S-adenosyl-L-methionine cycle I

MetaCyc:PWY-6151

The complete MetaCyc bacterial activated methyl cycle is represented with E. coli K-12 proteins: MetK makes SAM, a generic methyltransferase reaction yields SAH, Pfs cleaves SAH to adenine and S-ribosylhomocysteine, LuxS produces homocysteine and (S)-4,5-dihydroxypentane-2,3-dione, and methionine synthase regenerates methionine. The five native transformations are retained, with separate MetE triglutamate and documented MetH monoglutamate equations for the alternative final step. Generic methyl-acceptor states retain their native donor labels and unspecified chemical scope; no particular methylation target or catalyst is selected. LuxS-derived DPD is distinct from downstream cyclic or borated AI-2 signals, which are outside this cycle. The protein scope does not assert functionality in every K-12 derivative, universal quorum sensing, or simultaneous use of all annotated alternative metals.

Pathway type
amino acid metabolism
Organism scope

Read the source YAML

Pathway network

39 nodes · 54 asserted directed edges

Arrows show recorded subject → object relationships, not necessarily metabolic flow. Select a node for details or an arrow for evidence. Scroll, zoom or find a node to explore.

Pathway network: S-adenosyl-L-methionine cycle I 39 nodes · 54 asserted directed edges. Every arrow links to its evidence table row; nodes link to their component details. Isolated declared components are retained. CHEBI:57844 — consumes → RHEA:21081; Evidence: RHEA:21080consumes CHEBI:30616 — consumes → RHEA:21081; Evidence: RHEA:21080consumes CHEBI:15377 — consumes → RHEA:21081; Evidence: RHEA:21080consumes RHEA:21081 — produces → CHEBI:59789; Evidence: RHEA:21080produces RHEA:21081 — produces → CHEBI:43474; Evidence: RHEA:21080produces RHEA:21081 — produces → CHEBI:33019; Evidence: RHEA:21080produces CHEBI:57856 — consumes → RHEA:17806; Evidence: RHEA:17805consumes CHEBI:15377 — consumes → RHEA:17806; Evidence: RHEA:17805consumes RHEA:17806 — produces → CHEBI:58195; Evidence: RHEA:17805produces RHEA:17806 — produces → CHEBI:16708; Evidence: RHEA:17805produces CHEBI:58195 — consumes → RHEA:17754; Evidence: RHEA:17753consumes RHEA:17754 — produces → CHEBI:29484; Evidence: RHEA:17753produces RHEA:17754 — produces → CHEBI:58199; Evidence: RHEA:17753produces CHEBI:58207 — consumes → RHEA:21197; Evidence: RHEA:21196consumes CHEBI:58199 — consumes → RHEA:21197; Evidence: RHEA:21196consumes RHEA:21197 — produces → CHEBI:58140; Evidence: RHEA:21196produces RHEA:21197 — produces → CHEBI:57844; Evidence: RHEA:21196produces CHEBI:18608 — consumes → RHEA:11173; Evidence: RHEA:11172consumes CHEBI:58199 — consumes → RHEA:11173; Evidence: RHEA:11172consumes RHEA:11173 — produces → CHEBI:57453; Evidence: RHEA:11172produces RHEA:11173 — produces → CHEBI:57844; Evidence: RHEA:11172produces CHEBI:59789 — consumes → MetaCyc:RXN-7605; Evidence: MetaCyc:RXN-7605, MetaCyc:S-ADENOSYLMETHIONINEconsumes MetaCyc:Demethylated-methyl-acceptors — consumes → MetaCyc:RXN-7605; A generic chemical class is retained without identifying a particular small molecule, protein, RNA or DNA substrate.; Evidence: MetaCyc:RXN-7605, MetaCyc:Demethylated-methyl-acceptorsconsumes MetaCyc:RXN-7605 — produces → CHEBI:57856; Evidence: MetaCyc:RXN-7605, MetaCyc:ADENOSYL-HOMO-CYSproduces MetaCyc:RXN-7605 — produces → MetaCyc:Methylated-methyl-acceptors; A generic chemical class is retained without identifying a particular small molecule, protein, RNA or DNA substrate.; Evidence: MetaCyc:RXN-7605, MetaCyc:Methylated-methyl-acceptorsproduces MetaCyc:RXN-7605 — produces → CHEBI:15378; Evidence: MetaCyc:RXN-7605, MetaCyc:PROTONproduces RHEA:21081 — part_of → MetaCyc:PWY-6151; Evidence: MetaCyc:PWY-6151, MetaCyc:SAM-PWY, MetaCyc:S-ADENMETSYN-RXN, RHEA:21080part of RHEA:17806 — part_of → MetaCyc:PWY-6151; Evidence: MetaCyc:PWY-6151, MetaCyc:ADENOSYLHOMOCYSTEINE-NUCLEOSIDASE-RXN, RHEA:17805part of RHEA:17754 — part_of → MetaCyc:PWY-6151; Evidence: MetaCyc:PWY-6151, MetaCyc:RIBOSYLHOMOCYSTEINASE-RXN, RHEA:17753part of RHEA:21197 — part_of → MetaCyc:PWY-6151; Evidence: MetaCyc:PWY-6151, MetaCyc:HOMOCYSMET-RXN, RHEA:21196part of RHEA:11173 — part_of → MetaCyc:PWY-6151; MetH alternative, represented by the current monoglutamate Rhea equation; native HOMOCYSMETB12-RXN permits an unspecified folate glutamate-chain length. This does not make monoglutamate the exclusive cellular substrate.; Evidence: MetaCyc:PWY-6151, MetaCyc:HOMOCYSMETB12-RXN, RHEA:11172part of MetaCyc:RXN-7605 — part_of → MetaCyc:PWY-6151; Evidence: MetaCyc:PWY-6151part of RHEA:21197 — precedes → RHEA:21081; The source-defined cycle closes through CHEBI:57844; ordering does not assert an irreversible thermodynamic constraint.; Evidence: MetaCyc:PWY-6151, RHEA:21196, RHEA:21080precedes RHEA:21081 — precedes → MetaCyc:RXN-7605; The source-defined cycle closes through CHEBI:59789; ordering does not assert an irreversible thermodynamic constraint.; Evidence: MetaCyc:PWY-6151, RHEA:21080, MetaCyc:RXN-7605precedes MetaCyc:RXN-7605 — precedes → RHEA:17806; The source-defined cycle closes through CHEBI:57856; ordering does not assert an irreversible thermodynamic constraint.; Evidence: MetaCyc:PWY-6151, MetaCyc:RXN-7605, RHEA:17805precedes RHEA:17806 — precedes → RHEA:17754; The source-defined cycle closes through CHEBI:58195; ordering does not assert an irreversible thermodynamic constraint.; Evidence: MetaCyc:PWY-6151, RHEA:17805, RHEA:17753precedes RHEA:17754 — precedes → RHEA:21197; The source-defined cycle closes through CHEBI:58199; ordering does not assert an irreversible thermodynamic constraint.; Evidence: MetaCyc:PWY-6151, RHEA:17753, RHEA:21196precedes RHEA:17754 — provides_input_for → RHEA:11173; Material continuity for the documented MetH alternative, not an additional native reaction-ordering triple.; Evidence: MetaCyc:PWY-6151, RHEA:17753, RHEA:11172provides input for RHEA:11173 — provides_input_for → RHEA:21081; Material continuity for the documented MetH alternative, not an additional native reaction-ordering triple.; Evidence: MetaCyc:PWY-6151, RHEA:11172, RHEA:21080provides input for MetaCyc:S-ADENMETSYN-CPLX — has_part → UniProtKB:P0A817; Source subunit coefficient 4; the protein component is not asserted to independently catalyze the overall reaction.; Evidence: MetaCyc:S-ADENMETSYN-CPLX, MetaCyc:S-ADENMETSYN-MONOMER, UniProtKB:P0A817, PMID:14967023has part MetaCyc:CPLX0-1541 — has_part → UniProtKB:P0AF12; Source subunit coefficient 2; the protein component is not asserted to independently catalyze the overall reaction.; Evidence: MetaCyc:CPLX0-1541, MetaCyc:EG11090-MONOMER, UniProtKB:P0AF12, PMID:11591349has part MetaCyc:S-ADENMETSYN-CPLX — catalyzes → RHEA:21081; Evidence: MetaCyc:S-ADENMETSYN-CPLX, UniProtKB:P0A817, RHEA:21080, PMID:6251075catalyzes MetaCyc:CPLX0-1541 — catalyzes → RHEA:17806; Evidence: MetaCyc:CPLX0-1541, UniProtKB:P0AF12, RHEA:17805, PMID:11489131catalyzes UniProtKB:P45578 — enables → RHEA:17754; Functional LuxS contribution; its homodimer annotation is by similarity (ECO:0000250). No independently verified E. coli assembly identifier or monomer sufficiency is asserted.; Evidence: UniProtKB:P45578, RHEA:17753, PMID:11489131enables UniProtKB:P25665 — enables → RHEA:21197; MetE is annotated monomeric; this edge preserves its gene-product activity and separately inspected experimental support without upgrading HAMAP