Understanding structure, function, and mutations in the mitochondrial ATP synthase

Abstract

The mitochondrial ATP synthase is a multimeric enzyme complex with an overall molecular weight of about 600,000 Da. The ATP synthase is a molecular motor composed of two separable parts: F₁ and F_o. The F₁ portion contains the catalytic sites for ATP synthesis and protrudes into the mitochondrial matrix. F_o forms a proton turbine that is embedded in the inner membrane and connected to the rotor of F₁. The flux of protons flowing down a potential gradient powers the rotation of the rotor driving the synthesis of ATP. Thus, the flow of protons though F_o is coupled to the synthesis of ATP. This review will discuss the structure/function relationship in the ATP synthase as determined by biochemical, crystallographic, and genetic studies. An emphasis will be placed on linking the structure/function relationship with understanding how disease causing mutations or putative single nucleotide polymorphisms (SNPs) in genes encoding the subunits of the ATP synthase, will affect the function of the enzyme and the health of the individual. The review will start by summarizing the current understanding of the subunit composition of the enzyme and the role of the subunits followed by a discussion on known mutations and their effect on the activity of the ATP synthase. The review will conclude with a summary of mutations in genes encoding subunits of the ATP synthase that are known to be responsible for human disease, and a brief discussion on SNPs.

Keywords: ATP synthase; F1 ATPase; F1Fo ATP synthase; mitochondrial diseases; petite mutations; uncoupling.

Figure 1. FIGURE 1: Structural representation of the ATP synthase.

A composite representation of the ATP synthase is shown on the right with the F₁, subunits of the stator, and the c₁₀-ring shown. The structure of the F₁ and c₁₀-ring were derived from the x-ray crystal structures (2HDL and 3U2F) while the structures of the stator (peripheral stalk) were derived from the x-ray crystal structures of the bovine components (2WSS and 2CLY). Note, that a number of subunits have not been represented in the structure, most notably, subunit-a, which forms the proton half-channels.

Figure 2. FIGURE 2: Possible scheme for site occupancy during ATP synthesis.

Shown is the one possible mechanism for ATP synthesis based on the data for the bacterial and yeast enzyme (A) and the human (B) F₁ ATPase . The direction from left to right is for ATP synthesis and right to left for ATP hydrolysis. The three binding sites are shown in magenta and the γ-subunit in grey with the arrow indicating the relative position. The asterisks (*) indicate the dwell angle observed during ATP hydrolysis.

Figure 3. FIGURE 3: Location of residues in the yeast ATP synthase classified as mgi.

The structural representation is derived from the x-ray structure of the yeast F₁ ATPase (2HDL). Shown are the αβγδε subunits, as indicated. The α₃β₃ core has been stripped down to a single α and β subunit to simplify the view. The mgi residues are as labeled. The N- and C- terminal ends of the γ-subunit are indicated as is the region of the orifice of the α₃β₃ assembly, which is located at residues 22 and 242 of the yeast γ-subunit. The nucleotide binding P-loop domain is colored red and labeled.

Figure 4. FIGURE 4: Primary sequence alignment of subunit-a.

(A)The partial primary sequence alignment of subunit-a from E. coli, yeast, and human is shown. The residues predicted to form transmembrane helices 3-5 (TMH3-5) are underlined and labeled . The highly conserved and essential R210 (E. coli numbering) is shaded blue. The residues shaded red are mutated in the discussed human diseases. The residues shaded gold are identified as important for proton movement . (B)(B) Hypothetical model of the arrangement of the helices from subunits a, b, and c. The helices from subunits a (5 helices), b (2 helices) and c (20 helices) are shown along with the side chains for a-Arg1876 (yellow/blue) and c-Glu59 (red). There is very little cross-linking data positioning Helix 1 of subunit-a and thus the position is inferred from the absence, rather than presence, of cross-linking. Subunit b is thought to have a stoichiometry of 2 in the E. coli enzyme and 1 in the mitochondrial enzyme and there is 1 transmembrane helix in the bacterial subunit and 2 in the mitochondrial subunit. This view is from the matrix side of the mitochondrion. Also shown is the relative direction for deportation/protonation of c-Glu59 during ATP synthesis. The black arrow indicates the direction of rotation during ATP synthesis. Also shown is a schematic of the orientation of the transmembrane helices (TMH) for subunits a, b, and c in the membrane. Note that the helices for the subunits-a and -b are representations of a possible placement and secondary structure, while the structure of the c-ring is a crystal structure obtained from yeast .

Figure 5. FIGURE 5: Relative location in the ATP synthase of residues mutated by known single nucleotide polymorphisms.

The structural representation is derived from the x-ray crystal structure of the bovine ATPase (1E79). To simplify the image, only a single copy of the α- (salmon) and β- (cyan) subunits is shown along with the γ- (purple), δ- (orange), and ε- (green) subunits. The residues, which are altered by known SNPs in the γ-subunit are shown in sphere representation and numbered using the human numbering system with 1 as the first residue in the mature peptide (the initiating Met is -25 for the γ-subunit). The two boxes represent the regions corresponding to Catch 1 and Catch 2 regions.