phosphatidylcholine Flippases

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