evidence.; Evidence: UniProtKB:P25665, RHEA:21196, MetaCyc:HOMOCYSMET-MONOMER, PMID:16618098enables UniProtKB:P13009 — enables → RHEA:11173; Evidence: UniProtKB:P13009, RHEA:11172, PMID:9201956enables UniProtKB:P0A817 — has_cofactor → CHEBI:18420; Mn2+ and Co2+ are tested alternatives to Mg2+, not a requirement that all three divalent metals bind simultaneously; potassium is a separate monovalent cofactor.; Evidence: UniProtKB:P0A817, PMID:6251075has cofactor UniProtKB:P0A817 — has_cofactor → CHEBI:29035; Mn2+ and Co2+ are tested alternatives to Mg2+, not a requirement that all three divalent metals bind simultaneously; potassium is a separate monovalent cofactor.; Evidence: UniProtKB:P0A817, PMID:6251075has cofactor UniProtKB:P0A817 — has_cofactor → CHEBI:48828; Mn2+ and Co2+ are tested alternatives to Mg2+, not a requirement that all three divalent metals bind simultaneously; potassium is a separate monovalent cofactor.; Evidence: UniProtKB:P0A817, PMID:6251075has cofactor UniProtKB:P0A817 — has_cofactor → CHEBI:29103; Mn2+ and Co2+ are tested alternatives to Mg2+, not a requirement that all three divalent metals bind simultaneously; potassium is a separate monovalent cofactor.; Evidence: UniProtKB:P0A817has cofactor UniProtKB:P45578 — has_cofactor → CHEBI:24875; This is an inferred E. coli annotation at the generic iron-cation level. No exact oxidation state, direct E. coli metal measurement or zinc-independent activity is asserted.; Evidence: UniProtKB:P45578has cofactor UniProtKB:P25665 — has_cofactor → CHEBI:29105; Evidence: UniProtKB:P25665, PMID:11170420has cofactor UniProtKB:P13009 — has_cofactor → CHEBI:29105; Evidence: UniProtKB:P13009, PMID:9398304has cofactor UniProtKB:P13009 — has_cofactor → CHEBI:28115; Cobalamin cycling is internal to the net methionine-synthase equation. Reductive reactivation is not added as a second methyl-transfer step of the native cycle.; Evidence: UniProtKB:P13009, PMID:9201956has cofactor water; CHEBI:15377; Declared type: small_molecule small molecule water hydron; CHEBI:15378; Declared type: small_molecule small molecule hydron adenine; CHEBI:16708; Declared type: small_molecule small molecule adenine magnesium(2+); CHEBI:18420; Declared type: cofactor cofactor magnesium(2+) (6S)-5-methyltetrahydrofolate(2-); CHEBI:18608; Declared type: small_molecule small molecule (6S)-5- methyltetrahydrofolate(2-) iron cation; CHEBI:24875; Declared type: cofactor cofactor iron cation methylcobalamin; CHEBI:28115; Declared type: cofactor cofactor methylcobalamin manganese(2+); CHEBI:29035; Declared type: cofactor cofactor manganese(2+) potassium(1+); CHEBI:29103; Declared type: cofactor cofactor potassium(1+) zinc(2+); CHEBI:29105; Declared type: cofactor cofactor zinc(2+) (S)-4,5-dihydroxypentane-2,3-dione; CHEBI:29484; Declared type: small_molecule small molecule (S)-4,5-dihydroxypentane- 2,3-dione ATP(4-); CHEBI:30616; Declared type: small_molecule small molecule ATP(4-) diphosphate(3-); CHEBI:33019; Declared type: small_molecule small molecule diphosphate(3-) hydrogenphosphate; CHEBI:43474; Declared type: small_molecule small molecule hydrogenphosphate cobalt(2+); CHEBI:48828; Declared type: cofactor cofactor cobalt(2+) (6S)-5,6,7,8-tetrahydrofolate(2-); CHEBI:57453; Declared type: small_molecule small molecule (6S)-5,6,7,8- tetrahydrofolate(2-) L-methionine zwitterion; CHEBI:57844; Declared type: small_molecule small molecule L-methionine zwitterion S-adenosyl-L-homocysteine zwitterion; CHEBI:57856; Declared type: small_molecule small molecule S-adenosyl-L-homocysteine zwitterion tetrahydropteroyltri-L-glutamate(4-); CHEBI:58140; Declared type: small_molecule small molecule tetrahydropteroyltri-L- glutamate(4-) S-(5-deoxy-D-ribos-5-yl)-L-homocysteine