Amino Acid Metabolism: Nitrogen Fixation, Transamination and NH Transport
Amino Acid Metabolism: Nitrogen Fixation, Transamination and NH Transport
Amino Acid Metabolism: Nitrogen Fixation, Transamination and NH Transport
synthesis degradation
reduction
(microorganisms, (animals &
(plants & some plants & animals) microorganisms)
anaerobic
bacteria)
denitrification nitrogen
fixation
nitrate NO3- N2 NH4+ ammonium
(anaerobic (Rhizobium &
bacteria) some other
bacteria)
nitrification nitrification
NO2-
(Nitrobacter & (Nitrosomonas &
other soil bacteria) nitrite other soil bacteria)
N2 3H2
2 NH3
The roots of leguminous plants have
nodules that contain N2-fixing bacteria
nodule cell
nucleus
bacteroids
Azotobacter are
free-living, aerobic
soil bacteria.
Mo-Fe-S cluster
(Mo:7Fe:9S)
8Fe:7S cluster
Mg ADP (2)
Two ATP-binding sites, structurally
homologous to G-proteins
1n2c.pdb
Cys residue
S-CH2CH
of the protein
The Fe-Mo cofactor
contains homocitrate
Homocitrate (3-hydroxy-3-
carboxyadipic acid)
~16 ADP
~16 ATP + 16 Pi
8 e-
CO2- CO2-
+
H3N-C-H C=O
amino acid R R -keto
acid
CO2- CO2-
C=O +
H3N C H
CH2 CH2
CH2 CH2
CH2O- P CH2OH
+
H3NCH2 NH
+ HOCH2 NH + Cl -
HO CH3 HO CH3
pyridoxamine phosphate pyridoxine hydrochloride (vitamin B6)
Pyridoxal phosphate transfers the amino group
by shuttling between aldehyde and amine forms
H
amino -
O2C C R1 -
O2C C R1 -keto
acid 1 NH3+ acid 1
O
CH=O CH2NH3+
HO CH2O- P HO CH2O- P
pyridoxal pyridoxamine
phosphate CH CH3 N phosphate
3 N
H+ H+
(on enzyme) (on enzyme)
H
amino -
O2C C R2 -
O2C C R2 -keto
acid 2 NH3+ O acid 2
pyridoxal
CH3 N CH3 N CH3 N
H+ phosphate H+ H+
H+
-keto -
acid O2C C R H2O -
O2C C R -
O2C C R
O N
+
H
N
CH2NH2 CH2 CH
CH2O- P HO CH2O- P
HO HO CH2O- P
Arg 222
Lys 258
Asn 194
Schiff base
formed from PLP
& 2-methyl-Asp
aspartate
aminotransferase
Asp 222
1ajs.pdb
Related enzymes use pyridoxal phosphate to catalyze
amino acid racemizations and decarboxylations
H
H Schiff
-
O2C C R base
-
O2C C R H2O N CO2
amino NH2
acid CH
HO CH2O- P
H C R
CH=O N
CH3 N
H+ CH
HO CH2O- P
HO CH2O- P
H
CH3 N H C R
H+ N
N CH3
H
CH
amine
HO CH2O- P
H
H2O
H C R H+
CH3 N
NH2 H+ Schiff
base
Amino acid decarboxylases generate
amines that serve as neurotransmitters
-
CO2- CO2-
CO2 +
H3N C H +
H3N C H
+
H3 N C H
CH2 CH2
CH2 5-hydroxy-Trp
Glu dihydroxy-Phe
CH2 (DOPA) HO NH
- OH
CO2 OH
CO2 CO2
CO2
NH3+ NH3+ NH3+
CH2 CH2 CH2
CH2 CH2 CH2
CH2
HO NH
- OH
CO2
-aminobutyrate OH
(GABA) dopamine serotonin
CO2- CO2-
+
H3N-C-H O=C -keto-
Glutamate dehydrogenase (1) glutarate
CH2 CH2
and glutamine synthetase (2)
are found in all organisms. CH2 CH2
Reaction (3) occurs in plants & Glu
bacteria, but not animals. CO2- CO2-
Glutamine serves as a donor of amine groups
for synthesis of many other molecules
carbamoyl-phosphate
glucosamine-6-P
-
CO2
+
H3N-C-H alanine
CH2
CH2 glycine
C-NH2
O histidine
tryptophan
In most terrestrial animals, Gln also
carries ammonia in the blood to the AMP
CTP
liver & kidneys for excretion as urea.
Glutamine synthetase catalyzes formation
of glutamine from glutamate and NH4+
glutamine
synthetase
- CO2-
CO2 CO2-
+
+ H3N-C-H +
H3N-C-H H3N-C-H
CH2
CH2 ATP ADP NH4+ Pi CH2
CH2
CH2 CH2
C-O- P
CO2 - O C-NH2
Glu O Gln
The reaction proceeds through an enzyme-
bound -glutamylphosphate intermediate
NH4+ H2O
glutaminase
In terrestrial animals, Gln carries ammonia in the blood to the
liver & kidneys, where it is hydrolyzed for excretion as urea.
Glutamine synthetase is inhibited
allosterically by many of the end-products
carbamoyl-
Glu Gln phosphate
glutamine
synthetase glucosamine-
CO2-
ATP ADP CO2- 6-P
+
H3N-C-H NH4+ Pi + alanine
H3N-C-H
CH2 CH2
CH2 CH2 glycine
X X X X X X X X
CO2- C-NH2
O histidine
Gln
ATP PPi
adenylylation
glutamine glutamine
synthetase --OH synthetase --O-AMP
(active) deadenylylation (inactive)
ADP Pi
-keto-
adenyl group
glutarate
O
enz O P OCH2 O Adenine
O
2gls.pdb
Alanine carries amino groups from
muscle to the liver for excretion
muscle
muscle blood liver O
protein
H2N-C-NH2
glucose glucose
urea
amino acids
NH4+
CO2 - CO2-
Glu
C=O C=O Glu
CO2- CO2-
-keto- +
H3N C H +
H3N C H
Ala -keto-
glutarate
CH3 CH3 glutarate
Ala