One Carbon Metabolism (Homo sapiens)

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Description

This one-carbon metabolism pathway is centered around folate. Folate has two key carbon-carbon double bonds. Saturating one of them yields dihydrofolate (DHF) and adding an additional molecule of hydrogen across the second yields tetrahydrofolate (THF). Folates serve as donors of single carbons in any one of three oxidation states: 5-methyl-THF (CH3THF; reduced), 5,10 methylene-THF (CH2THF; intermediate) and 10-formyl-THF (CHOTHF; oxidized). The single carbon donor CH3THF is used to convert homocysteine into methionine which can then be used to methylate DNA, the donor CH2THF is used (along with a molecule of hydrogen at the site of one of the double bonds) to convert dUMP (deoxyuridylate) into dTMP (thymidylate) and the donor CHOTHF is used to set up ring closure reactions in de novo purine synthesis. CH3THF is the primary methyl-group donor for processes such as DNA methylation reactions. Purines are used both in RNA synthesis and in DNA synthesis and dTMP is synthesized srtictly for DNA synthesis, be it for DNA repair or DNA replication.

The folate pathway is central to any study related to DNA methylation, dTMP synthesis or purine synthesis.

Differential methylation (e.g. hypermethylation of tumor suppressors) as well as disturbances in nucleotide synthesis and repair, are associated with several forms of cancer. There are also indications that hypermethylation is involved in the progression of adenomas to cancer.

The pathway is also illustrative of the role of a number of B vitamins, including vitamin B12 (cobalamine) which is important for the sythesis of folate (vitamin B9) and of methionine.

Ontology Tags

 

Bibliography

  1. Ludwig ML, Matthews RG; ''Structure-based perspectives on B12-dependent enzymes.''; Annu Rev Biochem, 1997 PubMed
  2. Hazra A, Wu K, Kraft P, Fuchs CS, Giovannucci EL, Hunter DJ; ''Twenty-four non-synonymous polymorphisms in the one-carbon metabolic pathway and riskof colorectal adenoma in the Nurses' Health Study.''; Carcinogenesis, 2007 PubMed

History

View all...
CompareRevisionActionTimeUserComment
68025view08:18, 29 June 2013EgonwAdded a missing metabolite identifiers.
68024view08:08, 29 June 2013EgonwConverted two labels into Metabolite DataNodes.
65710view13:11, 11 June 2013EgonwConverted three labels to metabolite DataNodes.
61699view23:32, 16 April 2013MaintBotupdated data node type "Unkown" to "GeneProduct" for annotated genes
49064view08:35, 4 July 2012Eveloimproved homocysteine annotatopn
45325view20:12, 7 October 2011KhanspersOntology Term : 'folate mediated one-carbon metabolic pathway' added !
41078view23:20, 1 March 2011MaintBotRemoved redundant pathway information and comments
38794view06:48, 24 September 2010Thomaslinked to dna repair pathways
36799view12:04, 4 May 2010EveloMTHFR Riboflavin complex
36797view11:56, 4 May 2010EveloModified description
36795view11:38, 4 May 2010EveloAdded MTR reference
36794view11:29, 4 May 2010EveloModified description
36793view11:12, 4 May 2010EveloAdded more vitamins as metabolites, multiline labels
36792view10:28, 4 May 2010EveloAdded vitamin names to metabolite labels
36779view09:04, 4 May 2010Eveloadded connection
36699view12:09, 16 April 2010MichielMinor edits
36698view12:07, 16 April 2010MichielMinor cleanup
36697view12:03, 16 April 2010MichielAdded metabolites
36696view12:00, 16 April 2010MichielCorrected Cobalamin
36695view11:58, 16 April 2010MichielCorrected reactions
36689view11:08, 15 April 2010Evelocorrected typos in metabolite names
36181view14:36, 5 March 2010EveloPeriodical save, work in progress
35855view17:59, 18 February 2010AlexanderPicotest
34894view00:30, 3 February 2010AlexanderPicoModified description
32642view14:39, 24 August 2009Eveloalignment
32010view13:19, 14 August 2009MaintBotFixed group labels
21183view11:30, 14 November 2008MaintBot[[Pathway:Homo sapiens:One-carbon metabolism]] moved to [[Pathway:WP241]]: Moved to stable identifier
20613view12:44, 12 November 2008Thomasfixed duplicate literature reference
15833view13:34, 5 June 2008EgoyenecheaPeriodical save, work in progress
15301view11:31, 27 May 2008Michielanchors
15218view07:50, 26 May 2008MichielAnchor correction
14657view14:13, 23 May 2008Michielcu
14654view14:08, 23 May 2008MichielCleaned up
14652view14:07, 23 May 2008MichielConnected all genes to reaction arrows
14649view13:55, 23 May 2008MichielSpecify description
14647view13:34, 23 May 2008MichielConnected genes to reaction arrows
14645view13:28, 23 May 2008MichielConnected some genes to reactions
14643view13:13, 23 May 2008MichielCleaned up some more
14641view13:09, 23 May 2008MichielCleaned up
14639view13:08, 23 May 2008MichielCorrected arrows
14637view13:07, 23 May 2008MichielCurated: grouped genes, arrows connected, cleaned up
12494view10:52, 15 May 2008MichielPeriodical save, work in progress
12488view10:43, 15 May 2008MichielCurved arrow enhancements #1
11556view01:22, 11 April 2008Txr24Modified description
11555view01:19, 11 April 2008Txr24Modified description
11554view00:53, 11 April 2008Txr24fosfaat -> phosphate
8308view13:46, 7 January 2008MaintBot[[Pathway:Human:One-carbon metabolism]] moved to [[Pathway:Homo sapiens:One-carbon metabolism]]: Renaming species
7559view11:46, 18 December 2007Thomasadded to metabolic category
7554view08:56, 18 December 2007MichielUpdated description
7553view08:51, 18 December 2007MichielAdded description

