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Amino Acid Catabolism: N
Copyright © 1999-2008 by Joyce J. i!an.
All rights reser"ed.
#olec$lar %iochemistry &&
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'here are m$ltiple transaminase en(ymes !hich vary in
substrate specificity.
)ome sho! pre*erence *or partic$lar amino acids or
classes o* amino acids as amino gro$p donors+ and,or *or
partic$lar -keto acid acceptors.
H
R1 C COO- + R2 C COO
-
NH3+ O
Transaminase
H
R1 C COO
-
+ R2 C COO
-
O NH3+
Transaminases aminotrans*erases
cataly(e the
re"ersible reaction
at right.
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/ample o* a Transaminase reaction:
Aspartate donates its amino gro$p+ becoming the
α-eto acid oaloacetate.
α-etogl$tarate accepts the amino gro$p+
becoming the amino acid gl$tamate.
aspartate α-etogl$tarate oaloacetate gl$tamate
Aminotrans*erase 'ransaminase
COO−
CH2
CH2
C
COO−
O
COO−
CH2
HC
COO−
NH3+
COO−
CH2
CH2
HC
COO−
NH3+
COO−
CH2
C
COO−
O3 3
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&n another eample+ alanine becomes pyr$"ate as
the amino gro$p is trans*erred to α-etogl$tarate.
alanine α-etogl$tarate pyr$"ate gl$tamate
Aminotrans*erase 'ransaminase
COO−
CH2
CH2
C
COO−
O
CH3
HC
COO−
NH3+
COO−
CH2
CH2
HC
COO−
NH3+
CH3
C
COO−
O3 3
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'ransaminases equilibrate amino groups among
a"ailable α-eto acids.
'his permits synthesis o* non-essential amino acids+
$sing amino gro$ps *rom other amino acids 4 carbon
seletons synthesi(ed in a cell.
'h$s a balance o* di**erent amino acids is maintained+
as proteins o* "aried amino acid contents are
synthesi(ed.
Altho$gh the amino N o* one amino acid can be $sed
to synthesi(e another amino acid+ N must be
obtained in the diet as amino acids proteins.
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Essential amino acids m$st be cons$med in the diet.
#ammalian cells lac en(ymes to synthesi(e theircarbon seletons α-eto acids. 'hese incl$de:
&sole$cine+ le$cine+ 4 "aline
5ysine
'hreonine
'ryptophan
6henylalanine 'yr can be made *rom 6he.
#ethionine Cys can be made *rom #et.
7istidine /ssential *or in*ants.
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'he prosthetic gro$p o* 'ransaminase is
pyridoxal phosphate PLP+ a deri"ati"e o*
"itamin %8.
pyrido0al phosphate -656.
NH
CO
P
O−
O
O
OH
CH3
CH O−
+
H2
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&n the resting state+ the aldehyde gro$p o* pyridoal
phosphate is in a Schiff base linage to the ε-amino
gro$p o* an en(yme lysine side-chain.
NH
C
O
P
O−
O
O
O−
CH3
HC−
+
H2
N
(CH2)4
Enz
H
3
RHC COO−
NH2
/n(yme 5ys-656 )chi** base
Amino acid
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'he acti"e site lysine etracts 73+ promoting
ta$tomeri(ation+ *ollo!ed by reprotonation 4 hydrolysis.
NH
CO
P
O−
O
O
O−
CH3
HC−
+
H2
N
HC
H
3
R COO−
Enz−Lys−NH2
Amino acid-656 )hi** base aldimine
'he α-amino gro$p
o* a s$bstrate amino
acid displaces the
en(yme lysine+ to
*orm a )chi** base
linage to 656.
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'he amino gro$p remains on !hat is no! pyridoxamine
phosphate PP.
A di**erent α-eto acid reacts !ith 6#6 and the process
reverses+ to complete the reaction.
NH
CO
P
O−
O
O
OH
CH3
CH2
NH2
H2
R C COO−
O
−
+
Enz−Lys−NH2
6yridoamine phosphate 6#6
α-eto acid
hat !as anamino acidlea"es as an
-keto acid.
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)e"eral other en!ymes that cataly(e metabolism or
synthesis o* amino acids also $tili(e PLP as prosthetic
gro$p+ and ha"e mechanisms in"ol"ing a )chi** base
linage o* the amino gro$p to 656.
