PDBsum entry 3b8c

Hydrolase

PDB id: 3b8c

Contents

Protein chains

833 a.a. *

Ligands

ACP ×2

Metals

_MG ×2

* Residue conservation analysis

Superseded by:

5ksd

PDB id:

3b8c

Name:

Hydrolase

Title:

Crystal structure of a plasma membrane proton pump

Structure:

Atpase 2, plasma membrane-type. Chain: a, b. Fragment: aha2delta73 c-terminal truncated. Synonym: proton pump 2, aha2. Engineered: yes

Source:

Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: aha2. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932.

Resolution:

3.60Å R-factor: 0.351 R-free: 0.366

Authors:

B.P.Pedersen,M.J.Buch-Pedersen,J.P.Morth,M.G.Palmgren,P.Nissen

Key ref:

B.P.Pedersen et al. (2007). Crystal structure of the plasma membrane proton pump. Nature, 450, 1111-1114. PubMed id: 18075595 DOI: 10.1038/nature06417

Date:

01-Nov-07 Release date: 18-Dec-07

Protein chains

P19456  (PMA2_ARATH) -  ATPase 2, plasma membrane-type from Arabidopsis thaliana

Seq: 948 a.a.

Struc: 833 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.3.6 - Transferred entry: 7.1.2.1.
• Reaction: ATP + H₂O + H⁺(In) = ADP + phosphate + H⁺(Out)

ATP + H(2)O + H(+)(In) = ADP (Bound ligand (Het Group name = ACP) matches with 81.25% similarity) + phosphate + H(+)(Out)

• Cofactor: Mg(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/nature06417

Nature 450:1111-1114 (2007)

PubMed id: 18075595

Crystal structure of the plasma membrane proton pump.

B.P.Pedersen, M.J.Buch-Pedersen, J.P.Morth, M.G.Palmgren, P.Nissen.

ABSTRACT

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.

Selected figure(s)

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.

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.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2007, 450, 1111-1114) copyright 2007.

Figures were selected by the author.