1. Amino Acid Catabolism: Carbon Skeletons Copyright © 1999-2007 by Joyce J. Diwan. All rights reserved. Molecular Biochemistry II

2. Amino Acid Carbon Skeletons Amino acids, when deaminated, yield  -keto acids that, directly or via additional reactions, feed into major metabolic pathways (e.g., Krebs Cycle). Amino acids are grouped into 2 classes, based on whether or not their carbon skeletons can be converted to glucose:  glucogenic  ketogenic.

3. Carbon skeletons of glucogenic amino acids are degraded to:  pyruvate, or  a 4-C or 5-C intermediate of Krebs Cycle. These are precursors for gluconeogenesis. Glucogenic amino acids are the major carbon source for gluconeogenesis when glucose levels are low. They can also be catabolized for energy, or converted to glycogen or fatty acids for energy storage.

4. Carbon skeletons of ketogenic amino acids are degraded to:  acetyl-CoA, or  acetoacetate. Acetyl CoA, & its precursor acetoacetate, cannot yield net production of oxaloacetate, the gluconeogenesis precursor. For every 2-C acetyl residue entering Krebs Cycle, 2 C leave as CO 2. Carbon skeletons of ketogenic amino acids can be catabolized for energy in Krebs Cycle, or converted to ketone bodies or fatty acids. They cannot be converted to glucose.

5. The 3-C  -keto acid pyruvate is produced from alanine, cysteine, glycine, serine, & threonine. Alanine deamination via Transaminase directly yields pyruvate.

6. Serine is deaminated to pyruvate via Serine Dehydratase. Glycine, which is also product of threonine catabolism, is converted to serine by a reaction involving tetrahydrofolate (to be discussed later).

7. The 4-C Krebs Cycle intermediate oxaloacetate is produced from aspartate & asparagine. Aspartate transamination yields oxaloacetate. Aspartate is also converted to fumarate in Urea Cycle. Fumarate is converted to oxaloacetate in Krebs cycle.

8. Asparagine loses the amino group from its R-group by hydrolysis catalyzed by Asparaginase. This yields aspartate, which can be converted to oxaloacetate, e.g., by transamination.

9. The 4-C Krebs Cycle intermediate succinyl-CoA is produced from isoleucine, valine, & methionine. Propionyl-CoA, an intermediate on these pathways, is also a product of  -oxidation of fatty acids with an odd number of C atoms.

10. The branched chain amino acids initially share in part a common pathway. Branched Chain  -Keto Acid Dehydrogenase (BCKDH) is a multi-subunit complex homologous to Pyruvate Dehydrogenase complex. Genetic deficiency of BCKDH is called Maple Syrup Urine Disease (MSUD). High concentrations of branched chain keto acids in urine give it a characteristic odor.

11. Propionyl-CoA is carboxylated to methylmalonyl-CoA. A racemase yields the L-isomer essential to the subsequent reaction. Methylmalonyl-CoA Mutase catalyzes a molecular rearrangement: the branched C chain of methylmalonyl-CoA is converted to the linear C chain of succinyl-CoA. The carboxyl that is in ester linkage to the thiol of coenzyme A is shifted to an adjacent carbon atom, with opposite shift of a hydrogen atom.

12. Recall that coenzyme A is a large molecule.

13. Coenzyme B 12, a derivative of vitamin B 12 (cobalamin), is the prosthetic group of Methylmalonyl-CoA Mutase.

14. A crystal structure of the enzyme-bound coenzyme B 12. Coenzyme B 12 contains a heme-like corrin ring with a cobalt ion coordinated to 4 ring N atoms.

15.  methyl C atom of 5'-deoxyadenosine (not shown).  an enzyme histidine N When B 12 is free in solution, a ring N of the dimethylbenzimidazole serves as axial ligand to the cobalt. When B 12 is enzyme-bound, a His side-chain N substitutes for the dimethylbenzimidazole. See also a diagram in an NIH website.website Within the active site, the Co atom of coenzyme B 12 has 2 axial ligands:

16. Homolytic cleavage of the deoxyadenosyl C-Co bond during catalysis yields a deoxyadenosyl carbon radical, as Co 3+ becomes Co 2+. Reaction of this with methylmalonyl-CoA generates a radical substrate intermediate and 5'-deoxyadenosine. Following rearrangement of the substrate, the product radical abstracts a H atom from the methyl group of 5'-deoxyadenosine. This yields succinyl-CoA and the 5'-deoxyadenosyl radical, which reacts with coenzyme B 12 to reestablish the deoxyadenosyl C-Co bond.

17. Methyl group transfers are also carried out by B 12 (cobalamin). Methyl-B 12 (methylcobalamin), with a methyl axial ligand substituting for the deoxyadenosyl moiety of coenzyme B 12, is an intermediate of such transfers. E.g., B 12 is a prosthetic group of the mammalian enzyme that catalyzes methylation of homocysteine to form methionine (to be discussed later).

18.  Vitamin B 12 is synthesized only by bacteria. Ruminants get B 12 from bacteria in their digestive system. Humans obtain B 12 from meat or dairy products.  Vitamin B 12 bound to the protein gastric intrinsic factor is absorbed by cells in the upper part of the human small intestine via receptor-mediated endocytosis. B 12 synthesized by bacteria in the large intestine is unavailable. Strict vegetarians eventually become deficient in B 12 unless they consume it in pill form.  Vitamin B 12 is transported in the blood bound to the protein transcobalamin, which is recognized by a receptor that mediates uptake into body cells.