NH
CO
P
O−
O
O
O−
CH3
HC−
+
H2
N
HC
H
3
R COO−
Enz−Lys−NH2
Amino acid-656 )hi** base aldimine
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Chime /ercise
'!o neighboring st$dents or st$dent gro$ps sho$ld
team $p+ each displaying one o* the *ollo!ing:
'ransaminase !ith PLP in )chi** base linage to
the acti"e site lysine resid$e.
'ransaminase in the PP *orm+ !ith glutarate+ an
analog o* α-etogl$tarate+ at the acti"e site.
)t$dents sho$ld then sho! and eplain the str$ct$re
displayed by them to the neighboring st$dent or
st$dent gro$p.
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&n addition to e$ilibrating amino gro$ps among
a"ailable α-eto acids+ transaminases funnel amino
groups *rom ecess dietary amino acids to those amino
acids e.g.+ gl$tamate that can be deaminated.
"arbon skeletons o* deaminated amino acids can be
cataboli(ed *or energy+ or $sed to synthesi(e gl$cose or
*atty acids *or energy storage.
;nly a *e! amino acids are deaminated directly.
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&t is one o* the *e! en(ymes that can $se N#$% or N#$P% as e− acceptor.
;idation at the α-carbon is *ollo!ed by hydrolysis+
releasing N7<3.
−OOC
H2
C
H2
C C COO−
O
+ NH4+
NAD(P)+
NAD(P)H
−OOC
H2
CH2
C C COO−
NH3+
Hgl$tamate
α-etogl$tarate
=l$tamate ehydrogenase
H2O&lutamate$ehydrogenase
cataly(es a ma>or
reaction that e**ects
net removal of N *rom the amino
acid pool.
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)$mmari(ed abo"e:'he role o* transaminases in *$nneling amino N to
gl$tamate+ !hich is deaminated "ia =l$tamate
ehydrogenase+ prod$cing N7<3.
Amino acid -ketoglutarate NADH + NH4
+
-keto acid glutamate NAD+ + H2O
Transaminase Glutamate Dehydrogenase
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)ome other path!ays *or deamination o* amino acids:
1. Serine $ehydratase cataly(es:
serine pyruvate % N'(%
2. Peroxisomal 5- and -amino acid oidases cataly(e:
amino acid % )#$ % '*+
-keto acid % N'(% % )#$'*
)#$'* % +* )#$ % '*+*
"atalase cataly(es: 2 '*+* * '*+ % +*
HO CH2
HC COO
−
NH3
+
C COO−
OH2O NH4+
C COO−
NH3
+
H2C H3C
H2O
serine aminoacrylate pyr$"ate
)erine ehydratase
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#ost terrestrial land animals con"ert ecess nitrogen to
urea+ prior to ecreting it.
?rea is less toic than ammonia.
'he ,rea "ycle occ$rs mainly in liver.
'he 2 nitrogen atoms o* $rea enter the ?rea Cycle as N'-
prod$ced mainly "ia =l$tamate ehydrogenase and asthe amino N of aspartate.
'he N7@ and 7C;@− carbonyl C that !ill be part o* $rea
are incorporated *irst into carbamoyl phosphate.
H2N C
O
NH2
$rea
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"arbamoyl Phosphate
Synthase 'ype & cataly(es
a @-step reaction+ !ith
carbonyl phosphate and
carbamate intermediates.#mmonia is the N inp$t.
'he reaction+ !hich
in"ol"es clea"age o* * .P bonds o* A'6+ is essentially
irreversible.H2N C OPO3
2−
O
H2N C O−
O
HO C
O
OPO32−
HCO3−
ATP
NH3
ADP
ATP
Pi
ADP
carbonyl phosphate
carbamate
carbamoyl phosphate
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Alternate *orms o*
"arbamoyl Phosphate
Synthase Types // 0 ///
initially generate ammonia
by hydrolysis o* glutamine.'he type && en(yme incl$des
a long internal tunnel
thro$gh !hich ammonia 4
reaction intermediates s$ch
as carbamate pass *rom one
acti"e site to another. H2N C OPO32−
O
H2N C O−
O
HO C
O
OPO32−
HCO3−
ATP
NH3
ADP
ATP
Pi
ADP
carbonyl phosphate
carbamate
carbamoyl phosphate
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"arbamoyl Phosphate Synthase is the committed step o*
the ?rea Cycle+ and is s$b>ect to reg$lation.