zwitterion; CHEBI:58195; Declared type: small_molecule small molecule S-(5-deoxy-D- ribos-5-yl)-L-homocysteine zwitterion L-homocysteine zwitterion; CHEBI:58199; Declared type: small_molecule small molecule L-homocysteine zwitterion 5-methyltetrahydropteroyltri-L-glutamate(4-); CHEBI:58207; Declared type: small_molecule small molecule 5- methyltetrahydropteroyltri- L-glutamate(4-) S-adenosyl-L-methionine zwitterion; CHEBI:59789; Declared type: small_molecule small molecule S-adenosyl-L-methionine zwitterion a demethylated methyl donor; MetaCyc:Demethylated-methyl-acceptors; Declared type: chemical_entity chemical entity a demethylated methyl donor a methylated methyl donor; MetaCyc:Methylated-methyl-acceptors; Declared type: chemical_entity chemical entity a methylated methyl donor S-adenosylmethionine synthase; UniProtKB:P0A817; Declared type: protein protein S-adenosylmethionine synthase 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; UniProtKB:P0AF12; Declared type: protein protein 5'-methylthioadenosine/S- adenosylhomocysteine nucleosidase S-ribosylhomocysteine lyase; UniProtKB:P45578; Declared type: protein protein S-ribosylhomocysteine lyase Methionine synthase; UniProtKB:P13009; Declared type: protein protein Methionine synthase 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase; UniProtKB:P25665; Declared type: protein protein 5- methyltetrahydropteroyltrigl utamate--homocysteine methyltransferase methionine adenosyltransferase; MetaCyc:S-ADENMETSYN-CPLX; Declared type: complex complex methionine adenosyltransferase 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; MetaCyc:CPLX0-1541; Declared type: complex complex 5'-methylthioadenosine/S- adenosylhomocysteine nucleosidase L-methionine + ATP + H2O => S-adenosyl-L-methionine + phosphate + diphosphate; RHEA:21081; Declared type: reaction/activity; Source reaction direction: left_to_right reaction / activity L-methionine + ATP + H2O => S-adenosyl-L-methionine + phosphate + diphosphate S-adenosyl-L-methionine + a demethylated methyl donor -> S-adenosyl-L-homocysteine + a methylated methyl donor + H+; MetaCyc:RXN-7605; Declared type: reaction/activity; Source reaction direction: left_to_right reaction / activity S-adenosyl-L-methionine + a demethylated methyl donor -> S-adenosyl-L-homocysteine + a methylated methyl donor + H+ S-adenosyl-L-homocysteine + H2O => S-(5-deoxy-D-ribos-5-yl)-L-homocysteine + adenine; RHEA:17806; Declared type: reaction/activity; Source reaction direction: left_to_right reaction / activity S-adenosyl-L-homocysteine + H2O => S-(5-deoxy-D- ribos-5-yl)-L-homocysteine + adenine S-(5-deoxy-D-ribos-5-yl)-L-homocysteine => (S)-4,5-dihydroxypentane-2,3-dione + L-homocysteine; RHEA:17754; Declared type: reaction/activity; Source reaction direction: left_to_right reaction / activity S-(5-deoxy-D- ribos-5-yl)-L-homocysteine => (S)-4,5-dihydroxypentane- 2,3-dione + L-homocysteine 5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine => tetrahydropteroyltri-L-glutamate + L-methionine; RHEA:21197; Declared type: reaction/activity; Source reaction direction: left_to_right reaction / activity 5- methyltetrahydropteroyltri- L-glutamate + L-homocysteine => tetrahydropteroyltri-L- glutamate + L-methionine (6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine => (6S)-5,6,7,8-tetrahydrofolate + L-methionine; RHEA:11173; Declared type: reaction/activity; Source reaction direction: left_to_right reaction / activity (6S)-5-methyl-5,6,7,8- tetrahydrofolate + L-homocysteine => (6S)- 5,6,7,8-tetrahydrofolate + L-methionine S-adenosyl-L-methionine cycle I; MetaCyc:PWY-6151; Declared type: pathway pathway S-adenosyl-L-methionine cycle I

