Biosynthesis of Nucleotides

April 23, 2003

Bryant Miles

Nucleotides play a variety of crucial roles in cells. They are the precursors of DNA and RNA.
Nucleoside triphosphates are carriers of metabolic energy. Let’s begin by looking at the de novo
biosynthesis of pyrimidines.

I. Pyrimidine Biosynthesis.

The pyrimidine ring is synthesized first and then attached to ribose to form the pyrimidine nucleotide.
Pyrimidines are synthesized from bicarbonate, aspartate and ammonia.

Carbamoyl Phosphate Synthetase II.

Remember carbamoyl phosphate synthetase I? This enzyme is found in the mitochondria of the liver and
uses 2 molecules of ATP to take bicarbonate and ammonia and form carbamoyl phosphate. CPS I uses
ammonia as the nitrogen source. CPS II catalyzes the same reaction, but the nitrogen source comes from
the hydrolysis of glutamine. The subunit that hydrolyzes glutamine to pruduce the ammonia for
biosynthesis is called a glutamine amidotransferase.

ADP H3N CH C O
ATP
O O O CH2
P CH2
C C O-
HO O- HO O
O -
C O
NH2

NH3

O
H3N CH C O
Pi
CH2
ADP ATP
O O CH2
O
- C O
O P C C
- O NH2 O NH2 O
O

The crystal structure of this enzyme is shown above. This enzyme has three active sites. The first one is
in the yellow subunit which catalyzes the hydrolysis of glutamine to produce glutamate and ammonia.
The second active site is shown in Blue this site activates bicarbonate with ATP to form
carboxyphosphate which then reacts with the nascent ammonia to form the carbamate. The third active
site is shown in red. This site catalyzes the phosphorylation of carbamate to form carbamoyl phosphate.
These three active sites are separated from each other by 45 Å. How are the intermediates shuttled from
one active site to the next?

Running through the interior of this enzyme there is a channel completely protected from the solvent that
connects all three active sites together. Ammonia is channel form the glutaminase domain to the
 carboxyphosphate domain to form carbamate. Carbamate is then channeled to the second ATP site to
form carbamoyl phosphate. Each of these three reactions is synchronized such that for every glutamine
hydrolyzed one carbamoyl phosphate is produced.

The channel running through carbamoyl phosphate synthetase connecting the

three active sites is shown to the left.

The carbamoyl phosphate produced in this reaction reacts with aspartate in a

reaction catalyzed by aspartate transcarbamylase to form carbamoylaspartate.
O O
O O Pi

-
O
-
P
O
C
NH2
+ H 3N CH C O
-
O2 C
HN
C
NH2
O CH2 Aspartate
Transcarbamoylase CO2-
C O H C
H2
O Carbamoyl
Aspartate
H+

Dihydroorotase
H 2O
O O
O NADH + H
+
NAD
+ O
-O P O H
O O O C
C H H C
HN NH O- HN NH HN NH
H O P O P O- -
OH OH O2 C
C - - C
-
O2C O O- O O2 C O Dihydroorotate C
O
C + C
H Dehydrogenase H C
H PRPP H2
Orotate Orotate Dihydroorotat
e

Pyrimidine phosphoribosyltransferase O

C
HN CH
PPi
O C
N
O H
O
C -O P O O
HN CH O- H H
H H
OH OH
C
O N CO2 - UMP
O
-O P O O ATP
O- H H
H H Nucleoside Monophosphate Kinase
OH OH
ADP
Oritidylate O
H+ C
HN CH

C
O O N H
O
Oritidylate Decarboxylase -
O P O P O O
O
- O- H H
H H
OH OH

CO2 UDP
O
ATP
C
HN CH Nucleoside Diphosphate Kinase

C
O N H ADP
O
O
C
-O P O O HN CH

O- H H O
C
N H
O O
H H O
OH OH -
O P O P O P O O
- - O- H H UTP
UMP
O O
H H
OH OH
Cytosine Biosynthesis.
This yet another enzyme that has a glutamine amidotransferase domain.
CTP Synthetase NH 2

N
N

O O O N N
-
O P O P O P O
O
O- O- O- H H
H H
OH OH Glutamine
O
B: H C O
N CH
ADP -
O P O-
C
O O O N H O
O
-
O P O P O P O O C NH3
N CH
H H
O- O- O-
H H C
OH OH
O N H Glutamate
UTP O O O
-
O P O P O P O
O
H H
O- O- O-
H H
OH OH

NH2

C
N CH

O
C
N H
Pi
O O O
-
O P O P O P O
O
H H
O- O- O-
H H
OH OH
CTP

II. Purine Biosynthesis

Glutamine phosphoribosyl amidotransferase Purine are synthesized from PRPP. PRPP is the
Glutamine Glutamate foundation upon which the purines are built. The first
step of purine biosynthesis is the displacement of the
NH3 pyrophosphate group of PRPP by ammonia to form 5-
O phosphoribosyl amine. The enzyme involved is
-O P O
O
H glutamine phosphoribosyl amidotransferase. This
O O
O- H H enzyme also has a glutamine amidotransferase
O P O P O-
H
OH OH
-
domain to produce the ammonia for biosynthesis.
O- O

PRPP
O O
-
O P O P O-

- -
O O

O
NH2
-O P O
O
O- H H
H H

OH OH

5-Phosphoribosyl-1-amine
Glycinamide Ribonucleotide synthetase O

H2N C N
C
ADP
CH
O O O O C
H3N CH C O + ATP H3N CH C O P O
H2N N
- -O P O
H H O-
O- H H
H H

O OH OH
NH2
-O P O
O 5-Aminoimidazole-4-carboxamide ribonucleotide
O- H H
H H
CO2-
OH OH
CH
5-Phosphoribosyl-1-amine CH
-
CO2
Adenylosuccinate lyase
Pi
CO2- O
CH2 NH3
HC N C N
O C C
-
H
O O2C CH2 CH
NH O C
-O P O
O H2N N
O- H H -O P O
H H
O- H H
OH OH H
H
Glycinamide Ribonucleotide OH OH

N10-Formyl-THF N-Succinyl-5-aminoimidazole-4-carboxamide ribonucleotide

Glycinamide Ribonucleotide ADP + Pi

Transformylase

THF H
SAICAR Synthetase
N
CH2 C O
H Aspartate + ATP
O C
O -
O2C N
C
NH
-O P O CH
O
O C
O- H H H2N N
H H -O P O

OH OH O- H H
H H
Formylglycinamide Ribonucleotide OH OH

ATP +Gln + H2O

ADP + Pi
FGAM Synthetase
AIR Carboxylase
ADP + Pi + Glu -
H ATP + HCO3
N
CH2 C
H
O ATP ADP + Pi N
HC
HN C CH
O
O C
NH H 2N N
-O P O
O -O P O
O- H H AIR Synthetase O- H H
H H
H H
OH OH
OH OH
Formylglycinamidine Ribonucleotide
5-Amidoimidazole
Ribonucleotide
 O

H2N C N
C
CH
O C
H2N N
-O P O

O- H H
H H

OH OH

5-Aminoimidazole-4-carboxamide ribonucleotide
N10-Formyl-THF

AICAR
Transformylase
THF
O

H2N C N
C
CH
H
O O C C
N N
-O P O H

O- H H
H H

OH OH

N-Formylaminoimidazole-4-carboxamide FAICAR

IMP Synthase
H2O
O

N
NH
HC
CH
N
O N

-O P O
O

O- H H

H H
IMP
OH OH