Page last updated: 2024-10-24

nucleotide biosynthetic process

Definition

Target type: biologicalprocess

The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates). [GOC:go_curators]

Nucleotide biosynthesis is a fundamental biological process that involves the synthesis of nucleotides, the building blocks of DNA and RNA. These molecules play crucial roles in various cellular functions, including genetic information storage, protein synthesis, and energy transfer.

The process can be broadly divided into two major pathways: de novo synthesis and salvage pathways.

**De Novo Synthesis**

This pathway involves the synthesis of nucleotides from simpler precursors. It begins with the synthesis of purine and pyrimidine bases, which are then attached to a ribose-5-phosphate molecule to form nucleoside monophosphates (NMPs). The key steps in de novo purine biosynthesis include the sequential addition of amino acids and other small molecules to a pre-existing ribose-5-phosphate molecule. Pyrimidine biosynthesis involves the formation of a pyrimidine ring structure from a carbamoyl phosphate and aspartate.

Once the NMPs are formed, they are further phosphorylated to diphosphates (NDPs) and triphosphates (NTPs). This phosphorylation is crucial for the incorporation of nucleotides into DNA and RNA.

**Salvage Pathways**

The salvage pathways utilize pre-existing purine and pyrimidine bases or nucleosides that are obtained from the breakdown of nucleic acids. These molecules are converted into NMPs and then further processed into NDPs and NTPs. Salvage pathways are crucial for maintaining nucleotide pools and reducing the need for de novo synthesis, which is a more energy-intensive process.

**Regulation**

Nucleotide biosynthesis is tightly regulated at multiple levels to ensure a balanced supply of nucleotides for DNA and RNA synthesis. The availability of precursors, the activity of enzymes, and the feedback inhibition mechanisms are all involved in regulating this process.

**Clinical Significance**

Disruptions in nucleotide biosynthesis can lead to various genetic disorders. These disorders often involve defects in enzymes involved in nucleotide metabolism, leading to the accumulation of toxic metabolites or deficiencies in essential nucleotides. Examples include Lesch-Nyhan syndrome, a severe neurological disorder caused by a deficiency in hypoxanthine-guanine phosphoribosyltransferase (HGPRT), an enzyme involved in purine salvage, and orotic aciduria, a disorder caused by a deficiency in uridine monophosphate synthase (UMPS), an enzyme involved in pyrimidine biosynthesis.

Overall, nucleotide biosynthesis is a complex and highly regulated process that is essential for all living organisms. Understanding the intricate details of this pathway is crucial for comprehending fundamental cellular processes and for developing therapies for genetic disorders associated with nucleotide metabolism.'
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Proteins (4)

ProteinDefinitionTaxonomy
Thymidylate synthaseA thymidylate synthase that is encoded in the genome of Escherichia coli K-12. [OMA:P0A884, PRO:DNx]Escherichia coli K-12
Deoxycytidylate deaminaseA deoxycytidylate deaminase that is encoded in the genome of human. [PRO:DNx, UniProtKB:P32321]Homo sapiens (human)
Purine nucleoside phosphorylaseA purine nucleoside phosphorylase that is encoded in the genome of human. [PRO:DNx, UniProtKB:P00491]Homo sapiens (human)
Thymidine kinase 2, mitochondrialA thymidine kinase 2, mitochondrial that is encoded in the genome of human. [PRO:DNx, UniProtKB:O00142]Homo sapiens (human)

Compounds (37)

CompoundDefinitionClassesRoles
phenolphthaleinPhenolphthalein: An acid-base indicator which is colorless in acid solution, but turns pink to red as the solution becomes alkaline. It is used medicinally as a cathartic.phenols
trimethoprimtrimethoprim : An aminopyrimidine antibiotic whose structure consists of pyrimidine 2,4-diamine and 1,2,3-trimethoxybenzene moieties linked by a methylene bridge.

Trimethoprim: A pyrimidine inhibitor of dihydrofolate reductase, it is an antibacterial related to PYRIMETHAMINE. It is potentiated by SULFONAMIDES and the TRIMETHOPRIM, SULFAMETHOXAZOLE DRUG COMBINATION is the form most often used. It is sometimes used alone as an antimalarial. TRIMETHOPRIM RESISTANCE has been reported.
aminopyrimidine;
methoxybenzenes
antibacterial drug;
diuretic;
drug allergen;
EC 1.5.1.3 (dihydrofolate reductase) inhibitor;
environmental contaminant;
xenobiotic
cytarabinebeta-D-arabinoside;
monosaccharide derivative;
pyrimidine nucleoside
antimetabolite;
antineoplastic agent;
antiviral agent;
immunosuppressive agent
1,8-naphthalenedicarboxylic acid anhydride1,8-naphthalenedicarboxylic acid anhydride: used as seed protector from herbicidescyclic dicarboxylic anhydride
deoxycytidine monophosphate2'-deoxycytosine 5'-monophosphate : A pyrimidine 2'-deoxyribonucleoside 5'-monophosphate having cytosine as the nucleobase.