Components and activities

Declared biological components and source reaction directions
NodeKind or roleSource direction
Escherichia coli K-12
NCBITaxon:83333		taxon
water
CHEBI:15377		small molecule
hydron
CHEBI:15378		small molecule
adenine
CHEBI:16708		small molecule
magnesium(2+)
CHEBI:18420		cofactor
(6S)-5-methyltetrahydrofolate(2-)
CHEBI:18608		small molecule
iron cation
CHEBI:24875		cofactor
methylcobalamin
CHEBI:28115		cofactor
manganese(2+)
CHEBI:29035		cofactor
potassium(1+)
CHEBI:29103		cofactor
zinc(2+)
CHEBI:29105		cofactor
(S)-4,5-dihydroxypentane-2,3-dione
CHEBI:29484		small molecule
ATP(4-)
CHEBI:30616		small molecule
diphosphate(3-)
CHEBI:33019		small molecule
hydrogenphosphate
CHEBI:43474		small molecule
cobalt(2+)
CHEBI:48828		cofactor
(6S)-5,6,7,8-tetrahydrofolate(2-)
CHEBI:57453		small molecule
L-methionine zwitterion
CHEBI:57844		small molecule
S-adenosyl-L-homocysteine zwitterion
CHEBI:57856		small molecule
tetrahydropteroyltri-L-glutamate(4-)
CHEBI:58140		small molecule
S-(5-deoxy-D-ribos-5-yl)-L-homocysteine zwitterion
CHEBI:58195		small molecule
L-homocysteine zwitterion
CHEBI:58199		small molecule
5-methyltetrahydropteroyltri-L-glutamate(4-)
CHEBI:58207		small molecule
S-adenosyl-L-methionine zwitterion
CHEBI:59789		small molecule
a demethylated methyl donor
MetaCyc:Demethylated-methyl-acceptors		chemical entity
a methylated methyl donor
MetaCyc:Methylated-methyl-acceptors		chemical entity
S-adenosylmethionine synthase
UniProtKB:P0A817		protein
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
UniProtKB:P0AF12		protein
S-ribosylhomocysteine lyase
UniProtKB:P45578		protein
Methionine synthase
UniProtKB:P13009		protein
5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
UniProtKB:P25665		protein
methionine adenosyltransferase
MetaCyc:S-ADENMETSYN-CPLX		complex
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
MetaCyc:CPLX0-1541		complex
L-methionine + ATP + H2O => S-adenosyl-L-methionine + phosphate + diphosphate
RHEA:21081		reactionleft to right
S-adenosyl-L-methionine + a demethylated methyl donor -> S-adenosyl-L-homocysteine + a methylated methyl donor + H+
MetaCyc:RXN-7605		reactionleft to right
S-adenosyl-L-homocysteine + H2O => S-(5-deoxy-D-ribos-5-yl)-L-homocysteine + adenine
RHEA:17806		reactionleft to right
S-(5-deoxy-D-ribos-5-yl)-L-homocysteine => (S)-4,5-dihydroxypentane-2,3-dione + L-homocysteine
RHEA:17754		reactionleft to right
5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine => tetrahydropteroyltri-L-glutamate + L-methionine
RHEA:21197		reactionleft to right
(6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine => (6S)-5,6,7,8-tetrahydrofolate + L-methionine
RHEA:11173		reactionleft to right

