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COO-
C
NH2
+
CH2H2C
H2C
H
COO-
C
NH+
CH2H2C
HC
H
+H3NC
COO-
CH2 HCH2
C
O
H
+H3NC
COO-
CH2 HCH2
C
O
-O
Proline
Glutamate-γ-semialdehydedehydrogenase
Glutamate kinase andGlutamate-γ-semialdehyde
dehydrogenase
Non-enzymatic
Non-enzymatic
Proline oxidase
∆1-Pyrroline-5-carboxylatereductase
∆1-Pyrroline-5-carboxylate
Glutamate-γ-semialdehyde
Glutamate
KG + 3NADPH + NH3 + 2ATP ---> proline + 3NADP+ + 2ADP + 2Pi
KG + NADPH + NH3 + ATP ---> glutamate + NADP+ + ADP + Pi
Proline degradation
Proline
Pyrroline-5-carboxylate
H+
NC
COO-
H
N
N
NH
N
R
O
O
N
C
O
NH2
R
H H
FAD
NADPH
N
N
NH
N-
R
O
OHO
O
N
N
NH
N
R
O
OHO
HA
O
H
Reactive Flavin
H
H
H
B
H A
N
N
NH
N
R
O
OHHO
NH+
CCOO-
H
BH A
N
N
NH
N
R
O
O
NH+
CCOO-
H
HO
H
B
H A
NH2
+
CCOO-
H
H A
O
H
B
H C
COO-
NH3+
CH2 CH2 C
O
H
Glutamate semialdehyde
Pyrroline-5-carboxylate
Non-enzymatic
H C
COO-
NH3+
CH2 CH2 C
O
H
ES
H
B
H C
COO-
NH3+
CH2 CH2 C
O-
H
ES
N+
CNH2
O
R
H C
COO-
NH3+
CH2 CH2 C
O
ES
N
CNH2
O
R
NADP+
NADPH
H C
COO-
NH3+
CH2 CH2 C
O
ES
HO-
B
H
A
H C
COO-
NH3+
CH2 CH2 C
O
O-
Glutamate semialdehyde dehydrogenase
Glutamate semialdehyde
Glutamate
So….Proline = glutamate
If: Glu = -ketoglutarate + NADPH + NH3
Then: Pro = -ketoglutarate + NADPH + NH3
If: -ketoglutarate = 4 NADH + 2 GTP + 2 FADH2 + NADPH
Then: Pro = 4 NADH +2 GTP + 2 FADH2 + 2 NADPH + NH3
If: NADH = 3 ATPGTP = ATP
FADH2 = 2 ATPNH3 = -2 ATP
Then: Pro = 16 ATP + 2 NADPH
COO-
C+H3N
CH2 H
HNC
COO-
CH2 HCH2
C
O
H
HNC
COO-
CH2 HCH2
C
O
-O
Arginine
N-acetylglutamate-γ-semialdehydedehydrogenase
N-acetylglutamate kinase andN-acetylglutamate-γ-semialdehyde
dehydrogenaseN-acetylglutamate-γ-
semialdehyde
Glutamate
CH2
CH2
HN
C
+H3NC
COO-
CH2 HCH2
C
O
-O
C
O
H3C
N-acetylglutamateAcetylglutamate
synthase
C
O
H3C
HNC
COO-
CH2 HCH2
CH2+H3N
C
O
H3C
N-acetylornithine
NH2+
H2N
+H3NC
COO-
CH2 HCH2
CH2+H3N
Ornithine
N-acetylornithinase
aminotransferase aminotransferase
Urea cycle
NH2+
C
NH
CH2
CH2
CH2
CH NH3+
COO-
NH2H
OH
B NH2
C
NH
CH2
CH2
CH2
CH NH3+
COO-
NH2O
H
B
H
A
NH2
C
NH2
CH2
CH2
CH2
CH NH3+
COO-
NH2
O
Arginine
Ornithine
Arginine Degradation
ArginaseArginase
Ornithine
H C
COO-
NH3+
CH2 CH2 CH2 NH2
NH+
2-O3POO-
CH O
NH+
2-O3POO-
CH NH+
C
CH2
CH2
C
H
NH3+-OOC
B
NH
2-O3POO-
