HOMOCYSTEINE METABOLIC PATHWAY (PW:0000398)

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Description

Homocysteine (Hcy) metabolism is at the cross-roads of several pathways; Hcy itself is a byproduct in the de novo pathway of methionine metabolic cycle. The first reaction of the methionine cycle produces S-adenosylmethionine, also known as AdoMet or SAM, which is the major methyl donor for nucleic acids, proteins, lipids and small molecules. The methyltransfer reaction, carried by a large number of methyltransferases (MTs) generates S-adenosylhomocysteine (SAH), the precursor of Hcy and also a

Pathway Diagram:

Ariadne Genomics Inc. homocysteine ---> methionine S-adenosylmethionine ---> S-adenosylhomocysteine S-adenosylmethionine S-adenosylhomocysteine Cbl Mtr Bhmt remethylation pathway of homocysteine metabolism - cobalamin independent, betaine dependent remethylation pathway of homocysteine metabolism - cobalamin dependent transsulfuration pathway of homocysteine metabolism methionine cycle/metabolic pathway folate mediated one-carbon metabolic pathway folate cycle metabolic pathway cysteine, donwstream metabolites S-adenosylmethionine ---| remethylation pathway of homocysteine metabolism - cobalamin dependent 5-methyl-THF homocysteine <--> S-adenosylhomocysteine Ahcy methionine dimethylglycine betaine homocysteine adenosine THF Mtrr Mtrr ---> Mtr dimethylglycine ---| Bhmt betaine ---> dimethylglycine S-adenosylhomocysteine ---> adenosine Mthfr homocysteine ---> cysteine, donwstream metabolites S-adenosylmethionine --+> transsulfuration pathway of homocysteine metabolism 5-methyl-THF ---> THF
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Genes in Pathway:

