Principles of Biochemistry/Nucleic acid III: Sythesis of nucleotides

Purines Synthesis

Purines are biologically synthesized as nucleotides (bases attached to ribose 5-phosphate). A key regulatory step is the production of ribose-5-phospho-α-D-ribosyl 1-pyrophosphate (PRPP) by PRPP synthetase, which is activated by inorganic phosphate and inactivated by purine ribonucleotides. It is not the committed step to purine synthesis because PRPP is also used in pyrimidine synthesis and salvage pathways. The first committed step is the reaction of PRPP, glutamine and water to 5'-phosphoribosylamine, glutamine, and pyrophosphate - catalyzed by pyrophosphate amidotransferase, which is activated by PRPP and inhibited by AMP, GMP and IMP.

Both adenine and guanine are derived from the nucleotide inosine monophosphate (IMP), which is synthesised on a pre-existing ribose-phosphate through a complex pathway using atoms from the amino acids glycine, glutamine, and aspartic acid, as well as formate ions transferred from the coenzyme tetrahydrofolate.

GMP

• IMP dehydrogenase converts IMP into XMP
• GMP synthase converts XMP into GMP

In enzymology, a GMP synthase (glutamine-hydrolysing) (EC 6.3.5.2) is an enzyme that catalyzes the chemical reaction

ATP + xanthosine 5'-phosphate + L-glutamine + H₂O $\rightleftharpoons$ AMP + diphosphate + GMP + L-glutamate

The 4 substrates of this enzyme are ATP, xanthosine 5'-phosphate, L-glutamine, and H2O, whereas its 4 products are AMP, diphosphate, GMP, and L-glutamate. This enzyme belongs to the family of ligases, specifically those forming carbon-nitrogen bonds carbon-nitrogen ligases with glutamine as amido-N-donor. The systematic name of this enzyme class is xanthosine-5'-phosphate:L-glutamine amido-ligase (AMP-forming). Other names in common use include GMP synthetase (glutamine-hydrolysing), guanylate synthetase (glutamine-hydrolyzing), guanosine monophosphate synthetase (glutamine-hydrolyzing), xanthosine 5'-phosphate amidotransferase, and guanosine 5'-monophosphate synthetase. This enzyme participates in purine metabolism and glutamate metabolism. At least one compound, Psicofuranin is known to inhibit this enzyme.

• GMP reductase converts GMP back into IMP

AMP

• adenylosuccinate synthase converts IMP to adenylosuccinate
• adenylosuccinate lyase converts adenylosuccinate into AMP
• AMP deaminase converts AMP back into IMP

Phosphoribosyl pyrophosphate (PRPP) is a pentosephosphate.

It is formed from ribose 5-phosphate by the enzyme ribose-phosphate diphosphokinase.

It plays a role in transferring phospho-ribose groups in several reactions:

Enzyme	Reactant	Product
adenine phosphoribosyltransferase	adenine	AMP
hypoxanthine-guanine phosphoribosyltransferase	guanine	GMP
hypoxanthine-guanine phosphoribosyltransferase	hypoxanthine	IMP
orotate phosphoribosyltransferase	orotate	OMP
uracil phosphoribosyltransferase	uracil	UMP

In de novo generation of purines, the enzyme amidophosphoribosyltransferase acts upon PRPP to create phosphoribosylamine. Six enzymes take part in IMP synthesis. Three of them are multifunctional:

GART (reactions 2, 3, and 5)

PAICS (reactions 6, and 7)

ATIC (reactions 9, and 10)

Trifunctional purine biosynthetic protein adenosine-3 is an enzyme that in humans is encoded by the gene GART . This protein is a trifunctional polypeptide. It has phosphoribosylglycinamide formyltransferase (EC 6.3.4.13), phosphoribosylglycinamide synthetase (EC 6.3.3.1), phosphoribosylaminoimidazole synthetase (EC 2.1.2.2) activity which is required for de novo purine biosynthesis.

Phosphoribosylaminoimidazole carboxylase (or AIR carboxylase) is an enzyme involved in nucleotide synthesis. It catalyzes the conversion of 5'-phosphoribosyl-5-aminoimidazole ("AIR") into 5-phosphoribosyl-4-carboxy-5-aminoimidazole ("CAIR").

Bifunctional purine biosynthesis protein PURH is a protein that in humans is encoded by the ATIC gene. ATIC encodes an enzyme which generates inosine monophosphate from aminoimidazole carboxamide ribonucleotide. It has two functions: EC 2.1.2.3 - 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase EC 3.5.4.10 - IMP cyclohydrolase

Inosinate synthesis

The biosynthetic origins of purine ring atoms N1 arises from the amine group of Asp C2 and C8 originate from formate N3 and N9 are contributed by the amide group of Gln C4, C5 and N7 are derived from Gly C6 comes from HCO3- (CO2)

The synthesis of UMP.