External references

View all...
NameTypeDatabase referenceComment
10-Formyl TetrahydrofolateMetabolite2800-34-2 (CAS)
MIsmatch repairPathwayWP531 (WikiPathways)
SHMT1GeneProduct6470 (Entrez Gene)
SHMT2GeneProduct6472 (Entrez Gene) KEGG database: One carbon pool by folate - Homo sapiens (human)
ALDH1L1GeneProduct10840 (Entrez Gene)
FOLH1GeneProduct2346 (Entrez Gene)
TCN IIGeneProduct6948 (Entrez Gene)
S-AdenosylmethionineMetabolite29908-03-0 (CAS)
MTHFRGeneProduct4524 (Entrez Gene)
5-Formyl TetrahydrofolateMetabolite135-16-0 (CAS)
BHMTGeneProduct635 (Entrez Gene)
serineMetabolite617 (PubChem-compound)
DNMT1GeneProduct1786 (Entrez Gene)
5,10-Methylene TetrahydrofolateMetabolite25513-46-6 (CAS)
MTRGeneProduct4548 (Entrez Gene)
MethionineMetabolite63-68-3 (CAS)
MTRRGeneProduct4552 (Entrez Gene)
HomocysteineMetaboliteHMDB00742 (HMDB)
MTHFD1GeneProduct4522 (Entrez Gene)
Cobalamin Vitamin B12MetaboliteHMDB02174 (HMDB)
GARTGeneProduct2618 (Entrez Gene)
Pyridoxal 5'-phosphate Vitamin B6MetaboliteHMDB01491 (HMDB)
ATICGeneProduct471 (Entrez Gene)
Thymidylate SynthesisPathway
DHFRGeneProduct1719 (Entrez Gene) KEGG database: One carbon pool by folate - Homo sapiens (human)
Deoxythymidine monophosphateMetabolite9700 (PubChem-compound)
MTHFD1LGeneProduct25902 (Entrez Gene) KEGG database: One carbon pool by folate - Homo sapiens (human)
Dihydrofolate Vitamin B9Metabolite4033-27-6 (CAS)
MTFMTGeneProduct123263 (Entrez Gene) KEGG database: One carbon pool by folate - Homo sapiens (human)
5-Methyl TetrahydrofolateMetabolite134-35-0 (CAS)
DNMT3aGeneProduct1788 (Entrez Gene) KEGG Database Methionine metabolism - Homo sapiens (human)
5,10-Methenyl TetrahydrofolateMetabolite7444-29-3 (CAS)
DNMT3bGeneProduct1789 (Entrez Gene) KEGG database: Methionine metabolism - Homo sapiens (human)
BetaineMetabolite107-43-7 (CAS)
MTHFD2GeneProduct10797 (Entrez Gene) KEGG database: One carbon pool by folate - Homo sapiens (human)
S-adenosylhomocysteineMetabolite979-92-0 (CAS)
FTCDGeneProduct10841 (Entrez Gene) KEGG database: One carbon pool by folate - Homo sapiens (human)
AMTGeneProduct275 (Entrez Gene) KEGG database: One carbon pool by folate - Homo sapiens (human)
MTHFSGeneProduct10588 (Entrez Gene) KEGG database: One carbon pool by folate - Homo sapiens (human)
TYMSGeneProduct7298 (Entrez Gene) KEGG database: One carbon pool by folate - Homo sapiens (human)
AHCYGeneProduct191 (Entrez Gene) KEGG Database Methionine metabolism - Homo sapiens (human)
MethylcobalaminMetaboliteHMDB02274 (HMDB)
KIAA0828GeneProduct23382 (Entrez Gene) KEGG Database Methionine metabolism - Homo sapiens (human)
5-Formimino TetrahydrofolateMetabolite135-16-0 (CAS)
MAT2BGeneProduct27430 (Entrez Gene) KEGG Database Methionine metabolism - Homo sapiens (human)
Riboflavin Vitamin B2MetaboliteHMDB00244 (HMDB)
MAT1AGeneProduct4143 (Entrez Gene) KEGG Database Methionine metabolism - Homo sapiens (human)
Non-homologous end joiningPathwayWP438 (WikiPathways)
PolyglutamateMetabolite25513-46-6 (CAS)
glycineMetaboliteHMDB00123 (HMDB)
MonoglutamateMetabolite59-30-3 (CAS)
AlcoholMetabolite702 (PubChem-compound)
TetrahydrofolateMetabolite135-16-0 (CAS)
Deoxyuridine monophosphateMetabolite65063 (PubChem-compound)
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