Pathway · 2 proteins

Oxidative phosphorylation

Proteins of this group that KEGG places on its “Oxidative phosphorylation” map for Aquifex aeolicus.

How it works

This map covers the membrane complexes that pass electrons along a chain and use the energy to pump protons, and ATP synthase, which uses the proton flow to make ATP. The proteins here belong to complex I, the cytochrome bc1 complex, cytochrome c and cytochrome oxidase, together with the enzymes that make heme A for the oxidase.

Grouped by KEGG pathway map. The explanation above is the atlas’s own; the map itself covers more organisms than Aquifex.

Its proteins

Protein	EC	Reaction (UniProt)	Metal or cluster	Amino acids	Certainty
NADH-quinone oxidoreductase subunit I	7.1.1.-	a quinone + NADH + 5 H(+)(in) = a quinol + NAD(+) + 4 H(+)(out)	[4Fe-4S] cluster	201	Step named
NADH dehydrogenase I chain M	—	—	—	491	Step named

Also part of this pathway

These proteins are described under another pathway, but also take part here.

Protein	EC	Reaction (UniProt)	Metal or cluster	Amino acids	Certainty
Cytochrome cHome: Oxidative phosphorylation	—	—	heme c	240	Step named
Cytochrome bHome: Oxidative phosphorylation	—	—	heme b	409	Step named
Heme O oxygenaseHome: Oxidative phosphorylation	—	—	heme b	296	Step named
Protoheme IX farnesyltransferaseHome: Oxidative phosphorylation	2.5.1.141	heme b + (2E,6E)-farnesyl diphosphate + H2O = Fe(II)-heme o + diphosphate	—	292	Step named
Cytochrome c oxidase subunit IHome: Oxidative phosphorylation	—	—	—	485	Step named
Rieske-I iron sulfur proteinHome: Quinone-linked electron transfer	—	—	[2Fe-2S] cluster	181	Step named
NADH-quinone oxidoreductase subunit AHome: Quinone-linked electron transfer	7.1.1.-	a quinone + NADH + 5 H(+)(in) = a quinol + NAD(+) + 4 H(+)(out)	—	118	Step named
NADH-quinone oxidoreductase subunit BHome: Quinone-linked electron transfer	7.1.1.-	a quinone + NADH + 5 H(+)(in) = a quinol + NAD(+) + 4 H(+)(out)	[4Fe-4S] cluster	179	Step named
NADH-quinone oxidoreductase subunit C/D 2Home: Quinone-linked electron transfer	7.1.1.-	a quinone + NADH + 5 H(+)(in) = a quinol + NAD(+) + 4 H(+)(out)	—	586	Step named
NADH-quinone oxidoreductase subunit HHome: Quinone-linked electron transfer	7.1.1.-	a quinone + NADH + 5 H(+)(in) = a quinol + NAD(+) + 4 H(+)(out)	—	336	Step named
NADH-quinone oxidoreductase subunit JHome: Quinone-linked electron transfer	7.1.1.-	a quinone + NADH + 5 H(+)(in) = a quinol + NAD(+) + 4 H(+)(out)	—	162	Step named
NADH-quinone oxidoreductase subunit K 1Home: Quinone-linked electron transfer	7.1.1.-	a quinone + NADH + 5 H(+)(in) = a quinol + NAD(+) + 4 H(+)(out)	—	100	Step named
NADH dehydrogenase I chain LHome: Quinone-linked electron transfer	—	—	—	622	Step named
NADH-quinone oxidoreductase subunit N 1Home: Quinone-linked electron transfer	7.1.1.-	a quinone + NADH + 5 H(+)(in) = a quinol + NAD(+) + 4 H(+)(out)	—	464	Step named
ATP synthase subunit bHome: ATP synthesis	—	—	—	144	Step named
ATP synthase subunit bHome: ATP synthesis	—	—	—	185	Step named
ATP synthase subunit deltaHome: ATP synthesis	—	—	—	181	Step named
ATP synthase subunit cHome: ATP synthesis	—	—	—	100	Step named
ATP synthase subunit aHome: ATP synthesis	—	—	—	216	Step named
ATP synthase subunit betaHome: ATP synthesis	7.1.2.2	ATP + H2O + 4 H(+)(in) = ADP + phosphate + 5 H(+)(out)	—	478	Step named
ATP synthase gamma chainHome: ATP synthesis	—	—	—	291	Step named
Cytochrome c oxidase subunit IIIHome: Oxygen reduction	—	—	—	258	Step named
Cytochrome c oxidase subunit 2Home: Oxygen reduction	7.1.1.9	4 Fe(II)-[cytochrome c] + O2 + 8 H(+)(in) = 4 Fe(III)-[cytochrome c] + 2 H2O + 4 H(+)(out)	Cu cation	236	Step named
NADH dehydrogenase I chain GHome: Quinone-linked electron transfer	—	—	[2Fe-2S] cluster, [4Fe-4S] cluster	632	Step named
NADH-quinone oxidoreductase subunit FHome: Quinone-linked electron transfer	7.1.1.-	a quinone + NADH + 5 H(+)(in) = a quinol + NAD(+) + 4 H(+)(out)	FMN, [4Fe-4S] cluster	426	Step named
NADH-quinone oxidoreductase subunit EHome: Quinone-linked electron transfer	7.1.1.-	a quinone + NADH + 5 H(+)(in) = a quinol + NAD(+) + 4 H(+)(out)	[2Fe-2S] cluster	160	Step named
ATP synthase epsilon chainHome: ATP synthesis	—	—	—	132	Step named
ATP synthase subunit alphaHome: ATP synthesis	7.1.2.2	ATP + H2O + 4 H(+)(in) = ADP + phosphate + 5 H(+)(out)	—	503	Step named
Inorganic pyrophosphataseHome: Not yet placed in a pathway	3.6.1.1	diphosphate + H2O = 2 phosphate + H(+)	Mg(2+)	178	Step named

Origins

Could cells have drawn energy from a proton gradient before membranes, pumps and ATP synthase existed?

How it was discovered

1961Peter Mitchell proposes that cells make ATP using a proton gradient across a membrane (the chemiosmotic hypothesis), later generally accepted (Nobel Prize 1978).Mitchell, Nature 191:144–148 (1961); Cairns-Smith, Genetic Takeover, p. 337

Naturalistic proposal

Martin and Russell proposed that the iron and nickel sulfide compartments of alkaline vents maintained a natural proton flow that could have powered early chemistry.

Design analysis

Deamer notes that the proposed proton potential across vent mineral walls has not yet been demonstrated. He adds that high salt and divalent ions in vent fluids inhibit membrane assembly.

In the cell, a proton gradient is useful only together with a sealed membrane, the pumps that build the gradient and ATP synthase that spends it. Each part is useless without the others.

From the books: Koonin, The Logic of Chance, PDF p. 244; Deamer, Assembling Life, p. 28.

The wider question for this part of the cell: origins for turning hydrogen into usable energy.

Sources

KEGG map aae00190 (enzymes of this organism highlighted)

Other pathways in this group: Quinone-linked electron transfer · ATP synthesis · Oxygen reduction · Hydrogen oxidation · Not yet placed in a pathway