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TitleStructural basis of polyamine transport by human ATP13A2 (PARK9).
Journal, issue, pagesMol Cell, Vol. 81, Issue 22, Page 4635-44649.e8, Year 2021
Publish dateNov 18, 2021
AuthorsSue Im Sim / Sören von Bülow / Gerhard Hummer / Eunyong Park /
PubMed AbstractPolyamines are small, organic polycations that are ubiquitous and essential to all forms of life. Currently, how polyamines are transported across membranes is not understood. Recent studies have ...Polyamines are small, organic polycations that are ubiquitous and essential to all forms of life. Currently, how polyamines are transported across membranes is not understood. Recent studies have suggested that ATP13A2 and its close homologs, collectively known as P5B-ATPases, are polyamine transporters at endo-/lysosomes. Loss-of-function mutations of ATP13A2 in humans cause hereditary early-onset Parkinson's disease. To understand the polyamine transport mechanism of ATP13A2, we determined high-resolution cryoelectron microscopy (cryo-EM) structures of human ATP13A2 in five distinct conformational intermediates, which together, represent a near-complete transport cycle of ATP13A2. The structural basis of the polyamine specificity was revealed by an endogenous polyamine molecule bound to a narrow, elongated cavity within the transmembrane domain. The structures show an atypical transport path for a water-soluble substrate, in which polyamines may exit within the cytosolic leaflet of the membrane. Our study provides important mechanistic insights into polyamine transport and a framework to understand the functions and mechanisms of P5B-ATPases.
External linksMol Cell / PubMed:34715013 / PubMed Central
MethodsEM (single particle)
Resolution2.5 - 3.7 Å
Structure data

EMDB-24212:
Cryo-EM structure of ATP13A2 in the E2-Pi state
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-24213:
Cryo-EM structure of ATP13A2 in the E2-Pi state
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-24214, PDB-7n70:
Cryo-EM structure of ATP13A2 in the BeF-bound E2P-like state
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-24215:
Cryo-EM structure of ATP13A2 in the E2-Pi state
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-24216:
Cryo-EM structure of ATP13A2 in the AlF-bound E2-Pi-like state
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-24217, PDB-7n72:
Cryo-EM structure of ATP13A2 in the AlF-bound E2-Pi-like state
Method: EM (single particle) / Resolution: 2.5 Å

EMDB-24218, PDB-7n73:
Cryo-EM structure of ATP13A2 in the ADP-AlF-bound E1P-ADP-like state
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-24219, PDB-7n74:
Cryo-EM structure of ATP13A2 D508N mutant in the E1-ATP-like state
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-24220, PDB-7n75:
Cryo-EM structure of ATP13A2 D458N/D962N mutant in the E1-apo state, Conformation 1
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-24221, PDB-7n76:
Cryo-EM structure of ATP13A2 D458N/D962N mutant in the E1-apo state, Conformation 2
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-24222, PDB-7n77:
Cryo-EM structure of ATP13A2 D458N/D962N mutant in the AlF-bound E1P-like state
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-24223, PDB-7n78:
Cryo-EM structure of ATP13A2 in the E2-Pi state
Method: EM (single particle) / Resolution: 3.0 Å

Chemicals

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

ChemComp-MG:
Unknown entry

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

ChemComp-SPM:
SPERMINE

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

ChemComp-HOH:
WATER

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

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-PO4:
PHOSPHATE ION

Source
  • homo sapiens (human)
KeywordsTRANSPORT PROTEIN / P-type ATPase / P5B-ATPase / polyamine transporter

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