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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Protein | Definition | Taxonomy |
---|---|---|
Thymidylate synthase | A thymidylate synthase that is encoded in the genome of Escherichia coli K-12. [OMA:P0A884, PRO:DNx] | Escherichia coli K-12 |
Deoxycytidylate deaminase | A deoxycytidylate deaminase that is encoded in the genome of human. [PRO:DNx, UniProtKB:P32321] | Homo sapiens (human) |
Purine nucleoside phosphorylase | A purine nucleoside phosphorylase that is encoded in the genome of human. [PRO:DNx, UniProtKB:P00491] | Homo sapiens (human) |
Thymidine kinase 2, mitochondrial | A thymidine kinase 2, mitochondrial that is encoded in the genome of human. [PRO:DNx, UniProtKB:O00142] | Homo sapiens (human) |
Compound | Definition | Classes | Roles |
---|---|---|---|
phenolphthalein | Phenolphthalein: 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 | |
trimethoprim | trimethoprim : 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 |
cytarabine | beta-D-arabinoside; monosaccharide derivative; pyrimidine nucleoside | antimetabolite; antineoplastic agent; antiviral agent; immunosuppressive agent | |
1,8-naphthalenedicarboxylic acid anhydride | 1,8-naphthalenedicarboxylic acid anhydride: used as seed protector from herbicides | cyclic dicarboxylic anhydride | |
deoxycytidine monophosphate | 2'-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-deazaguanine | 3-deazaguanine: structure | ||
adenosine | quinquefolan B: isolated from roots of Panax quinquefolium L.; RN not in Chemline 10/87; RN from Toxlit | adenosines; purines D-ribonucleoside | analgesic; anti-arrhythmia drug; fundamental metabolite; human metabolite; vasodilator agent |
thymine arabinoside | thymine arabinoside: selectively inhibits replication of herpes simplex virus | N-glycosyl compound | |
dansyl hydrazine | |||
3-deazaguanosine | 3-deazaguanosine: structure | ||
methotrexate | dicarboxylic 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'-deoxyuridine | 5-propyl-2'-deoxyuridine: RN given refers to parent cpd | ||
sorivudine | organic molecular entity | ||
ag 99 | tyrphostin A46: epidermal growth factor-urogastrone receptor antagonist | ||
galidesivir | |||
acyclovir | acyclovir : 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 monophosphate | guanosine 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 |
guanine | 2-aminopurines; oxopurine; purine nucleobase | algal metabolite; Escherichia coli metabolite; human metabolite; mouse metabolite; Saccharomyces cerevisiae metabolite | |
guanosine | ribonucleoside : Any nucleoside where the sugar component is D-ribose. | guanosines; purines D-ribonucleoside | fundamental metabolite |
inosine | inosines; purines D-ribonucleoside | Escherichia coli metabolite; human metabolite; mouse metabolite; Saccharomyces cerevisiae metabolite | |
raltitrexed | N-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 riboside | allopurinol riboside : A nucleoside analogue that is allopurinol with a beta-D-ribofuranosyl moiety at the 1-position. | nucleoside analogue | metabolite |
8-amino-9-benzylguanine | 8-amino-9-benzylguanine: structure given in first source | ||
forodesine | forodesine: structure in first source | dihydroxypyrrolidine; pyrrolopyrimidine | |
peldesine | peldesine: potent inhibitor of human CCRF-CEM T-cell proliferation; structure given in first source | ||
ci 972 | CI 972: structure given in first source | ||
8-aminoguanine | |||
acyclovir monophosphate | |||
cb 3717 | N-acyl-L-glutamic acid | ||
immucillin g | immucillin G: structure in first source | dihydroxypyrrolidine; pyrrolopyrimidine | |
ulodesine | ulodesine: a purine nucleoside phosphorylase inhibitor | ||
8-bromoguanosine | purine nucleoside | ||
9-arabinofuranosylguanine | 9-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 |