Transcript Amino Acid Catabolism: C

Molecular Biochemistry II
Amino Acid Catabolism:
Carbon Skeletons
Copyright © 1999-2007 by Joyce J. Diwan.
All rights reserved.
Amino Acid Carbon Skeletons
Amino acids, when deaminated, yield a-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.
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.
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 CO2.
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.
CH3
HC
COO
COO
CH2
CH2
CH2
NH3+
COO
alanine
+
C
CH3
O
COO
C
CH2
O
COO
+
HC
NH3+
COO
a-ketoglutarate
pyruvate glutamate
Aminotransferase (Transaminase)
The 3-C a-keto acid pyruvate is produced from
alanine, cysteine, glycine, serine, & threonine.
Alanine deamination via Transaminase directly yields
pyruvate.
+
H2O NH4
H2O
HO
CH2
H
C
COO
NH3+
serine
H2C
C
COO
O
H3C
C
COO
NH3+
aminoacrylate
pyruvate
Serine Dehydratase
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).
COO
COO
COO
CH2
COO
CH2
CH2
CH2
CH2
CH2
HC
NH3+
COO
+
C
O
COO
C
O
COO
+
HC
NH3+
COO
aspartate a-ketoglutarate oxaloacetate glutamate
Aminotransferase (Transaminase)
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.
H2N
O
H2O NH4+ COO
C
CH2
HC
CH2
NH3+
HC
COO
asparagine
NH3+
COO
aspartate
Asparaginase
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.
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 b-oxidation of fatty acids with an
odd number of C atoms.
The branched chain amino acids initially share in
part a common pathway.
Branched Chain a-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.
Propionyl-CoA
Methylmalonyl-CoA
Carboxylase (Biotin)
Racemase
H
HCO 3
H
C
CH3
C
S-CoA
O
COO

H
ATP ADP
+ Pi
propionyl-CoA
C
CH3
C
S-CoA
O
H
Methylmalonyl-CoA
Mutase (B12)
H
COO
C
C
H
H
C
S-CoA
H
COO
H
C
C
CoA-S
C
H
O
D-methylmalonyl-CoA L-methylmalonyl-CoA
H
O
succinyl-CoA
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.
SH
CH2
b-mercaptoethylamine
CH2
NH
C
O
CH2
pantothenate
CH2
Recall that coenzyme A
is a large molecule.
NH
C
NH2
O
HO
C
H
H3C
C
CH3 O
H2C
O
N
N
P
O
O
O
P
N
N
O
CH2
O
O
H
H
O
H
OH
H
ADP-3'-phosphate

Coenzyme A
O
P
O
O
H
Methylmalonyl-CoA
Mutase (B12)

H
COO
C
C
H
H
C
S-CoA
O
L-methylmalonyl-CoA
H
COO
H
C
C
CoA-S
C
H
H
O
succinyl-CoA
Coenzyme B12, a derivative of vitamin B12 (cobalamin),
is the prosthetic group of Methylmalonyl-CoA Mutase.
Two views of coenzyme B12
Co
dimethylbenzimidazole
corrin
ring
PDB 1REQ
A crystal structure of the enzyme-bound coenzyme B12.
Coenzyme B12 contains a heme-like corrin ring with a
cobalt ion coordinated to 4 ring N atoms.
Two views of coenzyme B12
More diagrams
in NIH website &
U. Bristol website.
Co
corrin
ring
Within the active
site, the Co atom
of coenzyme B12
has 2 axial
dimethylbenzimidazole
PDB 1REQ
ligands:
 methyl C atom of 5'-deoxyadenosine (not shown).
 an enzyme histidine N
When B12 is free in solution, a ring N of the
dimethylbenzimidazole serves as axial ligand to the cobalt.
When B12 is enzyme-bound, a His side-chain N substitutes
for the dimethylbenzimidazole.
Homolytic cleavage of the deoxyadenosyl C-Co bond
during catalysis yields a deoxyadenosyl carbon radical,
as Co3+ becomes Co2+.
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 B12 to reestablish
the deoxyadenosyl C-Co bond.
Methyl group transfers are also carried out by B12
(cobalamin).
Methyl-B12 (methylcobalamin), with a methyl axial
ligand substituting for the deoxyadenosyl moiety of
coenzyme B12, is an intermediate of such transfers.
E.g., B12 is a prosthetic group of the mammalian enzyme
that catalyzes methylation of homocysteine to form
methionine (to be discussed later).
 Vitamin B12 is synthesized only by bacteria.
Ruminants get B12 from bacteria in their digestive system.
Humans obtain B12 from meat or dairy products.
 Vitamin B12 bound to the protein gastric intrinsic factor
is absorbed by cells in the upper part of the human small
intestine via receptor-mediated endocytosis.
B12 synthesized by bacteria in the large intestine is
unavailable.
Strict vegetarians eventually become deficient in B12
unless they consume it in pill form.
 Vitamin B12 is transported in the blood bound to the
protein transcobalamin, which is recognized by a
receptor that mediates uptake into body cells.
SH
Two views of coenzyme B12
CH2
corrin
ring
Co
b-mercaptoethylamine
CH2
NH
C
O
CH2
pantothenate
CH2
NH
dimethylbenzimidazole
PDB 1REQ
Explore via Chime
Methylmalonyl-CoA Mutase
with its prosthetic group,
Coenzyme B12.
Desulfo-CoA (without the
thiol) is at the active site.
C
NH2
O
HO
C
H
H3C
C
CH3 O
H2C
O
N
N
P
O
O
O
P
N
N
O
CH2
O
O
H
H
O
H
OH
H
ADP-3'-phosphate

