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TitleStructural Basis of Substrate-Independent Phosphorylation in a P4-ATPase Lipid Flippase.
Journal, issue, pagesJ Mol Biol, Vol. 433, Issue 16, Page 167062, Year 2021
Publish dateAug 6, 2021
AuthorsMilena Timcenko / Thibaud Dieudonné / Cédric Montigny / Thomas Boesen / Joseph A Lyons / Guillaume Lenoir / Poul Nissen /
PubMed AbstractP4-ATPases define a eukaryotic subfamily of the P-type ATPases, and are responsible for the transverse flip of specific lipids from the extracellular or luminal leaflet to the cytosolic leaflet of ...P4-ATPases define a eukaryotic subfamily of the P-type ATPases, and are responsible for the transverse flip of specific lipids from the extracellular or luminal leaflet to the cytosolic leaflet of cell membranes. The enzymatic cycle of P-type ATPases is divided into autophosphorylation and dephosphorylation half-reactions. Unlike most other P-type ATPases, P4-ATPases transport their substrate during dephosphorylation only, i.e. the phosphorylation half-reaction is not associated with transport. To study the structural basis of the distinct mechanisms of P4-ATPases, we have determined cryo-EM structures of Drs2p-Cdc50p from Saccharomyces cerevisiae covering multiple intermediates of the cycle. We identify several structural motifs specific to Drs2p and P4-ATPases in general that decrease movements and flexibility of domains as compared to other P-type ATPases such as Na/K-ATPase or Ca-ATPase. These motifs include the linkers that connect the transmembrane region to the actuator (A) domain, which is responsible for dephosphorylation. Additionally, mutation of Tyr380, which interacts with conserved Asp340 of the distinct DGET dephosphorylation loop of P4-ATPases, highlights a functional role of these P4-ATPase specific motifs in the A-domain. Finally, the transmembrane (TM) domain, responsible for transport, also undergoes less extensive conformational changes, which is ensured both by a longer segment connecting TM helix 4 with the phosphorylation site, and possible stabilization by the auxiliary subunit Cdc50p. Collectively these adaptions in P4-ATPases are responsible for phosphorylation becoming transport-independent.
External linksJ Mol Biol / PubMed:34023399
MethodsEM (single particle)
Resolution2.9 - 3.8 Å
Structure data

12893

7oh4

EMDB-12893: Drs2p-Cdc50p in the E1 state
PDB-7oh4: Cryo-EM structure of Drs2p-Cdc50p in the E1 state with PI4P and Mg2+ bound
Method: EM (single particle) / Resolution: 3.0 Å

12894

7oh5

EMDB-12894: Drs2p-Cdc50p in the E1-AlFx-ADP state
PDB-7oh5: Cryo-EM structure of Drs2p-Cdc50p in the E1-AlFx-ADP state
Method: EM (single particle) / Resolution: 2.9 Å

12895

7oh6

EMDB-12895: Drs2p-Cdc50p in the [PS]E2-AlFx state
PDB-7oh6: Cryo-EM structure of Drs2p-Cdc50p in the [PS]E2-AlFx state
Method: EM (single particle) / Resolution: 3.0 Å

12896

7oh7

EMDB-12896: Drs2p-Cdc50p in the E1-AMPPCP state with PI4P bound
PDB-7oh7: Cryo-EM structure of Drs2p-Cdc50p in the E1-AMPPCP state with PI4P bound
Method: EM (single particle) / Resolution: 3.8 Å

Chemicals

ChemComp-2Y5:
(2R)-1-{[(R)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}-3-(octadecanoyloxy)propan-2-yl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate

ChemComp-MG:
Unknown entry

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

ChemComp-HOH:
WATER / Water

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

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

ChemComp-Q3G:
O-[(R)-[(2S)-2-(hexadecanoyloxy)-3-(octadecanoyloxy)propoxy](hydroxy)phosphoryl]-D-serine / phospholipid*YM

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

Source
  • Saccharomyces cerevisiae (brewer's yeast)
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
KeywordsMEMBRANE PROTEIN / Lipid Flippase / P4 ATPase / trans-Golgi Network / Phosphatidylserine transport

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