Deoxycytidine Monophosphate: Deoxycytidine (dihydrogen phosphate). A deoxycytosine nucleotide containing one phosphate group esterified to the deoxyribose moiety in the 2'-,3'- or 5- positions.
2'-deoxycytidine phosphate;
pyrimidine 2'-deoxyribonucleoside 5'-monophosphate
Escherichia coli metabolite;
mouse metabolite
3-deazaguanine3-deazaguanine: structure
adenosinequinquefolan B: isolated from roots of Panax quinquefolium L.; RN not in Chemline 10/87; RN from Toxlitadenosines;
purines D-ribonucleoside
analgesic;
anti-arrhythmia drug;
fundamental metabolite;
human metabolite;
vasodilator agent
thymine arabinosidethymine arabinoside: selectively inhibits replication of herpes simplex virusN-glycosyl compound
dansyl hydrazine
3-deazaguanosine3-deazaguanosine: structure
methotrexatedicarboxylic acid;
monocarboxylic acid amide;
pteridines
abortifacient;
antimetabolite;
antineoplastic agent;
antirheumatic drug;
dermatologic drug;
DNA synthesis inhibitor;
EC 1.5.1.3 (dihydrofolate reductase) inhibitor;
immunosuppressive agent
5-propyl-2'-deoxyuridine5-propyl-2'-deoxyuridine: RN given refers to parent cpd
sorivudineorganic molecular entity
ag 99tyrphostin A46: epidermal growth factor-urogastrone receptor antagonist
galidesivir
acycloviracyclovir : An oxopurine that is guanine substituted by a (2-hydroxyethoxy)methyl substituent at position 9. Used in the treatment of viral infections.

Acyclovir: A GUANOSINE analog that acts as an antimetabolite. Viruses are especially susceptible. Used especially against herpes.
2-aminopurines;
oxopurine
antimetabolite;
antiviral drug
guanosine monophosphateguanosine 5'-monophosphate : A purine ribonucleoside 5'-monophosphate having guanine as the nucleobase.

Guanosine Monophosphate: A guanine nucleotide containing one phosphate group esterified to the sugar moiety and found widely in nature.
guanosine 5'-phosphate;
purine ribonucleoside 5'-monophosphate
biomarker;
Escherichia coli metabolite;
metabolite;
mouse metabolite
guanine2-aminopurines;
oxopurine;
purine nucleobase
algal metabolite;
Escherichia coli metabolite;
human metabolite;
mouse metabolite;
Saccharomyces cerevisiae metabolite
guanosineribonucleoside : Any nucleoside where the sugar component is D-ribose.guanosines;
purines D-ribonucleoside
fundamental metabolite
inosineinosines;
purines D-ribonucleoside
Escherichia coli metabolite;
human metabolite;
mouse metabolite;
Saccharomyces cerevisiae metabolite
raltitrexedN-acyl-amino acid
8-amino-9-(2-thienylmethyl)guanine
n-(4(n-((2-amino-4-hydroxy-6-quinazolinyl)methyl)prop-2-ynylamino)benzoyl)-l-glutamic acid
allopurinol ribosideallopurinol riboside : A nucleoside analogue that is allopurinol with a beta-D-ribofuranosyl moiety at the 1-position.nucleoside analoguemetabolite
8-amino-9-benzylguanine8-amino-9-benzylguanine: structure given in first source
forodesineforodesine: structure in first sourcedihydroxypyrrolidine;
pyrrolopyrimidine
peldesinepeldesine: potent inhibitor of human CCRF-CEM T-cell proliferation; structure given in first source
ci 972CI 972: structure given in first source
8-aminoguanine
acyclovir monophosphate
cb 3717N-acyl-L-glutamic acid
immucillin gimmucillin G: structure in first sourcedihydroxypyrrolidine;
pyrrolopyrimidine
ulodesineulodesine: a purine nucleoside phosphorylase inhibitor
8-bromoguanosinepurine nucleoside
9-arabinofuranosylguanine9-arabinofuranosylguanine: RN given refers to (beta)-isomer

9-beta-D-arabinofuranosylguanine : A purine nucleoside in which guanine is attached to arabinofuranose via a beta-N(9)-glycosidic bond. It inhibits DNA synthesis and causes cell death.
beta-D-arabinoside;
purine nucleoside
antineoplastic agent;
DNA synthesis inhibitor
9-deaza-9-(3-thienylmethyl)guanine
8-aminoguanosine