CH NH+
CH
CH2
CH2
C
H
NH3+-OOC
H H
Ornithine--aminotransferase
NH
2-O3POO-
CH NH+
CH
CH2
CH2
C
H
NH3+-OOC
Schiff BaseHydrolysis
H
A
NH+
2-O3POO-
H2CNH+
CH
CH2
CH2
C
H
NH3+-OOC
NH+
2-O3POO-
H2CNH3
+
HC
CH2
CH2
C
H
NH3+-OOC
O
Glutamate-semialdehyde
Ornithine--aminotransferase
NH+
2-O3POO-
H2CNH3
+
-OOC CH2 CH2 C
O
COO-
Schiff BaseFormation
NH+
2-O3POO-
HCNH+
COO-CH2CH2
-OOC
H
B
NH
2-O3POO-
HCNH+
COO-CH2CH2
-OOC
HA
NH+
2-O3POO-
HCNH+
COO-CH2CH2
-OOCH
Schiff BaseHydrolysis
H C
COO-
NH3+
CH2 CH2 COO-
NH+
2-O3POO-
COH
Ornithine--aminotransferase
H C
COO-
NH3+
CH2 CH2 C
O
H
ES
H
B
H C
COO-
NH3+
CH2 CH2 C
O-
H
ES
N+
CNH2
O
R
H C
COO-
NH3+
CH2 CH2 C
O
ES
N
CNH2
O
R
NADP+
NADPH
H C
COO-
NH3+
CH2 CH2 C
O
ES
HO-
B
H
A
H C
COO-
NH3+
CH2 CH2 C
O
O-
Glutamate semialdehyde dehydrogenase
Glutamate semialdehyde
Glutamate
KG + Acetyl-CoA + 4NADPH + 3NH3 + 7ATP + CO2 --->arginine + 4NADP+ + 6ADP + 1AMP+ 6Pi + 1PPi
KG + NADPH + NH3 + ATP ---> glutamate + NADP+ + ADP + Pi
So…Arg = Glutamate + NADPH + NH3
If: Glu = -ketoglutarate + NADPH + NH3
Then: Arg = -ketoglutarate + 2 NADPH + 2 NH3
If: -ketoglutarate = 4 NADH + 2 GTP + 2 FADH2 + NADPH
Then: Arg = 4 NADH +2 GTP +2 FADH2 + 3 NADPH + 2NH3
If: NADH = 3 ATPGTP = ATP
FADH2 = 2 ATPNH3 = -2 ATP
Then: Arg = 14 ATP + 3 NADPH
What is the problem with arginine degradation?
alpha-ketoglutarate
glutamate
glutamate semialdehyde
proline N-acetylglutamate semialdehyde
arginine
Control point
oxaloacetate + NADPH + NH3 + ATP ---> aspartate + NADP+ + ADP + Pi
Remember the cost of aspartate
H
O
H2C
NH3+
H
COO-
-O
O O
CH2
H
B
H+
-OOC
O
OH
H2C
NH3+
H
COO-
Schiff Base Formation
N COO--OOC
H2C
OH
H
B
H+
N COO--OOC
N COO--OOC
H-
H+
N COO--OOC
SB Hydrolysis
COO-O
COO- NH3+
succinyl-CoA
COO-O
COO- NH
CO
CH2
CH2
COO-
glutamate
C
COO-+H3N
COO- NH
CO
CH2
CH2
COO-
H
Hydrolysis
COO-
+H3N H
CH2
CH2
NH3+H
COO-
COO-
+H3N H
CH2
CH2
NH3+H
COO-
COO-
+H3N H
CH2
CH2
H
COO-
ES-
HS
E
E
S H
-S
E
+H3N
Epimerase
oxaloacetate + 4NADPH + 2NH3 + 3ATP + pyruvate + succinyl-CoA --->lysine + 4NADP+ + 3ADP + 3Pi + CO2
+H3N
COO-
H
(CH2)3
O
O-
+H3N H
+H3N
COO-
H
(CH2)3
O
O-
NH+
HPLP
+H3N
COO-
H
(CH2)3
NH+
HPLP
H+
+H3N
COO-
H
(CH2)3
NH+
HPLP
H
This is this is not the only way to make lysine
Homocitrate synthase
Homoaconitase
