Amino Acid Catabolism

Digestion and Absorption of Proteins

There are multiple transaminase enzymes which vary in substrate specificity. Some show preference for particular amino acids or classes of amino acids as amino group donors, and/or for particular a-keto acid acceptors. Transaminases (aminotransferases) catalyze the reversible reaction at right.

H

R1 C COO- + R2 C COO-

NH3+ O

Transaminase

H

R1 C COO- + R2 C COO-

O NH3+

Example of a Transaminase reaction: Aspartate donates its amino group, becoming the a-keto acid oxaloacetate.a-Ketoglutarate accepts the amino group, becoming the amino acid glutamate.

aspartate -ketoglutarate oxaloacetate glutamate

Aminotransferase (Transaminase)

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In another example, alanine becomes pyruvate as the amino group is transferred to a-ketoglutarate.

alanine -ketoglutarate pyruvate glutamate



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Common -Keto Acids Used Pyruvate, oxaloacetate (OAA), -ketoglutarate (most common acceptors of amino group)Ala pyruvateGlu -ketoglutarate Asp oxaloacetate e.g. of transamination: glutamate + pyruvate -ketoglutarate + alanineNote: above rxn is reversible; reversibility links protein metab with the metab of carbohydrates and proteins

Transaminases equilibrate amino groups among available a-keto acids. This permits synthesis of non-essential amino acids, using amino groups from other amino acids & carbon skeletons synthesized in a cell. Thus a balance of different amino acids is maintained, as proteins of varied amino acid contents are synthesized. Although the amino N of one amino acid can be used to synthesize another amino acid, N must be obtained in the diet as amino acids (proteins).

Essential amino acids must be consumed in the diet.Mammalian cells lack enzymes to synthesize their carbon skeletons (a-keto acids). These include: Isoleucine, leucine, & valine Lysine Threonine Tryptophan Phenylalanine (Tyr can be made from Phe.) Methionine (Cys can be made from Met.) Histidine (Essential for infants.)

The prosthetic group of Transaminase is pyridoxal phosphate (PLP), a derivative of vitamin B6.

pyridoxal phosphate (PLP)


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In the resting state, the aldehyde group of pyridoxal phosphate is in a Schiff base linkage to the e-amino group of an enzyme lysine side-chain.


Enzyme (Lys)-PLP Schiff base

Amino acid

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The active site lysine extracts H+, promoting tautomerization, followed by reprotonation & hydrolysis. The a-amino group of a substrate amino acid displaces the enzyme lysine, to form a Schiff base linkage to PLP.


Amino acid-PLP Shiff base (aldimine)

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The amino group remains on what is now pyridoxamine phosphate (PMP). A different a-keto acid reacts with PMP and the process reverses, to complete the reaction.What was an amino acid leaves as an a-keto acid.


Pyridoxamine phosphate (PMP)

-keto acid

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Several other enzymes that catalyze metabolism or synthesis of amino acids also utilize PLP as prosthetic group, and have mechanisms involving a Schiff base linkage of the amino group to PLP.


Amino acid-PLP Shiff base (aldimine)

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In addition to equilibrating amino groups among available a-keto acids, transaminases funnel amino groups from excess dietary amino acids to those amino acids (e.g., glutamate) that can be deaminated.Carbon skeletons of deaminated amino acids can be catabolized for energy, or used to synthesize glucose or fatty acids for energy storage. Only a few amino acids are deaminated directly.

It is one of the few enzymes that can use NAD+ or NADP+ as e- acceptor. Oxidation at the a-carbon is followed by hydrolysis, releasing NH4+.Glutamate Dehydrogenase catalyzes a major reaction that effects net removal of N from the amino acid pool.


glutamate

-ketoglutarate

Glutamate Dehydrogenase

H2O

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Summarized above: The role of transaminases in funneling amino N to glutamate, which is deaminated via Glutamate Dehydrogenase, producing NH4+.

Amino acid -ketoglutarate NADH + NH4+

-keto acid glutamate NAD+ + H2O

Transaminase Glutamate

Dehydrogenase

Some other pathways for deamination of amino acids:1. Serine Dehydratase catalyzes: serine pyruvate + NH4+2. Peroxisomal L- and D-amino acid oxidases catalyze: amino acid + FAD + H2O a-keto acid + NH4+ + FADH2 FADH2 + O2 FAD + H2O2 Catalase catalyzes: 2 H2O2 2 H2O + O2


serine aminoacrylate pyruvate

Serine Dehydratase

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Most terrestrial land animals convert excess nitrogen to urea, prior to excreting it. Urea is less toxic than ammonia.The Urea Cycle occurs mainly in liver. The 2 nitrogen atoms of urea enter the Urea Cycle as NH3 (produced mainly via Glutamate Dehydrogenase) and as the amino N of aspartate. The NH3 and HCO3- (carbonyl C) that will be part of urea are incorporated first into carbamoyl phosphate.


