Limits...
High-resolution structure and mechanism of an F/V-hybrid rotor ring in a Na⁺-coupled ATP synthase.

Matthies D, Zhou W, Klyszejko AL, Anselmi C, Yildiz Ö, Brandt K, Müller V, Faraldo-Gómez JD, Meier T - Nat Commun (2014)

Bottom Line: Physiologically, however, F/A-type enzymes specialize in ATP synthesis driven by downhill ion diffusion, while eukaryotic V-type ATPases function as ion pumps.Molecular and kinetic simulations are used to dissect the mechanisms of Na(+) recognition and rotation of this c-ring, and to explain the functional implications of the V-type c-subunit.These structural and mechanistic insights indicate an evolutionary path between synthases and pumps involving adaptations in the rotor ring.

View Article: PubMed Central - PubMed

Affiliation: Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany.

ABSTRACT
All rotary ATPases catalyse the interconversion of ATP and ADP-Pi through a mechanism that is coupled to the transmembrane flow of H(+) or Na(+). Physiologically, however, F/A-type enzymes specialize in ATP synthesis driven by downhill ion diffusion, while eukaryotic V-type ATPases function as ion pumps. To begin to rationalize the molecular basis for this functional differentiation, we solved the crystal structure of the Na(+)-driven membrane rotor of the Acetobacterium woodii ATP synthase, at 2.1 Å resolution. Unlike known structures, this rotor ring is a 9:1 heteromer of F- and V-type c-subunits and therefore features a hybrid configuration of ion-binding sites along its circumference. Molecular and kinetic simulations are used to dissect the mechanisms of Na(+) recognition and rotation of this c-ring, and to explain the functional implications of the V-type c-subunit. These structural and mechanistic insights indicate an evolutionary path between synthases and pumps involving adaptations in the rotor ring.

No MeSH data available.


Related in: MedlinePlus

Structure of the heteromeric c-ring from the Acetobacterium woodii ATP synthase. The ring is viewed (a) along the membrane plane and (b) from the periplasm, highlighting the two c-subunit topologies (blue and orange cartoons), as well as the bound Na+ ions (yellow spheres) and the co-coordinating water molecules (red spheres). Note the site within subunit c1 does not bind Na+. Residues L55/F77 in c2/3, and L72/L155/F94/Y177 in c1 indicate the likely position of the ring within the membrane (gray). (c) Electrostatic potential at the outer surface of the c-ring, and (d) at the surface of the central hydrophobic pore. Detergent molecules (green) resolved in the electron density map are highlighted. Arrows indicate the position of the ion-binding sites. (e) Asymmetry of the electrostatic potential on the cytoplasmic face of the c-ring, where the central stalk binds. (f) The N-terminal extension of subunit c1 occludes the central pore almost completely.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4228694&req=5

Figure 1: Structure of the heteromeric c-ring from the Acetobacterium woodii ATP synthase. The ring is viewed (a) along the membrane plane and (b) from the periplasm, highlighting the two c-subunit topologies (blue and orange cartoons), as well as the bound Na+ ions (yellow spheres) and the co-coordinating water molecules (red spheres). Note the site within subunit c1 does not bind Na+. Residues L55/F77 in c2/3, and L72/L155/F94/Y177 in c1 indicate the likely position of the ring within the membrane (gray). (c) Electrostatic potential at the outer surface of the c-ring, and (d) at the surface of the central hydrophobic pore. Detergent molecules (green) resolved in the electron density map are highlighted. Arrows indicate the position of the ion-binding sites. (e) Asymmetry of the electrostatic potential on the cytoplasmic face of the c-ring, where the central stalk binds. (f) The N-terminal extension of subunit c1 occludes the central pore almost completely.

Mentions: The crystal structure of the c-ring from the A. woodii ATP synthase was resolved at 2.1 Å resolution (Supplementary Fig. 3; Supplementary Table 1). Consistent with our previous biochemical analysis22, the ring is an assembly of nine copies of single-hairpin c-subunits, referred to as c2/3, and one copy of a double-hairpin c-subunit, or c1 (Fig. 1a,b). Thus, the structure consists of 22 transmembrane α-helices, arranged in two concentric, staggered rings of eleven helices each. The c-ring is ~72 Å in height, and is shaped like an hourglass with a central pore perpendicular to the membrane plane (Fig. 1). The outermost diameter is widest (~55 Å) on the cytoplasmic and periplasmic sides, and is narrowest approximately halfway across the membrane (~45 Å). In the c2/3 subunits, the N-terminal (or inner) helix and the C-terminal (or outer) helix are connected on the cytoplasmic side by a short, rigid loop, which mediates crystal contacts (Supplementary Fig. 4). The c2/3 subunits are structurally very similar (RMSD < 1 Å) to other F-type single-hairpin c-subunits (Supplementary Fig. 5), particularly those in the Ilyobacter tartaricus c11 ring12 (RMSD ~ 0.4 Å).