Homoaconitase
Homoisocitrate DH
-ketoadipate
-KG + acetyl-CoA + + 2NH3 + 2NAD+ + 4ATP + 4NADPH --->Lysine + CO2 + 2NADH + 4NADP+ + 4ADP + 4Pi
H C
COO-
NH3+
CH2 CH2 CH2 CH2 NH
COO-
CH2
CH2
C
COO-
O
H
B
H C
COO-
NH3+
CH2 CH2 CH2 CH2 N
COO-
CH2
CH2
C
COO-
SB
H-
H+
H C
COO-
NH3+
CH2 CH2 CH2 CH N
COO-
CH2
CH2
CH
COO-HH
BNAD+
H C
COO-
NH3+
CH2 CH2 CH2 CH N
COO-
CH2
CH2
CH
COO-
SB
H C
COO-
NH3+
CH2 CH2 CH2 CHH2N
COO-
CH2
CH2
CH
COO-
O
Lysine DegradationNADPH
N
CH2N
O
R
H C
COO-
NH3+
CH2 CH2 CH2 C H
O
N+
CH2N
O
R
E
SH
B
H C
COO-
NH3+
CH2 CH2 CH2 C S
O-
H
E H C
COO-
NH3+
CH2 CH2 CH2 C S
O
E
H C
COO-
NH3+
CH2 CH2 CH2 C S
O
E
-OH
B
HA
H C
COO-
NH3+
CH2 CH2 CH2 C O-
O
Transamination
C
COO-
CH2 CH2 CH2 C O-
O
O-ketoadipate
NAD+
O C
COO-
CH2 CH2 CH2 C
O
O-O C CH2 CH2 CH2 C
O
O-
TPP dependentoxidative decarboxylation
S
CoA
glutaryl-CoA
alpha-ketoadipate
O C CH CH2 C
O
O-
S
CoA
Fatty acidbeta oxidation
CH2
-O C CH CH2
S
CoA
CH
H+
O CH CH3
S
CoA
CH
FADH2
NADH
O CH CH3
S
CoA
CH
FA beta oxidation
O CH2 CH3
S
CoA
CH
OH
O CH2 CH3
S
CoA
C
O
FA beta oxidation
2 H3C
O
S CoA
NADH
So…Lysine = NADH + -ketoadipate + 2 NH3
If: -ketoadipate = 2 NADH + FADH2 + 2 Acetyl-CoA
Then: Lys = 3 NADH + FADH2 + 2 Acetyl-CoA + 2 NH3
If: Acetyl-CoA = 3 NADH + FADH2 + GTP
Then: Lys = 9 NADH + 3 FADH2 + 2 GTP + 2 NH3
If GTP = ATP, NADH = 3 ATP FADH2 = 2 ATP and NH3 = -2 ATP
Then: Lys = 35 ATP
oxaloacetate + 3NADPH + NH3 + 3ATP ---> threonine + 3NADP+ + 3ADP + 3Pi
COO-
H
NH3+
H2C
H2C OPO3
2-
COO-
H
NH+
H2C
H2C OPO3
2-
NH+
B
H+
COO-
NH+
HC
H2C OPO3
2-
NH+
H
B
COO-
NH+
CH
CH2
NH+
OH-
H+
COO-
NH+
CH
CH3
NH+
OH
H
B
H+COO-
NH+
CH
CH3
NH+
OH
H
gamma lyase/beta synthase
Threonine can be degraded in three ways
(1) Threonine dehydrogenase pathway
ThreonineDehydrogenase
H C
+H3N
COO-
O
H
CH3
H
B
NAD+
H C
+H3N
COO-
O
CH3
H C
COO-
NH3+
C
OH
S
CH3
CoA
Must break C-C bond on an amino acidand stabilize a carbanion
H C
COO-
NH3+
C
OH
S
CH3
CoA
NH+
2-O3POO-
C
HO
Schiff BaseFormation
NH+
2-O3POO-
C
H
H C
COO-
NH+
C
O
S
CH3
CoA
H
B
NH
2-O3POO-
C
H
H C
COO-
NH+
H3CC
O
SCoA
HA
NH+
2-O3POO-
C
H
H C
COO-
NH+
H
Schiff BaseHydrolysis
H C
COO-
NH3+
C
O
CH3
HS
CoA
B
H
A
NH+
2-O3POO-
C
HO
COO-
CH H
NH3+
Glycine
-amino--ketobutyrate
2-amino--ketobutyrate lyase