The color scheme is as follows: enzymes, coenzymes, substrate names, inorganic molecules

The inosinate synthesis is complex, beginning with a 5-phosphoribosyl-1-pyrophosphate (PRPP). In the first step, an amino group given by glutamine is attached at carbon 1 of PRPP. The resulting molecule is 5-phosphoribosylamine, which is highly unstable, with a half-life of 30 seconds at physiologic pH. 5-Phosphoribosylamine gains an amino acid (glycine), becoming glycinamide ribonucleotide (GAR). Then, N10-formyltetrahydrofolate (THF) transfers a formyl group to glycinamide ribonucleotide to form formyl glycinamide ribonucleotide (FGAR).

Using an ATP molecule, ammonia is added to the compound to become formylglycinamidine ribonucleotide. Another ATP molecule causes an intermolecular reaction that produces an imidazole ring (5-aminoimidazole ribonucleotide).

The next step of the pathway is adding bicarbonate to make carboxyaminoimidazole ribonucleotide by using ATP (it only happens in fungi and bacteria; high eukaryotes simply add CO2 to form the ribonucleotide). Then, the imidazole’s carboxylate group phosphatises and adds aspartate.

As we have just seen, a six-step process links glycine, formate, bicarbonate, glutamine, and aspartate to lead to an intermediate that contains almost all the required atoms to synthesize a purine ring. This intermediate removes fumarate, and a second formyl group from THF is added. The compound gets cycled and forms inosinate after a sort of intermolecular reactions. Inosinate is the first intermediate in this synthesis pathway to have a whole purine ring.

Enzymes taking part in IMP synthesis constitute a multienzyme complex in the cell. Evidences demonstrate that there are multifunctional enzymes, and some of them catalyze non-sequential steps in the pathway.

Laboratory synthesis of purine

History

The name 'purine' (purum uricum) was coined by the German chemist Emil Fischer in 1884. He synthesized it for the first time in 1899. The starting material for the reaction sequence was uric acid (8), which had been isolated from kidney stones by Scheele in 1776. Uric acid (8) was reacted with PCl₅ to give 2,6,8-trichloropurine (10), which was converted with HI and PH₄I to give 2,6-diiodopurine (11). The product was reduced to purine (1) using zinc-dust.

In addition to in vivo synthesis of purines in purine metabolism, purine can also be created artificially.

Purine (1) is obtained in good yield when formamide is heated in an open vessel at 170 ^oC for 28 hours.

This remarkable reaction and others like it have been discussed in the context of the origin of life.

Procedure: Formamide (45 grams) was heated in an open vessel with a condenser for 28 hours in an oil bath at 170-190 ^oC. After removing excess formamide (32.1 grams) by vacuum distillation, the residue was refluxed with methanol. The methanol solvent was filtered, the solvent removed from the filtrate by vacuum distillation, and almost pure purine obtained; yield 4.93 grams (71% yield from formamide consumed). Crystallization from acetone afforded purine as colorless crystals; melting point 218 ^oC.

Oro, Orgel and co-workers have shown that four molecules of HCN tetramerize to form diaminomaleodinitrile (12), which can be converted into almost all natural-occurring purines.

The Traube purine synthesis (1900) is a classic reaction (named after Wilhelm Traube) between an amine-substituted pyrimidine and formic acid.

De novo biosynthesis of pyrimidine

Unlike purines, pyrimidines are assembled before being attached to 5-phosphoribosyl-1-pyrophosphate (PRPP).

The synthesis of UMP.

The color scheme is as follows: enzymes, coenzymes, substrate names, inorganic molecules

Enzyme	Product	Description
carbamoyl phosphate synthetase II	carbamoyl phosphate	This is the regulated step in the pyrimidine biosynthesis.
aspartic transcarbamolyase (aspartate carbamoyl transferase)	carbamoyl aspartic acid	-
dihhydroorotase	dihydroorotate	Dehydration
dihydroorotate dehydrogenase (the only mitochondrial enzyme)	orotate	Dihydroorotate then enters the mitochondria where it is oxidised through removal of hydrogens. This is the only mitochondrial step in nucleotide rings biosynthesis.
orotate phosphoribosyltransferase	OMP	PRPP is used.
OMP decarboxylase	UMP	Decarboxylation
uridine-cytidine kinase 2	UDP	Phosphorylation. ATP is used.
nucleoside diphosphate kinase	uridine 5'-triphosphate(UTP)	Phosphorylation. ATP is used.
CTP synthase	cytidine 5'triphosphate(CTP)	Glutamine and ATP are used.

