Wednesday, December 10, 2008

Succinate Dehydrogenase

The proper name for succinate dehydrogenase is succinate:ubiquinone oxidoreductase (EC 1,3,5,1). It catalyzes the following reaction,


This is an oxidation-reduction reaction where succinate is oxidized and ubiquinone (Q) is reduced to ubiquinol (QH2). In bacteria the quinone might be menaquinone.

The reaction is part of the citric acid cycle and it is also part of the membrane-associated electron transport system that couples oxidation-reduction reactions to the transfer of protons across a membrane. The resulting protonmotive force is used to drive the synthesis of ATP.

Each year I challenge my students to find a website that correctly depicts the reactions of the citric acid cycle. This year I issued the same challenge to Sandwalk readers: Biochemistry on the Web: The Citric Acid Cycle. Nobody could find a correct version except for a few websites that copied it from my textbook.

The succinate dehydrogenase reaction is one of the reactions that everyone gets wrong. It's incorrect on almost all websites, class powerpoint slides, and also in most biochemistry textbooks. The standard error is to describe the reaction as ....

succinate + FAD → fumarate + FADH2


Let's see how the enzyme works so we can understand why that reaction is incorrect.

The structure of the E. coli enzyme is shown on the right [PDB 1NEK]. There are two polypeptide chains (subunits) making up the head portion of the enzyme at the bottom of the figure. The genes for these polypeptides are present in all species and they are well-conserved. There are one or two membrane-associated subunits (top) and these can differ from species to species.

An FAD coenzyme is covalently bound to the head region of the enzyme. This is the site where succinate is oxidized to fumarate and it projects into the cytoplasm of bacterial cells or the mitochondrial matrix in eukaryotic cells. (Succinate dehdrogenase is a mitochondrial membrane protein.)

Electrons are passed sequentially to three iron-sulfur (Fe-S) clusters and then to quinone. (The reduced form, quinol or QH2, is shown in the structure.) Most versions of succinate dehydrogenase contain a heme b group in the membrane bound portion of the molecule. It's role is unclear. (See Succcinate Dehydrogenase and Evolution by Accident.)

Here's a schematic drawing of the oxidation-reduction reaction (right). The important point is that FAD is part of a short electron transfer chain from succinate to QH2. FADH2 can't be a product of the reaction because it never dissociates from the enzyme. The product is QH2, which can diffuse in the membrane to complex III where it is oxidized.

There are dozens of enzymes that have similar internal electron transfer chains involving FAD or FMN. One of them, α-ketoglutarate deydrogenase is part of the citric acid cycle and another (complex I) is part of the membrane-associated electron transport chain. In these cases the products of the reaction are NADH2 and NAD+. You never see flavin coenzyme listed as a product because it is a transient intermediate that never dissociates from the enzyme.

Succinate deydrogenase is the only example where there is confusion about the real product of the reaction. It's not clear why. Perhaps it's an historical anomaly dating back to the time forty years ago when the real product (QH2) was unknown. That's not a very good excuse for getting it wrong in 2008.

There's one other interesting feature of this enzyme that's worth mentioning. Note that the reduction of Q is accompanied by the uptake of two protons (H+) from the cytoplasmic side of the membrane. This is very important since these protons will eventually be released on the other side of the membrane in the next reaction. This contributes to the formation of a proton gradient across the membrane. (See Ubiquinone and the Proton Pump.)

Access to the active site of quinone reduction is restricted to a small channel that opens into the cytoplasmic side of the membrane. Cheng et al. (2008) have identified a proton wire that leads from the cytoplasm to the quinone. A proton wire is a chain of protons—they are shown as red balls in the figure below. The opening to the cytoplasm is in the middle of this mirror-image view and the ubiquinone is identified as UQ.


As two protons are taken up by ubiquinone, the remaining ones in the proton wire shuffle along the channel and two are added at the other end where it opens to the cytoplasm. (The protons come from the ionization of water.)


Cheng, V.W.T., Johnson, A., Rothery, R.A. and Weiner, J.H. (2008) Alternative Sites for Proton Entry from the Cytoplasm to the Quinone Binding Site in Escherichia coli Succinate Dehydrogenase. Biochemistry 47:9107–9116 [DOI: 10.1021/bi801008e]

2 comments :

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  2. Dear Larry,

    I just wanted to let you know that we just got your book for evaluation purposes, for consideration in our Biochemistry course for undergraduates. I look forward to reading it.

    PS. I really like reading your blog and I have recommended it to every one I meet.

    Cheers
    -A

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