Mechanistic edges

Mechanistic edges and their cited evidence
SubjectPredicate and descriptionObjectEvidence
L-methionine zwitterion
CHEBI:57844		consumes

L-methionine + ATP + H2O => S-adenosyl-L-methionine + phosphate + diphosphate
RHEA:21081
  • RHEA:21080

    Source assertion: Rhea RHEA:21081 lists CHEBI:57844 on its substrates side with coefficient 1.

    Source locationRHEA:21081/rh:substrates -> http://rdf.rhea-db.org/21080_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_21080_compound_2530/rh:compound -> http://rdf.rhea-db.org/Compound_2530/rh:accession
ATP(4-)
CHEBI:30616		consumes

L-methionine + ATP + H2O => S-adenosyl-L-methionine + phosphate + diphosphate
RHEA:21081
  • RHEA:21080

    Source assertion: Rhea RHEA:21081 lists CHEBI:30616 on its substrates side with coefficient 1.

    Source locationRHEA:21081/rh:substrates -> http://rdf.rhea-db.org/21080_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_21080_compound_6372/rh:compound -> http://rdf.rhea-db.org/Compound_6372/rh:accession
water
CHEBI:15377		consumes

L-methionine + ATP + H2O => S-adenosyl-L-methionine + phosphate + diphosphate
RHEA:21081
  • RHEA:21080

    Source assertion: Rhea RHEA:21081 lists CHEBI:15377 on its substrates side with coefficient 1.

    Source locationRHEA:21081/rh:substrates -> http://rdf.rhea-db.org/21080_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_21080_compound_1283/rh:compound -> http://rdf.rhea-db.org/Compound_1283/rh:accession
L-methionine + ATP + H2O => S-adenosyl-L-methionine + phosphate + diphosphate
RHEA:21081		produces

S-adenosyl-L-methionine zwitterion
CHEBI:59789
  • RHEA:21080

    Source assertion: Rhea RHEA:21081 lists CHEBI:59789 on its products side with coefficient 1.

    Source locationRHEA:21081/rh:products -> http://rdf.rhea-db.org/21080_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_21080_compound_6127/rh:compound -> http://rdf.rhea-db.org/Compound_6127/rh:accession
L-methionine + ATP + H2O => S-adenosyl-L-methionine + phosphate + diphosphate
RHEA:21081		produces

hydrogenphosphate
CHEBI:43474
  • RHEA:21080

    Source assertion: Rhea RHEA:21081 lists CHEBI:43474 on its products side with coefficient 1.

    Source locationRHEA:21081/rh:products -> http://rdf.rhea-db.org/21080_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_21080_compound_5518/rh:compound -> http://rdf.rhea-db.org/Compound_5518/rh:accession
L-methionine + ATP + H2O => S-adenosyl-L-methionine + phosphate + diphosphate
RHEA:21081		produces

diphosphate(3-)
CHEBI:33019
  • RHEA:21080

    Source assertion: Rhea RHEA:21081 lists CHEBI:33019 on its products side with coefficient 1.