O
Coenzyme A
The deoxyadenosyl moiety is lacking in the crystal.
P
O
O
COO
COO
COO
CH2
COO
CH2
CH2
CH2
CH2
CH2
HC
NH3+
COO
+
C
O
COO
C
O
COO
+
HC
NH3+
COO
aspartate a-ketoglutarate oxaloacetate glutamate
Aminotransferase (Transaminase)
The 5-C Krebs Cycle intermediate a-ketoglutarate is
produced from arginine, glutamate, glutamine,
histidine, & proline.
Glutamate deamination via Transaminase directly yields
a-ketoglutarate.
H2 H2

OOC C C
glutamate
NH3+
C
H
COO
NAD(P)+
NAD(P)H
O
H2 H2

OOC C C
a-ketoglutarate
C
COO + NH4+
Glutamate Dehydrogenase
Glutamate deamination by Glutamate Dehydrogenase
also directly yields a-ketoglutarate.
H2 N
N
H
N
H
Tetrahydrofolate (THF)
H
HN
N
H
O
pteridine
H
CH2
HN
COO
O
C
-aminobenzoate
N
H
C
H
C C COO
H2 H 2
glutamate
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.
THF exists in various
forms, with single-C units,
of varying oxidation state,
bonded at N5 or N10, or
bridging between them.
In these diagrams N10 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.
H2N
N
H
N
H
H
HN
N5
H H
10N
O
Tetrahydrofolate (THF)
H2N
N
CH2
H
N
R
H
H
H
HN
N5
H
O
N5-Methyl-THF
CH2
CH3 10N
H
R
H
H2N
H
N
N
H
H
HN
N5
H
O
C
HN
H
CH2
10N
R
H
N5-formimino-THF
N5-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.
HC
C
N
CH2
COO
NH3+
NH
C
H
In the pathway of
histidine degradation,
N-formiminoglutamate
is converted to
glutamate by transfer of
the formimino group
to THF, yielding
N5-formimino-THF.
H
C
histidine
NH4+
H2O
H2O
H
C