urea

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Carbamoyl Phosphate Synthase (Type I) catalyzes a 3-step reaction, with carbonyl phosphate and carbamate intermediates. Ammonia is the N input.The reaction, which involves cleavage of 2 ~P bonds of ATP, is essentially irreversible.


carbonyl phosphate

carbamate

carbamoyl phosphate

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Carbamoyl Phosphate Synthase is the committed step of the Urea Cycle, and is subject to regulation.


Carbamoyl Phosphate Synthase

carbamoyl phosphate

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Urea CycleEnzymes in mitochondria: 1. Ornithine Trans- carbamylaseEnzymes in cytosol:2. Arginino- Succinate Synthase3. Arginino- succinase4. Arginase.


ornithine

urea

citrulline

aspartate

argininosuccinate

fumarate

arginine

carbamoyl phosphate

Urea Cycle

1

2

3

4

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For each cycle, citrulline must leave the mitochondria, and ornithine must enter the mitochondrial matrix. An ornithine/citrulline transporter in the inner mitochondrial membrane facilitates transmembrane fluxes of citrulline & ornithine.

cytosol

mitochondrial matrix

carbamoyl phosphate

Pi

ornithine citrulline


urea aspartate

arginine argininosuccinate

fumarate

A complete Krebs Cycle functions only within mitochondria. But cytosolic isozymes of some Krebs Cycle enzymes are involved in regenerating aspartate from fumarate.

cytosol


carbamoyl phosphate

Pi



urea aspartate


fumarate

Fumarate is converted to oxaloacetate via Krebs Cycle enzymes Fumarase & Malate Dehydrogenase. Oxaloacetate is converted to aspartate via transamination (e.g., from glutamate). Aspartate then reenters Urea Cycle, carrying an amino group derived from another amino acid.

aspartate -ketoglutarate oxaloacetate glutamate



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Hereditary deficiency of any of the Urea Cycle enzymes leads to hyperammonemia - elevated [ammonia] in blood. Total lack of any Urea Cycle enzyme is lethal. Elevated ammonia is toxic, especially to the brain. If not treated immediately after birth, severe mental retardation results.

Treatment of deficiency of Urea Cycle enzymes (depends on which enzyme is deficient): limiting protein intake to the amount barely adequate to supply amino acids for growth, while adding to the diet the a-keto acid analogs of essential amino acids. Liver transplantation has also been used, since liver is the organ that carries out Urea Cycle.

tissues where they generate arginine & ornithine, which are precursors for other important molecules.E.g., Argininosuccinate Synthase, which catalyzes synthesis of the precursor to arginine, is in most tissues.Mitochondrial Arginase II, distinct from the cytosolic Urea Cycle Arginase, cleaves arginine to yield ornithine. The complete Urea Cycle is significantly only in liver. However some enzymes of the pathway are in other cells and

cytosol


carbamoyl phosphate

Pi



urea aspartate


fumarate

Fates of the Carbon Skeletons of Amino Acids Glucogenic amino acids are shaded pink, and ketogenicamino acids are shaded yellow. Most amino acids are both glucogenic and ketogenic.

Nucleotide catabolism

Purine Catabolism and SalvageAll purine degradation leads to uric acid (but it might not stop there)Ingested nucleic acids are degraded to nucleotides by pancreatic nucleases, and intestinal phosphodiesterases in the intestineGroup-specific nucleotidases and non-specific phosphatases degrade nucleotides into nucleosidesDirect absorption of nucleosides Further degradation Nucleoside + H2O base + ribose (nucleosidase) Nucleoside + Pi base + r-1-phosphate (n. phosphorylase)

NOTE: MOST INGESTED NUCLEIC ACIDS ARE DEGRADED AND EXCRETED.

Intracellular Purine CatabolismNucleotides broken into nucleosides by action of 5-nucleotidase (hydrolysis reactions)Purine nucleoside phosphorylase (PNP)Inosine HypoxanthineXanthosine XanthineGuanosine GuanineRibose-1-phosphate splits offCan be isomerized to ribose-5-phosphateAdenosine is deaminated to Inosine (ADA)

Degradation of PyrimidinesCMP and UMP degraded to bases similarly to purines DephosphorylationDeaminationGlycosidic bond cleavageUracil reduced in liver, forming -alanine Converted to malonyl-CoA fatty acid synthesis for energy metabolism

Amino Acid Catabolism

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