What happens to the glycine?Glycine Cleavage System: trifunctional enzyme
-OOC CH2 NH3+
N+
2-O3POO-
H
CH O
Schiff BaseFormation
N+
2-O3POO-
H
CH
C
C
NH+
H H
OO-
CO2
N
2-O3POO-
H
CH
C
NH+
H H
S
SE
N+
2-O3POO-
H
CH
C
NH+
H H
S
E
S-
H
A
STEP1: decarboxylation of glycine
N+
2-O3POO-
H
CH OSchiff Base
Hydrolysis
N+
2-O3POO-
H
CH
C
NH+
H H
S
E
SH
N
HN
NR
H
H
S
E
S-
CH2 NH2
B
N
HN
NR
H
CH2H2N
HS
E
HS
B
H
A
N
HN
NR
CH2
NH3
N5,N10-methylenetetrahydrofolate
Tetrahydrofolate
HA
THF
N5,N10-methylene-THF
STEP 2: formation of N5,N10-methylene-THF
S
E
S
H
H
N+
C
O
NH2
R
B
E
S S
N
C
O
NH2
RNAD+
NADH
STEP 3: regeneration of catalytic site
There is another pathway of glycine degradation
From glycine cleavage system
Combine the glycine cleavage system with a reverse of the serine hydroxymethyltransferase rxn
N
HN
NR
CH2
N5,N10-methylene-THF
-OOC CH2 NH3+
N+
2-O3POO-
H
CH O Schiff Base
Formation
N+
2-O3POO-
H
CH
C
C
NH+
H H
OO-
B
N
2-O3POO-
H
CH
C
C
NH+
H
OO-
HA
N+
2-O3POO-
H
CH
C
C
NH+
H
OO-
NH
HN
NR
CH2
HO
H
B
HA
N+
2-O3POO-
H
CH
C
C
NH+
H
OO-
HO
NH
HN
HNR
Schiff BaseHydrolysis
THF
H C CH2OH
COO-
NH3+
N+
2-O3POO-
H
CH O
Serine
So…2 glycine = 1 serine + NADH + NH3
If: Ser = pyruvate + NH3
If: 2 Gly = serine + NADH + NH3
Then: 2 Gly = 14 ATP, 1 Gly = 7 ATP
Then: 2 Gly = pyruvate + NADH + 2 NH3
If: Pyruvate = 4 NADH + GTP + FADH2
Then: 2 Gly = 5 NADH + GTP + FADH2 + 2 NH3
If: NADH = 3 ATPGTP = ATP
FADH2 = 2 ATPNH3 = -2 ATP
If: glycine is degraded by glycine cleavage system you get 1 N5,N10-methylene tetrahydrofolate, NH3 and NADH
If Acetyl-CoA = 3 NADH + GTP + FADH2
So… Thr = Gly + Acetyl-CoA + NADH
Then: Thr = N5,N10-THF + NH3 + 2 NADH + Acetyl-CoA
Then: Thr = N5,N10-THF + NH3 + 5 NADH + GTP + FADH2
If NADH = 3 ATPGTP = ATP
FADH2 = 2 ATPNH3 = -2 ATP
Then: Thr = N5,N10-THF + 16 ATP
If: 2 Thr are degraded to 2 Gly
If: 1 Gly = N5,N10- THF + 1 NH3 + 1 NADH by glycine cleavage system
Then: 2 Thr = 2 Gly + 2 NADH + 2 Acetyl-CoA
And 1 Gly + N5,N10-methylene tetrahydrofolate = serine by serine hydroxymethyltransferase
If: Ser = pyruvate + NH3
Then: 2 Thr = 1 NH3 + 3 NADH + 2 Acetyl-CoA + serine
Then: 2 Thr = 2 NH3 + 3 NADH + 2 Acetyl-CoA + pyruvate
If: Acetyl-CoA = 3 NADH + GTP + FADH2
Pyruvate = 4 NADH +GTP + FADH2
Then: 2 Thr = 2 NH3 + 13 NADH + 3GTP + 3 FADH2
