Question: Nutrition is my greatest area of interest in biochemistry, specifically in how the digestive system comes to acquire and process all its required components. Nutrient deficiency is a fascinating concept today because despite abundant food in developed countries, individuals continually contract diseases related to vitamin deficiency. Pernicious anemia is an autoimmune disorder which results from vitamin B12 deficiency. Vitamin B12 is an important compound in all cellular processes and is intriguing because its synthesis requires a family of enzymes which generate radical intermediates. Another important family of enzymes called S-adenosyl-L-methionine (SAM) enzymes generates analogous radical intermediates. What are SAM enzymes and how is our understanding of radical enzymes affected based on new findings regarding radical SAM intermediate compounds?
Answer: SAM enzymes belong to one of the largest classes of enzymes in biology and catalyze cellular processes like post-transcriptional and post-translational modifications, enzyme activation, RNA modification, and biosynthetic reactions. These enzymes utilize a functional domain comprised of four sulfur and four iron (4S-4Fe) atoms which cleave SAM molecules to form an important radical intermediate known as 5’-deoxyadenosyl. A radical is a compound with a highly reactive, unpaired electron whose reactivity can be both useful in chemical reactions and problematic by damaging cellular structures.
The 5’-deoxyadenosyl intermediate has not yet been detected, but scientists at Montana State University and Northwestern University sought to capture it in an experiment by reacting pyruvate formate-lyase activating enzyme (PFL-AE) with an inactive form of pyruvate formate lyase (PFL). PFL-AE forms a glycine radical on the inactivated PFL. By reacting the enzymes together and repeatedly freezing them over a few seconds to collect magnetic resonance data, the team catalogued the structure of radical intermediates.
Although the 5’-deoxyadenosyl intermediate was not detected, their results suggested the enzyme operates via an organometallic center in which an iron atom from the 4S-4Fe cluster forms a transient bond with the 5’ carbon of SAM to stabilize the radical. This proposed intermediate structure is analogous to an intermediate found in vitamin B12 synthesis in which adenosylcobalamin cofactor reacts with vitamin B12 radical enzyme to generate cobalamin and a radical compound which is again stabilized by a transient bond with a functionally-similar organometallic center.
As previously mentioned, radical compounds can be destructive to cells by denaturing proteins and nucleic acids, so they must be stabilized to prevent unwanted radical reactions. The proposed intermediate structure provides a means by which the cell can temporarily contain the radical by anchoring it to an organometallic functional group. Researchers speculate based on the role of SAM in the enzymatic reaction that all radical SAM enzymes might operate using a similar organometallic intermediate. Further research is required to confirm this. The study of organometallic intermediates in radical SAM enzymes and radical B12 enzymes enhances our understanding of both classes of enzymes on a mechanistic level as well as our understanding of vitamin metabolism.
- Horitani, M., Byer, A. S., Shisler, K. A., Chandra, T., Broderick, J. B., and Hoffman, B. M. (2015) Why Nature Uses Radical SAM Enzymes so Widely: Electron Nuclear Double Resonance Studies of Lysine 2,3-Aminomutase Show the 5′-dAdo• “Free Radical” Is Never Free. J. Am. Chem. Soc. Journal of the American Chemical Society. 137, 7111–712z
- Horitani, M., Shisler, K., Broderick, W. E., Hutcheson, R. U., Duschene, K. S., Marts, A. R., Hoffman, B. M., and Broderick, J. B. (2016) Radical SAM catalysis via an organometallic intermediate with an Fe-[5′-C]-deoxyadenosyl bond. Science.352, 822–825