H2N C OPO32−
O
HCO3− + NH3 + 2 ATP
+ 2 ADP + Pi
Carbamoyl 6hosphate)ynthase
carbamoyl phosphate
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"arbamoyl Phosphate Synthase has an absol$te
re$irement *or an allosteric acti"ator N -acetylglutamate.
'his deri"ati"e o* gl$tamate is synthesi(ed *rom
acetyl-CoA 4 gl$tamate !hen cell$lar gl$tamateB is high+signaling an excess of free amino acids d$e to protein
breado!n or dietary intae.
O CO NH
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H2N C OPO32−
O
CH2
CH2
CH2
HC
COO−
NH3+
NH3+
CH2
CH2
CH2
HC
COO−
NH3+
NH
CO NH2
COO−
CH2
HC
COO−
NH2
CH2
CH2
CH2
HC
COO−
NH3+
NH
C NH2+
COO−
CH2
HC
COO−
HN
AMP + PPi
ATP
CH2
CH2
CH2
HC
COO−
NH3+
NH
C
NH2+
H2N
COO−
HC
CH
COO−
C NH2H2N
O H2O
Pi
ornithine
$rea
citr$lline
aspartate
arginino-s$ccinate
*$marate
arginine
carbamoyl phosphate
?rea Cycle
1
2
@
<
,rea "ycle
/n(ymes inmitochondria:
1. ;rnithine'rans-
carbamylase
/n(ymes incytosol:
2. Arginino- )$ccinate
)ynthase@. Arginino- s$ccinase
<. Arginase.
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or each cycle+ citrulline m$st lea"e the mitochondria+ andornithine m$st enter the mitochondrial matri.
An ornithine1citrulline transporter in the inner mitochondrialmembrane *acilitates transmembrane *l$es o* citr$lline 4
ornithine.
cytosol
mitochondrial matrix
carbamoyl phosphate
6i
ornithine citr$lline
ornithine citr$lline
$rea aspartate
arginine argininos$ccinate
*$marate
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A complete 2rebs "ycle *$nctions only !ithin
mitochondria.
%$t cytosolic iso(ymes o* some rebs Cycle en(ymes are
in"ol"ed in regenerating aspartate *rom fumarate.
cytosol
mitochondrial matrix
carbamoyl phosphate6i
ornithine citr$lline
ornithine citr$lline$rea aspartate
arginine argininos$ccinate
*$marate
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)umarate is con"erted to oxaloacetate "ia rebs Cycle
en(ymes $marase 4 #alate ehydrogenase.+xaloacetate is con"erted to aspartate "ia
transamination e.g.+ *rom gl$tamate.
Aspartate then reenters ?rea Cycle+ carrying an amino
gro$p deri"ed *rom another amino acid.
aspartate α-etogl$tarate oaloacetate gl$tamateAminotrans*erase 'ransaminase
COO−
CH2
CH2
C
COO−
O
COO−
CH2
HC
COO−
NH3+
COO−
CH2
CH2
HC
COO−
NH3+
COO−
CH2
C
COO−
O3 3
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'ereditary deficiency o* any o* the ?rea Cycle
en(ymes leads to hyperammonemia - ele"ated
ammoniaB in blood.'otal lac o* any ?rea Cycle en(yme is lethal.
/le"ated ammonia is toic+ especially to the brain.
&* not treated immediately a*ter birth+ se"ere mental
retardation res$lts.
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6ost$lated mechanisms *or toicity o* high ammoniaB:
1. 7igh N7@B !o$ld dri"e &lutamine Synthase:
glutamate % #TP % N'- glutamine % #$P % Pi
'his !o$ld deplete gl$tamate D a ne$rotransmitter 4
prec$rsor *or synthesis o* the ne$rotransmitter =A%A.
2. epletion o* gl$tamate 4 high ammonia le"el !o$ld
dri"e &lutamate $ehydrogenase reaction to reverse:
glutamate % N#$3P4% -ketoglutarate %
N#$3P4' % N'(%
'he res$lting depletion o* α-etogl$tarate+ an essential
rebs Cycle intermediate+ co$ld impair energy
metabolism in the brain.