If: GTP = ATP, NADH = 3 ATP FADH2 = 2 ATP and NH3 = -2 ATP
Then: 2 Thr = 44 ATP, Thr = 22 ATP
(2) Threonine can be degraded by serine hydroxymethyltransferase
COO-
C
NH3+
H C CH3
N+
2-O3POO-
H
CH O
Schiff BaseFormation
N+
2-O3POO-
H
CH
COO-
C
NH+
H C CH3
B
N
2-O3POO-
H
CH
COO-
C
NH+
HH
A
N+
2-O3POO-
H
CH
COO-
C
NH+
H
H
OH
H
OH
H3CC
H
O
Acetaldehyde
Threonine
H
Schiff BaseHydrolysis
N+
2-O3POO-
H
CH O
H
COO-
H
NH3+
Glycine
What happens to acetaldehyde: can’t be put onto THF
H3CC
H
O
CoAS
H
B
CoAS
C
CH3
O-
H
N+
C
O
NH2
R
H3CC
O
SCoA
N
C
O
NH2
RNAD+
NADH
Thr = glycine + Acetyl-CoA + NADH
Acetaldehyde dehydrogenase
If: glycine is degraded by glycine cleavage system you get 1 N5,N10-methylene tetrahydrofolate, NH3 and NADH
If Acetyl-CoA = 3 NADH + GTP + FADH2
Thus: Thr = Gly + Acetyl-CoA + NADH
Then: Thr = N5,N10-THF + NH3 + 2NADH + Acetyl-CoA
Then: Thr = N5,N10-THF + NH3 + 5 NADH + GTP + FADH2
If NADH = 3 ATPGTP = ATP
FADH2 = 2 ATPNH3 = -2 ATP
Then: Thr = N5,N10-THF + 16 ATP
(3) Threonine can be converted to -ketobutyrate by threonine (serine) dehydratase
NH+
O-
2-O3PO
CH O
H C
COO-
NH3+
C
OH
CH3
H
Schiff BaseFormation
NH+
O-
2-O3PO
CH
H C
COO-
NH+
C
OH
CH3
HB
HA
NH+
O-
2-O3PO
CH
C
COO-
NH+
C CH3
H
H2O
Schiff BaseHydrolysis
NH+
O-
2-O3PO
CH O
-OOC
NH2
H
CH3
3-methyl-2-aminoacrylate
Threonine
-OOC
NH
H
CH3
H
B
H
A
-OOC C
NH
CH2 CH3
Schiff BaseHydrolysis
-OOC C
O
CH2 CH3
-ketobutyrate
What happens to -ketobutyrate? -ketobutyrate dehydrogenase Same mechanism as pyruvate dehydrogenase and -ketoglutarate
dehydrogenase.CH3
CH2
C O
COO-S
C-
N+X
Y
R
S
C
N+X
Y
R
C
CH2
CH3
O-
C
O-OS
C
NX
Y
R
C
CH2
CH3
O-
CO2
SS
H A
S
C
N+X
Y
R
C
CH2
CH3
O-
HSS
S
C-
N+X
Y
R
C
CH2
CH3
O
HSS
HS
CoAB
H3C CH2 C
O
S CoA
HSS-
Propionyl-CoA
SS-H
N+
C
O
NH2
SS
N
C
O
NH2
Thr = propionyl-CoA + NADH
NAD+NADH
S
NHN
O
R
O P
O
O-
O-ADP
C
O
O-
-O
S
NHN
O-
R
C
H
B
O
+ ADP
S
C
CH3
CoA
O
H H
Propionyl-CoA
S
NHN
O
R
Biotin
O
S
H
CH3
O
O-
CoA
(S)-methylmalonyl-CoA
S
NHN
O
R
C
O
-O
O
H B
H+
What happens to propionyl-CoA?: Propionyl-CoA carboxylase
Loss of ATP!
-OOC C
H
C
O
S
CH3
CoA
B
-OOC C- C
O
S
CH3
CoA
AH
-OOC C C
O-
S
CH3
CoA
-OOC C-
CH3
C
O
S CoA
-OOC C
CH3
C
O
S CoA
H
(S)-methylmalonyl-CoA(R)-methylmalonyl-CoA
Methylmalonyl-CoA epimerase: Why?