The first three enzymes are all coded by the same gene in Metazoa (CAD). In Fungi, a similar protein exists but lacks the dihydroorotase function: another protein catalyzes the second step.

In other organisms (Bacteria, Archaea and the other Eukaryota]]), the first three steps are done by three different enzymes.

CTP synthase (or CTP synthetase) is an enzyme involved in pyrimidine biosynthesis. It intraconverts UTP and CTP. The source of the amine/amino group in CTP is glutamine. CTP synthase is activated by GTP, a purine. This acts to balance the relative amounts of purine and pyrimidine nucleotides. CTP synthase is inhibited by reversible by CTP and irreversible for example by the glutamine analogon DON. The following human genes encode proteins that possess CTP synthase activity:

CTPS – CTP synthase 1

CTPS2 – CTP synthase 2 Pyrimidine synthesis inhibitors are used in active moderate to severe rheumatoid arthritis and psoriatic arthritis. Examples include Leflunomide and Teriflunomide.

Chemical synthesis

Pyrimidines can also be prepared within the laboratory by organic synthesis. One method is the classic Biginelli reaction. Many other methods rely on condensation of carbonyls with amines for instance the synthesis of 2-Thio-6-methyluracil from thiourea and ethyl acetoacetate or the synthesis of 4-methylpyrimidine with 4,4-dimethoxy-2-butanone and formamide.

A novel method is by reaction of certain amides with carbonitriles under electrophilic activation of the amide with 2-chloro-pyridine and trifluoromethanesulfonic anhydride :

Salvage pathway

A salvage pathway is a Metabolic pathway|pathway in which nucleotides (purine and pyrimidine) are synthesized from intermediates in the degradative pathway for nucleotides.

Salvage pathways are used to recover bases and nucleosides that are formed during degradation of RNA and DNA. This is important in some organs because some tissues cannot undergo de novo synthesis.

The salvaged bases and nucleosides can then be converted back into nucleotides.

Substrates

The salvage pathway requires distinct substrates:

Pyrimidines

Uridine phosphorylase adds ribose-1-phospate to the free base uracil, forming uridine monophosphate. Uridine kinase then phosphorylates this nucleoside into its diphosphate and triphosphate forms. Deoxythymidine phosphorylase adds deoxyribose-1-phosphate to thymine, forming deoxythymidine monophosphate. Thymidine kinase can then phosphorylate this compound to deoxythymidine diphosphate and triphosphate.

Thymidine kinase Higher organisms have two isoenzymes, that are chemically very different, TK1 and TK2. The former was first found in fetal tissue, the second was found to be more abundant in adult tissue, and initially they were termed fetal and adult thymidine kinase. Soon it was shown that TK1 is present in the cytoplasm only in anticipation of cell division (cell cycle-dependent), whereas TK2 is located in mitochondria and is cell cycle-independent. The genes of the two types were localized in the mid-1970s. The gene for TK1 was cloned and sequenced. The corresponding protein has a molecular weight of about 25 kD. Normally, it occurs in tissue as a dimer. It can be activated by ATP. After activation, it has been converted to a tetramer. The recombinant TK1 cannot be activated and converted to a tetramer in this way, showing that the enzyme occurring in cells has been modified after synthesis. TK1 is synthesized by the cell during the S phase of cell division. After cell division is completed, TK1 is degraded intracellularly, so that it does not pass to body fluids after normal cell division. There is a feed-back regulation of the action of thymidine kinase in the cell: thymidine triphosphate (TTP), the product of the further phosphorylation of thymidine, acts as an inhibitor to thymidine kinase. This serves to maintain a balanced amount of TTP phosphate available for nucleic acid synthesis, not oversaturating the system. Genes for virus specific thymidine kinases have been identified in Herpes simplex virus, Varicella zoster virus and Epstein-Barr virus.

+ ATP ---> + ADP

Deoxythymidine reacts with ATP to give deoxythymidine monophosphate and ADP.

Purines

Phosphoribosyltransferases add activated ribose-5-phosphate (called phosphoribosyl pyrophosphate or PRPP) to bases, creating nucleotide monophosphates. There are two types of phosphoribosyltransferases: adenosine phosphoribosyltransferase (APRT) and hypoxanthine-guanine phosphoribosyltransferase (HGPRT). Lesch-Nyhan syndrome is associated with a deficiency of HGPRT.

Nucleoside	Enzyme	Nucleotide
hypoxanthine	hypoxanthine/guanine phosphoribosyl transferase (HGPRT)	IMP
guanine	hypoxanthine/guanine phosphoribosyl transferase (HGPRT)	GMP
adenine	adenine phosphoribosyltransferase (APRT)	AMP