High-resolution structure and mechanism of an F/V-hybrid rotor ring in a Na⁺-coupled ATP synthase.

Matthies D, Zhou W, Klyszejko AL, Anselmi C, Yildiz Ö, Brandt K, Müller V, Faraldo-Gómez JD, Meier T - Nat Commun (2014)

Structure of the heteromeric c-ring from the Acetobacterium woodii ATP synthase. The ring is viewed (a) along the membrane plane and (b) from the periplasm, highlighting the two c-subunit topologies (blue and orange cartoons), as well as the bound Na+ ions (yellow spheres) and the co-coordinating water molecules (red spheres). Note the site within subunit c1 does not bind Na+. Residues L55/F77 in c2/3, and L72/L155/F94/Y177 in c1 indicate the likely position of the ring within the membrane (gray). (c) Electrostatic potential at the outer surface of the c-ring, and (d) at the surface of the central hydrophobic pore. Detergent molecules (green) resolved in the electron density map are highlighted. Arrows indicate the position of the ion-binding sites. (e) Asymmetry of the electrostatic potential on the cytoplasmic face of the c-ring, where the central stalk binds. (f) The N-terminal extension of subunit c1 occludes the central pore almost completely.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4228694&req=5

Figure 1: Structure of the heteromeric c-ring from the Acetobacterium woodii ATP synthase. The ring is viewed (a) along the membrane plane and (b) from the periplasm, highlighting the two c-subunit topologies (blue and orange cartoons), as well as the bound Na+ ions (yellow spheres) and the co-coordinating water molecules (red spheres). Note the site within subunit c1 does not bind Na+. Residues L55/F77 in c2/3, and L72/L155/F94/Y177 in c1 indicate the likely position of the ring within the membrane (gray). (c) Electrostatic potential at the outer surface of the c-ring, and (d) at the surface of the central hydrophobic pore. Detergent molecules (green) resolved in the electron density map are highlighted. Arrows indicate the position of the ion-binding sites. (e) Asymmetry of the electrostatic potential on the cytoplasmic face of the c-ring, where the central stalk binds. (f) The N-terminal extension of subunit c1 occludes the central pore almost completely.
Mentions: The crystal structure of the c-ring from the A. woodii ATP synthase was resolved at 2.1 Å resolution (Supplementary Fig. 3; Supplementary Table 1). Consistent with our previous biochemical analysis22, the ring is an assembly of nine copies of single-hairpin c-subunits, referred to as c2/3, and one copy of a double-hairpin c-subunit, or c1 (Fig. 1a,b). Thus, the structure consists of 22 transmembrane α-helices, arranged in two concentric, staggered rings of eleven helices each. The c-ring is ~72 Å in height, and is shaped like an hourglass with a central pore perpendicular to the membrane plane (Fig. 1). The outermost diameter is widest (~55 Å) on the cytoplasmic and periplasmic sides, and is narrowest approximately halfway across the membrane (~45 Å). In the c2/3 subunits, the N-terminal (or inner) helix and the C-terminal (or outer) helix are connected on the cytoplasmic side by a short, rigid loop, which mediates crystal contacts (Supplementary Fig. 4). The c2/3 subunits are structurally very similar (RMSD < 1 Å) to other F-type single-hairpin c-subunits (Supplementary Fig. 5), particularly those in the Ilyobacter tartaricus c11 ring12 (RMSD ~ 0.4 Å).

Bottom Line: Physiologically, however, F/A-type enzymes specialize in ATP synthesis driven by downhill ion diffusion, while eukaryotic V-type ATPases function as ion pumps.Molecular and kinetic simulations are used to dissect the mechanisms of Na(+) recognition and rotation of this c-ring, and to explain the functional implications of the V-type c-subunit.These structural and mechanistic insights indicate an evolutionary path between synthases and pumps involving adaptations in the rotor ring.

View Article: PubMed Central - PubMed

Affiliation: Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany.

ABSTRACT
All rotary ATPases catalyse the interconversion of ATP and ADP-Pi through a mechanism that is coupled to the transmembrane flow of H(+) or Na(+). Physiologically, however, F/A-type enzymes specialize in ATP synthesis driven by downhill ion diffusion, while eukaryotic V-type ATPases function as ion pumps. To begin to rationalize the molecular basis for this functional differentiation, we solved the crystal structure of the Na(+)-driven membrane rotor of the Acetobacterium woodii ATP synthase, at 2.1 Å resolution. Unlike known structures, this rotor ring is a 9:1 heteromer of F- and V-type c-subunits and therefore features a hybrid configuration of ion-binding sites along its circumference. Molecular and kinetic simulations are used to dissect the mechanisms of Na(+) recognition and rotation of this c-ring, and to explain the functional implications of the V-type c-subunit. These structural and mechanistic insights indicate an evolutionary path between synthases and pumps involving adaptations in the rotor ring.

No MeSH data available.


Related in: MedlinePlus