19. Explore via Chime Methylmalonyl-CoA Mutase with its prosthetic group, Coenzyme B 12. Desulfo-CoA (without the thiol) is at the active site. The deoxyadenosyl moiety is lacking in the crystal.

20. The 5-C Krebs Cycle intermediate  -ketoglutarate is produced from arginine, glutamate, glutamine, histidine, & proline. Glutamate deamination via Transaminase directly yields  -ketoglutarate.

21. Glutamate deamination by Glutamate Dehydrogenase also directly yields  -ketoglutarate.

22. Histidine is first converted to glutamate. The last step in this pathway involves the cofactor tetrahydrofolate. Tetrahydrofolate (THF), which has a pteridine ring, is a reduced form of the B vitamin folate. Within a cell, THF has an attached chain of several glutamate residues, linked to one another by isopeptide bonds involving the R-group carboxyl.

23. THF exists in various forms, with single-C units, of varying oxidation state, bonded at N 5 or N 10, or bridging between them. In these diagrams N 10 with R is  -aminobenzoic acid, linked to a chain of glutamate residues. The cellular pool of THF includes various forms, produced and utilized in different reactions.

24. N 5 -formimino-THF is involved in the pathway for degradation of histidine. Reactions using THF as donor of a single-C unit include synthesis of thymidylate, methionine, f-methionine-tRNA, etc.

25. In the pathway of histidine degradation, N-formiminoglutamate is converted to glutamate by transfer of the formimino group to THF, yielding N 5 -formimino-THF.

26. Because of the essential roles of THF as acceptor and donor of single carbon units, dietary deficiency of folate, genetic deficiencies in folate metabolism or transport, and the increased catabolism of folate seen in some disease states, result in various metabolic effects leading to increased risk of developmental defects, cardiovascular disease, and cancer.

27. Aromatic Amino Acids Aromatic amino acids phenylalanine & tyrosine are catabolized to fumarate and acetoacetate. Hydroxylation of phenylalanine to form tyrosine involves the reductant tetrahydrobiopterin. Biopterin, like folate, has a pteridine ring. Dihydrobiopterin is reduced to tetrahydrobiopterin by electron transfer from NADH. Thus NADH is secondarily the e  donor for conversion of phenylalanine to tyrosine.

28. Overall the reaction is considered a mixed function oxidation, because one O atom of O 2 is reduced to water while the other is incorporated into the amino acid product.

29. O 2, tetrahydrobiopterin, and the iron atom in the ferrous (Fe ++ ) oxidation state participate in the hydroxylation. O 2 is thought to react initially with the tetrahydrobiopterin to form a peroxy intermediate. Phenylalanine Hydroxylase includes a non-heme iron atom at its active site. X-ray crystallography has shown the following are ligands to the iron atom: His N, Glu O & water O. (Fe shown in spacefill & ligands in ball & stick).

30. deamination via transaminase) accumulate in blood & urine. Mental retardation results unless treatment begins immediately after birth. Treatment consists of limiting phenylalanine intake to levels barely adequate to support growth. Tyrosine, an essential nutrient for individuals with phenylketonuria, must be supplied in the diet. Genetic deficiency of Phenylalanine Hydroxylase leads to the disease phenylketonuria. Phenylalanine & phenylpyruvate (the product of phenylalanine

31. Tyrosine is a precursor for synthesis of melanins and of epinephrine and norepinephrine. High [phenylalanine] inhibits Tyrosine Hydroxylase, on the pathway for synthesis of the pigment melanin from tyrosine. Individuals with phenylketonuria have light skin & hair color.

32. Methionine  S-Adenosylmethionine by ATP-dependent reaction.

33. SAM is a methyl group donor in synthetic reactions. The resulting S-adenosylhomocysteine is hydrolyzed to homocysteine. Homocysteine may be catabolized via a complex pathway to cysteine & succinyl-CoA.

34. Or methionine may be regenerated from homocysteine by methyl transfer from N 5 -methyl-tetrahydrofolate, via a methyltransferase enzyme that uses B 12 as prosthetic group. The methyl group is transferred from THF to B 12 to homocysteine. Another pathway converts homocysteine to glutathione.

35. In various reactions, S-adenosylmethionine (SAM) is a donor of diverse chemical groups including methylene, amino, ribosyl and aminoalkyl groups, and a source of 5'-deoxyadenosyl radicals. But SAM is best known as a methyl group donor.

36. Examples: S-adenosylmethionine as methyl group donor  methylation of bases in tRNA  methylation of cytosine residues in DNA  methylation of norepinephrine  epinephrine

37.  conversion of the glycerophospholipid phosphatidyl ethanolamine  phosphatidylcholine via methyl transfer from SAM. Enzymes involved in formation and utilization of S-adenosylmethionine are particularly active in liver. Liver has important roles in synthetic pathways involving methylation reactions, & in regulation of blood methionine.

38. Methyl Group Donors Methyl group donors in synthetic reactions include:  methyl-B 12  S-adenosylmethionine (SAM)  N 5 -methyl-tetrahydrofolate (N 5 -methyl-THF)

39. Lysine & Tryptophan The complex pathways for degradation of lysine and tryptophan will not be covered.

40. Check out the OMIM website for an example of an inborn error of metabolism, phenylketonuria, a disease resulting from deficiency of Phenylalanine Hydroxylase.OMIM website