OOC
HN
CH2
CH2 COO
N-formiminoglutamate
NH
C
H
THF
N 5-formimino-THF

OOC
H
C
CH2
NH3+
CH2 COO
glutamate
H2N
N
H
N
H
H
HN
N5
H H
O
Tetrahydrofolate (THF)
CH2
10 N
R
H
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.
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.
NH3+
CH2
CH
COO
phenylalanine
Phenylalanine
Hydroxylase
O2 + tetrahydrobiopterin
H2O + dihydrobiopterin
NH3+
HO
CH2
CH
COO
tyrosine
Overall the reaction is considered a mixed function
oxidation, because one O atom of O2 is reduced to water
while the other is incorporated into the amino acid product.
7,8-dihydrobiopterin
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).
Glu
His
His
PDB 1DMW
Phenylalanine
Hydroxylase
O2, tetrahydrobiopterin, and the iron atom in the ferrous
(Fe++) oxidation state participate in the hydroxylation.
O2 is thought to react initially with the tetrahydrobiopterin
to form a peroxy intermediate.
Genetic deficiency
of Phenylalanine
Hydroxylase leads
to the disease
phenylketonuria.
Transaminase
Phenylalanine
Phenylpyruvate
(Phenylketone)
Phenylalanine Deficient in
Hydroxylase
Phenylketonuria
Tyrosine
Melanins
Phenylalanine &
Multiple
Reactions
phenylpyruvate
(the product of
Fumarate + Acetoacetate
phenylalanine
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.
Transaminase
Phenylalanine
Phenylpyruvate
(Phenylketone)
Phenylalanine Deficient in
Hydroxylase
Phenylketonuria
Tyrosine
Melanins
Multiple
Reactions
Fumarate + Acetoacetate
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.
H3C
H3C
S
H2
C
methionine
H2 H
C C
COO
NH3+

H2 H2 H
C C C
+
S
CH2
NH3+
Adenine
O
ATP PPi + Pi
H
H
H
OH
H
OH
N5-methyl-THF
methylated acceptor
adenosine H2O
H2 H2 H
C C C
homocysteine
S-adenosylmethionine
(SAM)
acceptor
THF
HS
COO
COO

H2 H2 H
C C C
S
CH2
NH3+
Adenine
O
NH3+
H
COO
H
H
OH
H
OH
S-adenosylhomocysteine
Methionine  S-Adenosylmethionine by ATP-dependent reaction.
SAM is a methyl group
H 3C
donor in synthetic reactions.
The resulting
S-adenosylhomocysteine is
hydrolyzed to homocysteine.
Homocysteine may be
catabolized via a complex
pathway to cysteine &
succinyl-CoA.
adenosine H2O
HS
C
H2
C
H2
H
C

COO
+
S
H
C
C C
H2 H2
CH2
NH3+
Adenine
O
H
COO
H
H
OH
H
OH
S-adenosylmethionine
(SAM)
acceptor
methylated acceptor
S
CH2
C
H2
C
H2
homocysteine
H
COO
NH3+
Adenine
O
NH3+
H
C
S-adenosylH homocysteine
H
H
OH
OH
Or methionine may be
regenerated from
homocysteine by
H3C S C
H2
methyl transfer from
N5-methyl-tetrahydrofolate,
methionine
via a methyltransferase
enzyme that uses B12 as
THF
prosthetic group.
N5-methyl-THF
The methyl group is
transferred from THF to B12
to homocysteine.
Another pathway converts
homocysteine to glutathione.
HS
C
H2
C C
H2 H2
H
C
COO
NH3+
H
C
COO
NH3+
homocysteine
H 3C
+
S
C C
H2 H2
CH2
COO
NH3+
Adenine
O
H
H
C
H
H
OH
H
OH
S-adenosylmethionine (SAM)
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.
HO
H 3C
+
S
C C
H2 H2
CH2
OH
COO
HO
CH
Adenine
H
H
OH
H
OH
S-adenosylmethionine (SAM)
CH2
NH3+
norepinephrine
NH3+
O
H
H
C
S-adenosylmethionine
S-adenosylhomocysteine
HO
OH
HO
CH
CH2
H
N
CH3
epinephrine
Examples:
S-adenosylmethionine as methyl group donor
 methylation of bases in tRNA
 methylation of cytosine residues in DNA
 methylation of norepinephrine  epinephrine
O
O
R1
C
H2C
O
O
CH
H2C
C
R2
O
O
P
CH3
O
CH2
O
CH2
+
N CH3
CH3
phosphatidylcholine
 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.
Methyl Group Donors
Methyl group donors in synthetic reactions include:
 methyl-B12
 S-adenosylmethionine (SAM)
 N5-methyl-tetrahydrofolate (N5-methyl-THF)
Lysine & Tryptophan
The complex pathways for degradation of lysine
and tryptophan will not be covered.
Check out the OMIM website for an example of an
inborn error of metabolism, phenylketonuria, a
disease resulting from deficiency of Phenylalanine
Hydroxylase.