Sunday, February 24, 2019

Life (22) FeNi hydrogenase

OK, more doodles. More on Yu's paper.

Back in 2015 I produced this diagram based around Nick Lane's ideas and labwork:

Please note that the inclusion of three FeS clusters in the diagram is a complete fluke. No prescience involved! I went on to concentrate on the left hand side of the diagram to give this:

I apologised at the start of the following post because the diagram is upside down by modern convention. So let me turn it the correct way up here and alter the shapes a little, not changing anything basic. Like this:

This is the basic plan for a membrane bound FeNi hydrogenase. Obviously the exact shape is a cheat.  Lets look at the basic structure of a real life type 4 FeNi hydrogenase, say the one from the MBH of Pyrococcus furiosus. Which looks like this, ignoring the pumping/antiporting subunits (not shown):

Which is clear as mud. Until you overlay the doodle:

Look at those three embedded FeS clusters from the nickel catalytic core to the ferredoxin docking site, perfectly set up for electron tunneling! The H+ exit track is really as shown (though the blue arrow is my guess) and the hollow core of the gold section (MbhM) does connect to the outside. I omitted, by accident, that the track to ferredoxin is that of electrons freed from hydrogen. I'm showing the hydrogenase splitting hydrogen as per vent conditions. Nowadays it runs the other way (usually fed on fructose of all things) with hydrogen as waste.

Stuff makes sense.



Ken Strain said...

It's amazing work, but I feel it might take me a couple of billion years to fully appreciate the Yu paper.

"The structural conservation between MBH and complex I in the redox site is somewhat unexpected, given they utilize very different electron donors and acceptors. "

Peter said...

Yes Kenneth, they are not always as clear as you might like. I think here they are looking at the parallels between ComplexI’s N2 FeS cluster and MBH’s proximal FeS cluster. The surrounding amino acids are remarkably well conserved even though the electron transfer is from N2 to CoQ in complex I vs proximal FeS to the FeNiS cluster in MBH. They say elsewhere that the head of the CoQ molecule is in the region of the conserved active linker proteins which (I think) transfer physical movement to the membrane section. Would have helped if CoQ had been in figure 4D too. Looks like there is room…

I also spent many more hours than I should have looking at the rotation of MbhH to give Nqo14. That was clear as mud. And don’t start me on the flip of one half of MbhH to superimpose on the second half. Mud is utterly transparent by comparison, but I think I have it now.

I have to say I think we are a long, long way from understanding complex I. MBH is logical, complex I is complex. It can be made to anti port Na+ under the correct conditions. That means there is a Na+ channel somewhere, probably Nqo12, ie NuoL in the mammalian complex I.

I also find it very irresistible that the membrane anchor MbhM is essentially identical to the bacterial complex I membrane anchor Nqo8. Both are clearly channels. Both do “nothing”. Yet form is conserved over vast evolutionary distances and timescales. Hmmmmmmmm. We have a way to go!