Featured Article - March 2010
Short description: The mystery of how formate crosses the membrane is now solved.
Bacteria produce formate during anaerobic respiration. Rapid movement of this acidic molecule out of the cell is vital for bacterial survival, yet how does it leave the cell?
It is transported across the inner membrane by the protein FocA, a member of the formate nitrite transporter family. But exactly how formate is selected and how it travels through FocA was not known.
In fact, it wasn't even clear whether FocA was a channel or a transporter.
Now two groups have the answer.
And Yigong Shi and colleagues, from the Ministry of Education Protein Science Laboratory in Beijing, solved the structure of FocA from Escherichia coli at 2.25 Å resolution. 2
Both groups report a pentameric structure, with each monomer making extensive interactions with its neighbor. Together these subunits form a central pore, which was filled with detergent in both crystal structures, suggesting that it is usually occupied by lipids.
Each monomer has a kite-shaped structure, when viewed from above, and is hourglass-shaped if viewed from within the membrane.
The monomer itself has pseudo-twofold symmetry, with each having an internal structural repeat, although the symmetry is not perfect.
The surprise was that the overall structure of the FocA monomer is similar to that of the water channel aquaporin — despite a lack of detectable sequence homology.
The sequence identity between FocA and aquaporin is only 9–12%, yet their protein fold shares a strong likeness, despite marked differences such as aquaporin forming tetramers, and FocA pentamers.
Like aquaporin, each monomer has a hole through the middle, running from one side to the other. In FocA, the entrance is funnel-shaped and positively charged; the exit too is funnel-shaped, but is negatively charged.
The structures did not reveal a structural 'gate' in the middle of this pore, which would be expected in a transporter; instead FocA is a channel with a narrow, charged, entrance to the pore and hole that is just wide enough for formate to pass through.
Wang's team also provide experimental evidence that a pH gradient is not needed for formate transport; the only gradient required is that of formate. This biological evidence supports the structural evidence that FocA is a channel.
Wang's group also solved the 2.5 Å structure of FocA with formate bound. The overall structure was very similar, as would be expected for a channel, but they observed many specific interactions with formate in the narrow pore of the monomer, suggesting it acts as a selectivity filter.
So FocA probably works by concentrating deprotonated formate within its positively charged funnel. The formate ions then enter the pore and form hydrogen bonds and van der Waal contacts that pin formate in place — a bit like a coin in a slot.
Travel though the pore proceeds smoothly, and the negatively charged surface on the periplasmic side repels the format, 'shooting' it out of the channel.
Comparison of the formate-free and formate-bound structures also suggested a possible gating mechanism in which movements of a cytosolic loop open and close the channel.
This is the first time that the ion selectivity and gating mechanism are understood for an organic-ion channel. This structural and biochemical work will stimulate new interest in developing drugs against FocA and the formate transporter family, a family that does not exist in mammals.
A. B. Waight, J. Love & D.-N. Wang Structure and mechanism of a pentameric formate channel.
Nature Struct. Mol. Biol. 17, 31-37 (2010).
Y. Wang et al. Structure of the formate transporter FocA reveals a pentameric aquaporin-like channel.
Nature 462, 467-472 (2009).