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PDBsum entry 3b8c
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References listed in PDB file
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Key reference
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Title
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Crystal structure of the plasma membrane proton pump.
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Authors
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B.P.Pedersen,
M.J.Buch-Pedersen,
J.P.Morth,
M.G.Palmgren,
P.Nissen.
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Ref.
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Nature, 2007,
450,
1111-1114.
[DOI no: ]
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PubMed id
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Abstract
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A prerequisite for life is the ability to maintain electrochemical imbalances
across biomembranes. In all eukaryotes the plasma membrane potential and
secondary transport systems are energized by the activity of P-type ATPase
membrane proteins: H+-ATPase (the proton pump) in plants and fungi, and
Na+,K+-ATPase (the sodium-potassium pump) in animals. The name P-type derives
from the fact that these proteins exploit a phosphorylated reaction cycle
intermediate of ATP hydrolysis. The plasma membrane proton pumps belong to the
type III P-type ATPase subfamily, whereas Na+,K+-ATPase and Ca2+-ATPase are type
II. Electron microscopy has revealed the overall shape of proton pumps, however,
an atomic structure has been lacking. Here we present the first structure of a
P-type proton pump determined by X-ray crystallography. Ten transmembrane
helices and three cytoplasmic domains define the functional unit of ATP-coupled
proton transport across the plasma membrane, and the structure is locked in a
functional state not previously observed in P-type ATPases. The transmembrane
domain reveals a large cavity, which is likely to be filled with water, located
near the middle of the membrane plane where it is lined by conserved hydrophilic
and charged residues. Proton transport against a high membrane potential is
readily explained by this structural arrangement.
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Figure 1.
Figure 1: Overall structure of the plasma membrane H^+-ATPase.
The structure represents an active form of the proton pump,
without its auto-inhibitory C terminus, in complex with
Mg-AMPPCP. Ten transmembrane helices, orange, green and brown,
as indicated; nucleotide-binding domain (N), red; the
phosphorylation domain (P), blue; and the actuator domain (A),
yellow. Mg-AMPPCP is found at the interface between the N and P
domains and is shown as a ball-and-stick reprentation. Key
residues mentioned in the text are shown as sticks. The grey box
depicts the approximate location of the plasma membrane.
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Figure 4.
Figure 4: Mechanism of proton transport by plasma membrane
H^+-ATPase. E2-model forms of the H^+-ATPase were made by
structural alignment of our E1-AMPPCP structure with the E2P
structure of the Ca^2+-ATPase^26 and the E2-P* structure (E2
occluded state of the pump) of the Ca^2+-ATPase (PDB code 1XP5).
Asp 684 is the central proton donor/acceptor of the pump, and
together with Arg 655 it lines a centrally located water-filled
cavity. In the E1 conformation, hydrogen bonding between Asp 684
and Asn 106 gives preference to the protonated form of Asp 684
(E1-ATP structure). Conformational movements in the membrane
region, coupled to E1–E2 transitions, result in opening of the
cavity towards the proton exit pathway (E2P model) and interrupt
hydrogen bonding between Asn 106 and Asp 684; this results in
proton release from Asp 684, now exposed to the extracellular
environment. Placement of Arg 655 towards Asp 684 at the exit
channel also stimulates proton release from Asp 684, and
provides a positively charged plug in this area of the molecule
that prevents extracellular protons from re-protonating Asp
684. At the same time Arg 655 functions as a built-in
counter-ion that neutralizes the negative charge on Asp 684 and
promotes swift formation of the occluded E2-P* transition state
(E2P* model), dephosphorylation and transition to the E2 form.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2007,
450,
1111-1114)
copyright 2007.
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