Stability order of radicals allylic > R3C > R2CH > RCH2 > CH3 > vinylic
dA
CH2
Co3+NN
N N
dA
CH2
Co2+NN
N N
C C
H X
dA
CH2
H
Co2+NN
N N
C C
X
dA
CH2
H
Co2+NN
N N
C C
X
dA
CH2
Co2+NN
N N
C C
X H
So… Thr = succinyl-CoA - ATP + NADH
If: Succinyl-CoA = malate + GTP + FADH2
Then: Thr = malate + GTP - ATP + NADH + FADH2
If: Malate = pyruvate + NADPH - NADH
If: Pyruvate ---> 4 NADH + GTP + FADH2
Then: Thr = FADH2 + pyruvate + NADPH
Then: Thr = 4NADH + GTP + 2 FADH2 + NADPH
If GTP = ATP, NADH = 3 ATP FADH2 = 2 ATP and NH3 = -2 ATP
Then: Thr = 17 ATP + NADPH
If: GTP = ATP
Then: Thr = malate + NADH + FADH2
Degradation of glycine by this pathway makes 1 N5,N10-methylene tetrahydrofolate, NH3 and NADH
If: NADH is 3 ATP but NH3 is -2 ATP
Then: Gly = 1 ATP + 1 N5,N10-THF
+H3NC
COO-
H
S
CH3
+H3NC
COO-
H
C O-
O
+H3NC
COO-
H
C H
O
+H3NC
COO-
H
CH2
HO
+H3NC
COO-
H
CH2
OC
O
H2C
CH2
COO-
Aspartate Aspartate-γ-semialdehyde
HomoserineO-succinylhomoserine
succinyl-CoA
+H3NC
COO-
H
CH2
SCH2
CCOO-+H3N
H
Cystathionine
cysteine
succinate
Cystathionineγ-synthase
+H3NC
COO-
H
CH2
HS
Homocysteine
Cystathionine-lyase
Pyruvate + NH3
S-adenosylmethionine
S-adenosylhomocysteine
serine
Cystathionine-synthase
cysteine+
-ketobutyrateCystathionine
γ-lyase
Methionine
Asp semialdehyde
lysine threonine/methionine
homoserine
O-succinylhomoserine
O-phosphohomoserine
methionine
threonine
oxaloacetate + 3NADPH + 2ATP + succinyl-CoA + cysteine + N5-methyl-THF --->methionine + succinate + pyruvate + 3NADP+ + 2ADP + 2Pi
N5-methyl-THF comes from serine ---> glycine + N5,N10-methylene THF
N5,N10-methylene THF + NADH ---> N5-methyl THF + NAD+
2 ways to degrade serine.(1) Serine dehydratase breaks the C-Cγ bond
NH+
O-
2-O3PO
CH O
H C
COO-
NH3+
C
OH
H
H
Schiff BaseFormation
NH+
O-
2-O3PO
CH
H C
COO-
NH+
C
OH
H
HB
HA
NH+
O-
2-O3PO
CH
C
COO-
NH+
C H
H
+ H2O
Schiff BaseHydrolysis
NH+
O-
2-O3PO
CH O
-OOC
NH2
H
H
Aminoacrylate
Serine
Serine is converted to pyruvate + NH3 at no cost
-OOC
NH2
H
H
H
A
-OOC C
NH2+
CH3
Schiff BaseHydrolysis
-OOC C
O
CH3
Pyruvate
Aminoacrylate
+ NH3
If: Pyruvate = 4 NADH + 1 FADH2 + GTP
Then: Ser = 13 ATP
So: Ser = pyruvate + NH3
Then: Ser = 4 NADH + FADH2 + GTP + NH3
If: NADH = 3 ATPGTP = ATP
FADH2 = 2 ATPNH3 = -2 ATP
(2) Serine hydroxymethyltransferase: bifunctional enzyme
COO-
C
NH3+
H CH2 OH
N+
2-O3POO-
H
CH O
Schiff BaseFormation
N+
2-O3POO-
H
CH
COO-
C
NH+
H CH2 O
H
B
N
2-O3POO-
H
CH
COO-
C
NH+
H
H2C O
HA
N+
2-O3POO-
H
CH
COO-
C
NH+
H H
Serine
Formaldehyde
Schiff BaseHydrolysis
COO-
C
NH3+
H H
N+
2-O3POO-
H
CH O
Glycine
STEP 1: formation of glycine
What happens to formaldehyde?
