Never a Dull Enzyme
by Roberto
This post's title is taken directly from Arthur Kornberg's 1989 autobiographical chapter in Annual Reviews of Biochemistry. (For the uninitiated, Kornberg shared the 1959 Nobel Prize in Physiology or Medicine with Severo Ochoa "for their discovery of the mechanisms in the biological synthesis of ribonucleic acid and deoxyribonucleic acid." ) Arthur fell in love with enzymes early in his career and remained a devoted enzymologist all his life. To him, all enzymes, regardless of origin or function, were a source of excitement and certainly never ever dull. This memory of Arthur came to mind recently when Amy Cheng Vollmer reminded me of her 2010 STC post on metabolism. Therein, Amy notes that while enzymatic pathways might at first sight appear "dry and boring," vast secrets of biology can be gleaned from them. That is the reason she pointed me in the direction of a recent paper describing a fascinating structural feature of an enzyme from the tricarboxylic acid cycle, citrate synthase from the cyanobacteriumSynechococcus elongatus.
Fig.1. Sierpiński triangles formed by citrate synthase from S. elongatus. Top: 2D class averages of purified citrate synthase recorded by negative stained EM. Bottom: Cryo-EM density maps of Sierpiński triangles of the zeroth (hexamer), first (18-mer) and second (54-mer) fractal levels. Adapted from source.
Citrate synthase, from S. elongatus in particular, has the peculiar capacity to self-assemble into a type of fractal shape known as a Sierpiński triangle. This is not a universal feature of citrate synthases, there's something unique about the one from this cyanobacterium. Briefly, fractals are patterns that are self-similar across multiple length-scales, and Sierpiński triangles are equilateral triangles subdivided into smaller equilateral triangles. The citrate synthase from S. elongatus forms dimers that assemble into hexamers (a trimer of dimers) which in turn assemble into 18-mers that make Sierpiński triangles; these constitute about 80% of the enzyme isolated from cells. Larger multimers that also make fractals (36-mers and 54-mers) represent 3–4% of the purified enzyme. Interestingly, the 18-mers are less active than the hexamers and they are only stable at neutral pH. Since S. elongatus increases its intracellular pH to 8.4 during the day and returns it to 7.3 at night (as a function of its circadian rhythm) the authors posit that formation of the 18-mer could be a way to regulate the enzyme to be less active at night. To test this possibility the authors pinpointed the amino acid residues responsible for the formation of the fractal shapes and mutated them. The mutant enzyme no longer assembled into fractals and behaved differently in vitro. However, the mutant cells showed no alteration in their growth rate. So, there may be no adaptive benefit from fractal formation (at least under their experimental conditions). From these observations the authors conclude: "Although different stimuli modulate the formation of fractal complexes and these complexes can regulate the enzymatic activity of citrate synthase in vitro, the fractal may not serve a physiological function in vivo. We use ancestral sequence reconstruction to retrace how the citrate synthase fractal evolved from non-fractal precursors, and the results suggest it may have emerged as a harmless evolutionary accident." Does this make the enzyme dull? Not in the slightest. Stunningly beautiful I would say!
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