Enzyme Mechanism - Examples
The most abundant enzyme on earth is Ribulose bis-phosphate carboxylase (RuBisCO), the carbon dioxide (CO2) fixing enzyme of green plants. RuBisCO has some special interest on this campus because it was discovered by Melvin Calvin, who did his undergraduate B.S. on this campus. Calvin was awarded the Nobel Prize for discovery of RuBisCO and the understanding of the mechanism by which plants fix carbon dioxide. So Calvin is our only Nobel Prize winner and we should take a look at the enzyme which he discovered. Part of the 3-D structure of RuBisCO is a beta-barrel structure like TIM.
Figure 23. Structure of RuBisCO catalytic subunit.
How does the most abundant enzyme on earth work? The 5-carbon molecule Ribulose bis-P (RuBP) is the CO2 acceptor and binds to the enzyme first in the active site at the top of the beta barrel. RuBP binding to the active site has been studied using an inhibitor (CABP) which resembles the RuBP with CO2 attached to it. Mg2+ is directly involved in RuBP binding via a carboxylated form of Lys-201.
Figure 24. RuBP model molecule bound in the active site of RuBisCO with various key amino acid side chains identified.
I have made a diagram of the top of the beta barrel to show the positions of the amino acids involved in RuBP and carbon dioxide binding. This shows how the beta barrel brings together the important AA side chains of the active site.
Figure 25. Close-up of the active site of RuBisCO with key amino acids shown interacting with RuBP and CO2.
As it turns out, RuBP also forms an endiol like the triose did in the TIM reaction. This RuBP endiol is the highly reactive form of the substrate that can react with CO2 to form the 6 carbon intermediate that breaks down into 2 molecules of triose, which are used by the plant chloroplast to make sugars.
Figure 26. Reaction of RuBP in the active site of RuBisCO proposed to account for its reactivity with carbon dioxide.
Since the active form of RuBP is very reactive when bound to the RuBisCO's active site, it can also react with oxygen rather than CO2. This discovery explained how oxygen inhibits photosynthesis. So in the process of green plants filling the earth's atmosphere with oxygen, they produced a strong inhibitor of their most basic reaction. Of course, the oxygenation of the earth's atmosphere led to the rise of animals, which depend on plants for their food. So the plants really got a raw deal out of making oxygen.
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©Wilbur H. Campbell, 1995; wcampbel@mtu.edu