N
HN
NR
Tetrahydrofolate
H
BH
O C
H
H
A
H
N
HN
NR
H
CHHO
H
B
H
A
N
HN
NR
H2C
N5,N10-methylenetetrahydrofolate
STEP 2: formation of N5,N10-methylene-THF
Serine hydroxymethyl transferase can be run in reverse to make serine from glycine and N5,N10-methylene THF
3-phosphoglycerate + NAD+ + NADPH + NH4+ + ATP --->
Serine + NADH + NADP+ + ADP + 2Pi
3-phosphoglycerate + NAD+ + NADPH + NH4+ + ATP + THF --->
glycine + NADH + NADP+ + ADP + 2Pi + N5,N10-methylene THF
CO2 + NH4+ + N5,N10-methylene THF + NADH --->
Glycine + THF + NAD+
Reverse the glycine cleavage system
What happens to glycine?Glycine Cleavage System: trifunctional enzyme
-OOC CH2 NH3+
N+
2-O3POO-
H
CH O
Schiff BaseFormation
N+
2-O3POO-
H
CH
C
C
NH+
H H
OO-
CO2
N
2-O3POO-
H
CH
C
NH+
H H
S
SE
N+
2-O3POO-
H
CH
C
NH+
H H
S
E
S-
H
A
STEP1: decarboxylation of glycine
N+
2-O3POO-
H
CH OSchiff Base
Hydrolysis
N+
2-O3POO-
H
CH
C
NH+
H H
S
E
SH
N
HN
NR
H
H
S
E
S-
CH2 NH2
B
N
HN
NR
H
CH2H2N
HS
E
HS
B
H
A
N
HN
NR
CH2
NH3
N5,N10-methylenetetrahydrofolate
Tetrahydrofolate
HA
THF
N5,N10-methylene-THF
STEP 2: formation of N5,N10-methylene-THF
S
E
S
H
H
N+
C
O
NH2
R
B
E
S S
N
C
O
NH2
R
So…degradation of serine with serine hydroxymethyltransferase followed by the glycine cleavage system makes 2 N5,N10-
methylene-THF, NH3 and NADH
NAD+NADH
If: NADH is 3 ATP but NH3 is -2 ATP
Then: Ser = 1 ATP + 2 N5,N10-THF
STEP 3: regeneration of catalytic site
Degradation of glycine by this pathway makes 1 N5,N10-methylene tetrahydrofolate, NH3 and NADH
If: NADH is 3 ATP but NH3 is -2 ATP
Then: Gly = 1 ATP + 1 N5,N10-THF
There is another pathway of glycine degradation
From glycine cleavage system
Combine the glycine cleavage system with a reverse of the serine hydroxymethyltransferase rxn
N
HN
NR
CH2
N5,N10-methylene-THF
-OOC CH2 NH3+
N+
2-O3POO-
H
CH O Schiff Base
Formation
N+
2-O3POO-
H
CH
C
C
NH+
H H
OO-
B
N
2-O3POO-
H
CH
C
C
NH+
H
OO-
HA
N+
2-O3POO-
H
CH
C
C
NH+
H
OO-
NH
HN
NR
CH2
HO
H
B
HA
N+
2-O3POO-
H
CH
C
C
NH+
H
OO-
HO
NH
HN
HNR
Schiff BaseHydrolysis
THF
H C CH2OH
COO-
NH3+
N+
2-O3POO-
H
CH O
Serine
So…2 glycine = 1 serine + NADH + NH3
If: Ser = pyruvate + NH3
If: 2 Gly = serine + NADH + NH3
Then: 2 Gly = 14 ATP, 1 Gly = 7 ATP
Then: 2 Gly = pyruvate + NADH + 2 NH3
If: Pyruvate = 4 NADH + GTP + FADH2
Then: 2 Gly = 5 NADH + GTP + FADH2 + 2 NH3
If: NADH = 3 ATPGTP = ATP
FADH2 = 2 ATPNH3 = -2 ATP
Pyruvate + NH3 + ATP + NADPH ---> alanine + ADP + Pi + NADP+