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homocysteine metabolic pathway term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Ahcy adenosylhomocysteinase JBrowse link 3 150,587,833 150,603,057 RGD:730275
RGD:7242426
G As3mt arsenite methyltransferase JBrowse link 1 266,482,787 266,514,570 RGD:625365
G Asmt acetylserotonin O-methyltransferase JBrowse link 12 18,521,383 18,527,036 RGD:1359073
G Carm1 coactivator-associated arginine methyltransferase 1 JBrowse link 8 22,577,723 22,622,555 RGD:1359044
G Comt catechol-O-methyltransferase JBrowse link 11 86,715,981 86,735,630 RGD:1359089
G Dnmt1 DNA methyltransferase 1 JBrowse link 8 21,922,515 21,968,495 RGD:1359078
G Dot1l DOT1 like histone lysine methyltransferase JBrowse link 7 11,786,105 11,824,742 RGD:1359080
G Gamt guanidinoacetate N-methyltransferase JBrowse link 7 12,314,848 12,317,998 RGD:1359081
G Gnmt glycine N-methyltransferase JBrowse link 9 16,565,274 16,568,626 RGD:1359070
G Hnmt histamine N-methyltransferase JBrowse link 3 905,111 937,038 RGD:1359041
G Icmt isoprenylcysteine carboxyl methyltransferase JBrowse link 5 169,475,270 169,482,031 RGD:1359083
G Mrm2 mitochondrial rRNA methyltransferase 2 JBrowse link 12 16,398,749 16,403,656 RGD:1359074
G Mthfr methylenetetrahydrofolate reductase JBrowse link 5 164,844,642 164,864,360 RGD:7242426
G Nnmt nicotinamide N-methyltransferase JBrowse link 8 52,918,437 52,938,172 RGD:1359084
G Pcmt1 protein-L-isoaspartate (D-aspartate) O-methyltransferase 1 JBrowse link 1 1,734,863 1,767,759 RGD:729481
G Pemt phosphatidylethanolamine N-methyltransferase JBrowse link 10 46,339,821 46,404,640 RGD:729486
G Pnmt phenylethanolamine-N-methyltransferase JBrowse link 10 86,340,893 86,342,501 RGD:1359087
G Prmt1 protein arginine methyltransferase 1 JBrowse link 1 100,971,132 100,980,411 RGD:1359044
G Prmt3 protein arginine methyltransferase 3 JBrowse link 1 105,113,595 105,200,253 RGD:1359044
G Prmt5 protein arginine methyltransferase 5 JBrowse link 15 33,156,508 33,165,893 RGD:1359044
G Prmt6 protein arginine methyltransferase 6 JBrowse link 2 213,173,403 213,180,721 RGD:1359044
G Rnmt RNA (guanine-7-) methyltransferase JBrowse link 18 64,084,746 64,108,246 RGD:1359071
G Setdb1 SET domain, bifurcated 1 JBrowse link 2 196,495,867 196,527,412 RGD:1359072
G Suv39h2 suppressor of variegation 3-9 homolog 2 JBrowse link 17 78,762,897 78,782,016 RGD:1359810
G Trdmt1 tRNA aspartic acid methyltransferase 1 JBrowse link 17 80,824,652 80,859,585 RGD:1359088
remethylation pathway of homocysteine metabolism - cobalamin dependent term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Mthfr methylenetetrahydrofolate reductase JBrowse link 5 164,844,642 164,864,360 RGD:7242426
G Mtr 5-methyltetrahydrofolate-homocysteine methyltransferase JBrowse link 17 66,210,444 66,295,014 RGD:1359026
RGD:7242426
G Mtrr 5-methyltetrahydrofolate-homocysteine methyltransferase reductase JBrowse link 1 37,743,089 37,774,485 RGD:1359037
RGD:7242426
remethylation pathway of homocysteine metabolism - cobalamin independent, betaine dependent term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Ahcy adenosylhomocysteinase JBrowse link 3 150,587,833 150,603,057 RGD:10402751
G Aldh7a1 aldehyde dehydrogenase 7 family, member A1 JBrowse link 18 51,619,007 51,651,267 RGD:10402751
G Bhmt betaine-homocysteine S-methyltransferase JBrowse link 2 23,236,573 23,256,158 RGD:1359026
RGD:10402751
RGD:7242428
RGD:7242426
G Chdh choline dehydrogenase JBrowse link 16 6,078,083 6,109,386 RGD:10402751
G Mat2a methionine adenosyltransferase 2A JBrowse link 4 100,297,478 100,303,047 RGD:10402751
G Mat2b methionine adenosyltransferase 2B JBrowse link 10 25,832,096 25,848,045 RGD:10402751
G Mtr 5-methyltetrahydrofolate-homocysteine methyltransferase JBrowse link 17 66,210,444 66,295,014 RGD:10402751
G Pemt phosphatidylethanolamine N-methyltransferase JBrowse link 10 46,339,821 46,404,640 RGD:10402751
transsulfuration pathway of homocysteine metabolism term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Cbs cystathionine beta synthase JBrowse link 20 10,361,987 10,386,663 RGD:1359024
RGD:10402751
RGD:7242427
G Cdo1 cysteine dioxygenase type 1 JBrowse link 18 40,702,027 40,716,901 RGD:7242427
G Csad cysteine sulfinic acid decarboxylase JBrowse link 7 143,781,520 143,810,880 RGD:7242427
G Cth cystathionine gamma-lyase JBrowse link 2 264,266,959 264,293,040 RGD:1359024
RGD:7242427
RGD:10402751

