Purine Synthesis: Synthesis of Purine RiboNucleotides

Purine biosynthesis is how purines, which are essential components of DNA and other body molecules, are produced. This process starts with the chorismate, which is produced in plants. This is the first step in the biosynthesis of the purine ring systems.

This process is carried out by an enzyme known as chorismate mutase. There is also a reverse reaction in this process, which is the breakdown of the purine ring system. This takes place via the enzyme known as IMP dehydrogenase.

Adenine (adenine triphosphate, or ATP) and guanine are produced by this route (guanine triphosphate, or GTP). Glyceraldehyde-3-phosphate and dihydroxyacetone phosphate (DHAP) are the starting points for synthesizing the purine ring structure.

Purines are molecules that include adenine, guanine, and cytosine.

They are essential for the normal functioning of the genetic material in cells and are involved in many biochemical pathways. In this blog, we will discuss the purine biosynthesis pathway and the role of purines in health.

In 1948 “John Buchanor” obtained the first clues about how this process occurs. Denovo by feeding a variety of isotopically labeled compounds to pigeons and chemically determining the position of the labeled atoms in their excreted Uric acid.

The two purine nucleotides of nucleic acids are AMP and GMP, containing the purine bases Adenine (A) and Guanine (G).

The results of the studies are purine synthesis.

Sources of atoms for Purine Synthesis

The biosynthetic organs of Purine ring atoms note that C4, C5, and N7 come from a single Glycine molecule but each of the other atoms is derived from an independent precursor.

• N1→ came from Asparagine
• C2 and C8 → came from formate (THF)
• N3 and N9 → came from Glutamine
• C4, C5, and N7 → came from HCO₃^–

Purine Synthesis Pathways

Purine synthesis can be explained in two different pathways

1. De-Novo Pathway
2. Salvage Pathway (also called Dust-bin Pathway)

De Novo Purine Synthesis

In this de-novo synthesis of purines, each atom in the purine nucleotide came from different sources mentioned in the structure and data. There are three significant steps involved in this purine synthesis pathway.

1. Ribose-5-Phosphate to IMP synthesis
2. Synthesis of AMP from IMP
3. Synthesis of GMP from IMP

Ribose-5-Phosphate to IMP synthesis

Step 1: Amination

The starting material for purine biosynthesis is Ribose-5-P, a product of the Hexose MonoPhosphate Shunt or Pentose Phosphate pathway (HMP Shunt). The ribose-5-P is converted into phosphoribosyl pyrophosphate by Pyrophospho Kinase in this reaction ATP is consumed.

Step 2: Addition of N9

One nitrogen is added on Ribose-5-P, to form 5-phosphoribosyl-1-amine (PRA). The nitrogen is donated by Glutamine. Ribose-5-Phosphate is derived from PRPP.

The reaction needs energy from ATP hydrolysis. This is the rate-limiting enzyme of this pathway. This step is inhibited by azaserine, the anticancer drug.

Step 3: Incorporation of C4, C5, and N7

The phosphoribosyl amine (PRA) is condensed with glycine it forms Glycinamide ribotide (GAR). This reaction is catalyzed by GAR Synthase.

Step 4: Addition of C8

Glycinamide ribotide is converted into a Formyl glycine amide ribotide (FGAR). This reaction is catalyzed by transformylase. Here Formyl donor is N¹⁰-Formyl-THF.

Step 5: Addition of N3

Formyl Glycine ribotide is converted into Formylglycinaidine ribotide (FGAM) in the presence of the enzyme FGAM synthetase. Here amide donor is Glutamine and it is ATP consumed reaction. This enzyme is also inhibited by azaserine.

Step 6: Cyclisation (Closure of Ring)

FGAM is converted into 5-amino imidazole ribotide (AIR). This reaction is catalyzed by AIR synthetase. Here, ATP is consumed.

Step 7: Addition of C6

Amino imidazole ribotide is converted into 5-amino-4-carboxy-amino-imidazole ribonucleotide (CAIR). This reaction is catalyzed by AIR carboxylase. In this reaction, carbonic acid is substituted with a 4th carbon atom in the form of the carboxyl group (CAIR).

This carbon dioxide fixation reaction does not require biotin or ATP.

Step 8: Addition of N1

Carboxy Amino Imidazole has converted into 5-AminoImidazole (N-Succinylocarboxamide) ribotide (SACAIR). This reaction is catalyzed by SACAIR synthetase. In this reaction, one Aspartic acid linked with Carboxyl group ATP is consumed.

Step 9: Removal of Fumaric acid

SACAIR is converted into 5-AminoImidazole-4-CarboxyAmide Ribotide (AICAR). This reaction is catalyzed by adenosuccinate lyase. The linked aspartic acid is hydrolyzed into fumarate, which directly enters the TCA cycle.