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Treatment o* de*iciency o* ?rea Cycle en(ymes
depends on !hich en(yme is de*icient:
limiting protein intake to the amo$nt barely
ade$ate to s$pply amino acids *or gro!th+ !hile
adding to the diet the α-eto acid analogs o*
essential amino acids.
Liver transplantation has also been $sed+ sinceli"er is the organ that carries o$t ?rea Cycle.
t l
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tiss$es !here they generate arginine 4 ornithine+ !hich are
prec$rsors *or other important molec$les.
/.g.+ #rgininosuccinate Synthase+ !hich cataly(es
synthesis o* the prec$rsor to arginine+ is in most tiss$es.
#itochondrial #rginase //+ distinct *rom the cytosolic ?rea
Cycle Arginase+ clea"es arginine to yield ornithine.
cytosol
mitochondrial matrix
carbamoyl phosphate
6i ornithine citr$lline
ornithine citr$lline$rea aspartate
arginine argininos$ccinate
*$marate
'he complete,rea "ycle is
signi*icantly onlyin liver.
7o!e"er some en!ymes o* the
path!ay are inother cells and
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'he amino acid arginine+ in addition to being a constit$ento* proteins and an intermediate o* the ,rea "ycle+ is
prec$rsor *or synthesis o* creatine 4 the signal molec$le
nitric oxide.
H2N C N
NH2+
CH2
CH3
C
O
O−
creatine
NH2 NH2 NH2
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)ynthesis o* the radical species nitric oide 5N+ *rom
arginine is cataly(ed Nitric +xide Synthase+ a distant
relati"e o* cytochrome 6<E0.
$ifferent isoforms o* Nitric ;ide )ynthase e.g.+ eN+S
epressed in endothelial cells and nN+S in ne$ronal cells
are s$b>ect to di**ering reg$lation.
+H3N CH COO
−
CH2
CH2
CH2
NH
C
NH2
NH2+
NADPH NADP+
O2 H2O O2 H2O
+H3N CH COO−
CH2
CH2
CH2
NH
C
NH2
N OH
+H3N CH COO
−
CH2
CH2
CH2
NH
C
NH2
O
1/2 NADPH 1/2 NADP+
+ NO
Nitric ;ide )ynthase
arginine hydroyarginine citr$lline
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5N+ is a short-li"ed signal molecule !ith di"erse roles
in di**erent cell types+ incl$ding reg$lation o* smoothm$scle contraction+ gene transcription+ metabolism+ and
ne$rotransmission.
#any o* the regulatory effects of 5N+ arise *rom its
acti"ation o* a sol$ble cytosolic &uanylate "yclase
en(yme that cataly(es synthesis o* cyclic-&P
analogo$s in str$ct$re to cyclic-A#6.
"ytotoxic effects of 5N+ obser"ed $nder someconditions are attrib$ted to its non-en(ymatic reaction
!ith s$peroide ;2F− to *orm the strong oidant
peroxynitrite ;N;;−.
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Polyamines incl$de putrescine+spermidine+ spermine.
+rnithine is a ma>or precursor *or
synthesis o* polyamines.
Con"ersion o* ornithine to p$trescine is
cataly(ed by +rnithine $ecarboxylase.
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'he cationic polyamines ha"e di"erse roles in cell
gro!th 4 proli*eration.
isr$ption o* polyamine synthesis or metabolism leads
to disease in animals 4 h$mans.
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7o!e"er+ Ca33-acti"ated Peptidylarginine $eiminases con"ert arginine resid$es !ithin proteins to citrulline as
a post-translational modi*ication.
'here is no tGNA *or
citrulline 4 this amino acid
is not incorporated
translationally into proteins.
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is essential to terminal differentiation of skin cells.
/cessi"e protein citr$llination+ !ith prod$ction o*
antibodies against citrullinated proteins+ is *o$nd to be
a *actor in the autoimmune diseases s$ch as rhe$matoid
th iti d lti l l i
)$bstit$tion o* citrulline+
!hich lacks arginineHs
positive charge+ may alter
str$ct$re 4 properties s$ch as
binding a**inities o* a protein.
/.g.+ citrullination o* certain proteins+ incl$ding keratin
intermediate *ilament proteins+
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