Pathway Gene Annotations

Pathway Annotations Associated with Genes in the homocysteine metabolic pathway
Pathway TermsGene Symbols
5'-end pre-mRNA capping pathwayRnmt
alkaptonuria disease pathwayComt , Pnmt
altered folate cycle metabolic pathwayMthfr
altered folate mediated one-carbon metabolic pathwayMthfr
androgen signaling pathwayCarm1 , Prmt1
arginine and proline metabolic pathwayGamt
arginine:glycine amidinotransferase deficiency pathwayGamt
aromatic amino acid decarboxylase deficiency pathwayPnmt
catecholamine biosynthetic pathwayPnmt
choline metabolic pathwayAhcy , Pemt
creatine metabolic pathwayGamt
cysteine and methionine metabolic pathwayAhcy , Dnmt1 , Trdmt1
dihydropyrimidine dehydrogenase deficiency pathwayGamt , Gnmt
dimethylglycine dehydrogenase deficiency pathwayGamt , Gnmt
disulfiram pharmacodynamics pathwayComt , Pnmt
DNA modification pathwayDnmt1
dopamine beta hydroxylase deficiency pathwayComt , Pnmt
epinephrine biosynthetic pathwayPnmt
estrogen signaling pathwayCarm1 , Prmt1
folate cycle metabolic pathwayMthfr
folate mediated one-carbon metabolic pathwayGnmt , Mthfr
folate metabolic pathwayGnmt , Mthfr
glycerophospholipid metabolic pathwayPemt
glycine N-methyltransferase deficiency pathwayAhcy , Dnmt1 , Mthfr
glycine, serine and threonine metabolic pathwayGamt , Gnmt
guanidinoacetate methyltransferase deficiency pathwayGamt
gyrate atrophy pathwayGamt
hawkinsinuria disease pathwayComt , Pnmt
hereditary folate malabsorption disease pathwayMthfr
histidine metabolic pathwayHnmt , Prmt3
histidinemia disease pathwayHnmt , Prmt3
histone modification pathwayCarm1 , Dot1l , Prmt1 , Prmt5 , Suv39h2
homocysteine metabolic pathwayAhcy , As3mt , Asmt , Carm1 , Comt , Dnmt1 , Dot1l , Gamt , Gnmt , Hnmt , Icmt , Mrm2 , Mthfr , Nnmt , Pcmt1 , Pemt , Pnmt , Prmt1 , Prmt3 , Prmt5 , Prmt6 , Rnmt , Setdb1 , Suv39h2 , Trdmt1
homocystinuria disease pathwayAhcy , Dnmt1 , Mthfr
hypermethioninemia disease pathwayAhcy , Dnmt1 , Mthfr
hyperornithinemia-hyperammonemia-homocitrullinemia syndrome pathwayGamt
hyperprolinemia disease pathwayGamt
hyperprolinemia type II disease pathwayGamt
lysine degradation pathwayDot1l , Setdb1 , Suv39h2
methionine adenosyltransferase deficiency pathwayAhcy , Dnmt1 , Mthfr
methionine cycle/metabolic pathwayAhcy , As3mt , Asmt , Carm1 , Comt , Dnmt1 , Dot1l , Gamt , Gnmt , Hnmt , Icmt , Mrm2 , Mthfr , Nnmt , Pcmt1 , Pemt , Pnmt , Prmt1 , Prmt3 , Prmt5 , Prmt6 , Rnmt , Setdb1 , Suv39h2 , Trdmt1
methotrexate pharmacodynamics pathwayMthfr
methylenetetrahydrofolate reductase deficiency pathwayAhcy , Dnmt1 , Mthfr
monoterpenoid biosynthetic pathwayNnmt
mRNA decay pathwayRnmt
niacin metabolic pathwayNnmt
nonketotic hyperglycinemia disease pathwayGamt , Gnmt
Nonketotic hyperglycinemia disease pathwayGamt , Gnmt
p53 signaling pathwayPrmt5
phenytoin pharmacodynamics pathwayComt
prolidase deficiency pathwayGamt
remethylation pathway of homocysteine metabolism - cobalamin dependentMthfr
remethylation pathway of homocysteine metabolism - cobalamin independent, betaine dependentAhcy , Pemt
RNA transport pathwayPrmt5
sarcosinemia disease pathwayGamt , Gnmt
selenoamino acid metabolic pathwayAhcy
steroid hormone biosynthetic pathwayComt
tryptophan metabolic pathwayAsmt
tyrosine metabolic pathwayComt , Pnmt
tyrosinemia type I disease pathwayComt , Pnmt
Wnt signaling, non-canonical pathwaySetdb1
Phenotype Annotations Associated with Genes in the homocysteine metabolic pathway

References Associated with the homocysteine metabolic pathway:

Ontology Path Diagram:

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