The amino group of aspartic acid becomes the first nitrogen of the purine ring.

Step 10: Addition of C2

AICAR is converted into 5-FormaminoImidazole-4-Carboxamide Ribotide (FAICAR). This reaction is catalyzed by transformylase. Here formyl group donor is N¹⁰-Formyl THF. This carbon is derived from the one-carbon pool. In folic acid deficiency, this step is blocked; hence orange-colored FAICAR is excreted in the urine.

Step 11: Cyclization

FAICAR is converted into Inosine Mono Phosphate (IMP) by the catalyzation process. This reaction is catalyzed by IMP Cyclohydrolase. It contains purine, hypoxanthine.

Donor atom	Added features	Special	Product
Glutamine	N9	Rate-limiting	PRA
Glycine	C4, C5 and N7	ATP required	GAR
Methenyl-THFA	C8	–	FGAR
Glutamine	N3	ATP required	FGAM
–	Ring closure	ATP need	AIR
Carbon dioxide	C6	–	ACAIR
Aspartic acid	N1	ATP required	SAICAR
–	–	Fumarate removed	AICAR
Formyl THFA	C2	–	FAICAR
–	–	Ring closure	IMP

Synthesis of AMP from IMP

IMP is the central intermediate of both AMP and UMP.

Step 1: IMP to AdenyloSuccinate

The IMP is converted into adenyloSuccinate by taking Aspartate and GTP, which gives the power of the UTP to GTP and inorganic phosphate. This reaction is catalyzed by adenyl-succinate synthetase.

Step 2: AdenyloSuccinate to AMP

AdenyloSuccinate is converted into AMP by releasing Aspartate in the form of fumarate. This reaction is catalyzed by Adenylo Succinate Lyase.

Synthesis of GMP from IMP

Step 1: IMP to XMP

In the presence of the enzyme IMP-dehydrogenase, IMP is converted into Xanthosine Monophosphate. This is called dehydrogenation.

Step 2: XMP to GMP

XMP is converted into GMP by the enzyme GMP synthase. Here, the amino group donor is glutamate.

Regulation of Purine Biosynthesis

Activation:

• The activator molecule for purine synthesis is PRPP, which activates the enzyme AmidoPhospho Ribosyl transferase
• The initiator molecule for the synthesis is ribose-5-phosphate. The optimum concentration of Ribos-5-Phosphate is maintained by the enzyme Glucose-6-Phosphate dehydrogenase, which is the regulatory enzyme of Hexose Mono Phosphate Shunt.

Inhibition:

• The rate-limiting enzyme “Ribose-5-Phosphate Pyrophospho kinase” inhibited the nucleotides AMP, ADP, ATP, GMP, GDP, and GTP by a feedback inhibition mechanism.
• The enzyme amino phosphoribosyl transferase is inhibited by AMP, ADP, ATP, GMP, GDP, GTP adenylosuccinate and XMP.
• The amp inhibits Adenylo succinate synthatase GMP inhibits IMP dehydrogenase.

Salvage Pathway (or) Dust-bin Pathway

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This is another type of purine nucleotide synthesis from scratch. So, this is also called the “Dust-bin pathway”. Most cells have an active turnover of many of their nucleic acids, resulting in adenine, guanine, and Hypoxanthine.

Purines that result from the normal turnover of cellular nucleic acids or that are obtained from the diet are not degraded. It can be reconverted into nucleoside triphosphate and used by the body. This is referred to as the “salvage pathway” for purines.

Two enzymes are involved in this pathway.

APRT Enzyme

• APRT means Adenosyl Phosphoribosyl Transferase (APRTase)
• This enzyme catalyzes the reaction of Adenine to AMP conversion. In this reaction the secondary substrate is PRPP and byproduct is PPi.

Adenine + PRPP ↔ AMP + PPi

HGPRT Enzyme

• HGPRT means Hypoxanthine-Guanine Phospho Ribosyl Transferase (HGPRTase).
• This enzyme catalyzes the reaction of GMP formation from Hypoxanthine and PRPP.

Hypoxanthine + PRPP ↔ IMP + PPi

Guanine + PRPP ↔ GMP + PPi

The salvage pathway is of special importance in tissues like RBC and the brain, where the de-novo pathway is not operating.

The origin of the carbon and nitrogen atoms of the purine ring system was determined by John Buchanan using an isotopic tracer experiment.

The detailed explanation of purine biosynthesis was first explained by Buchanan and G.Robert Greenberg in the 1950s.

Frequently Asked Questions (FAQs)

Final words

Purine biosynthesis is how purines, which are essential components of DNA and other body molecules, are produced.
This process begins with converting the sugar ribose into two nucleotide molecules, 5-methylcytosine (5mC) and 2-deoxycytidine (2dC). A methyl group then links these two molecules together to form guanine. Finally, a phosphate group is added to the molecule to create purine.