    Source locationRHEA:21081/rh:products -> http://rdf.rhea-db.org/21080_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_21080_compound_2106/rh:compound -> http://rdf.rhea-db.org/Compound_2106/rh:accession
S-adenosyl-L-homocysteine zwitterion
CHEBI:57856		consumes

S-adenosyl-L-homocysteine + H2O => S-(5-deoxy-D-ribos-5-yl)-L-homocysteine + adenine
RHEA:17806
  • RHEA:17805

    Source assertion: Rhea RHEA:17806 lists CHEBI:57856 on its substrates side with coefficient 1.

    Source locationRHEA:17806/rh:substrates -> http://rdf.rhea-db.org/17805_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_17805_compound_4281/rh:compound -> http://rdf.rhea-db.org/Compound_4281/rh:accession
water
CHEBI:15377		consumes

S-adenosyl-L-homocysteine + H2O => S-(5-deoxy-D-ribos-5-yl)-L-homocysteine + adenine
RHEA:17806
  • RHEA:17805

    Source assertion: Rhea RHEA:17806 lists CHEBI:15377 on its substrates side with coefficient 1.

    Source locationRHEA:17806/rh:substrates -> http://rdf.rhea-db.org/17805_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_17805_compound_1283/rh:compound -> http://rdf.rhea-db.org/Compound_1283/rh:accession
S-adenosyl-L-homocysteine + H2O => S-(5-deoxy-D-ribos-5-yl)-L-homocysteine + adenine
RHEA:17806		produces

S-(5-deoxy-D-ribos-5-yl)-L-homocysteine zwitterion
CHEBI:58195
  • RHEA:17805

    Source assertion: Rhea RHEA:17806 lists CHEBI:58195 on its products side with coefficient 1.

    Source locationRHEA:17806/rh:products -> http://rdf.rhea-db.org/17805_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_17805_compound_5411/rh:compound -> http://rdf.rhea-db.org/Compound_5411/rh:accession
S-adenosyl-L-homocysteine + H2O => S-(5-deoxy-D-ribos-5-yl)-L-homocysteine + adenine
RHEA:17806		produces

adenine
CHEBI:16708
  • RHEA:17805

    Source assertion: Rhea RHEA:17806 lists CHEBI:16708 on its products side with coefficient 1.

    Source locationRHEA:17806/rh:products -> http://rdf.rhea-db.org/17805_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_17805_compound_4174/rh:compound -> http://rdf.rhea-db.org/Compound_4174/rh:accession
S-(5-deoxy-D-ribos-5-yl)-L-homocysteine zwitterion
CHEBI:58195		consumes

S-(5-deoxy-D-ribos-5-yl)-L-homocysteine => (S)-4,5-dihydroxypentane-2,3-dione + L-homocysteine
RHEA:17754
  • RHEA:17753

    Source assertion: Rhea RHEA:17754 lists CHEBI:58195 on its substrates side with coefficient 1.

    Source locationRHEA:17754/rh:substrates -> http://rdf.rhea-db.org/17753_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_17753_compound_5411/rh:compound -> http://rdf.rhea-db.org/Compound_5411/rh:accession
S-(5-deoxy-D-ribos-5-yl)-L-homocysteine => (S)-4,5-dihydroxypentane-2,3-dione + L-homocysteine
RHEA:17754		produces

(S)-4,5-dihydroxypentane-2,3-dione
CHEBI:29484
  • RHEA:17753

    Source assertion: Rhea RHEA:17754 lists CHEBI:29484 on its products side with coefficient 1.

    Source locationRHEA:17754/rh:products -> http://rdf.rhea-db.org/17753_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_17753_compound_5596/rh:compound -> http://rdf.rhea-db.org/Compound_5596/rh:accession
S-(5-deoxy-D-ribos-5-yl)-L-homocysteine => (S)-4,5-dihydroxypentane-2,3-dione + L-homocysteine
RHEA:17754		produces

L-homocysteine zwitterion
CHEBI:58199
  • RHEA:17753

    Source assertion: Rhea RHEA:17754 lists CHEBI:58199 on its products side with coefficient 1.

    Source locationRHEA:17754/rh:products -> http://rdf.rhea-db.org/17753_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_17753_compound_3869/rh:compound -> http://rdf.rhea-db.org/Compound_3869/rh:accession
5-methyltetrahydropteroyltri-L-glutamate(4-)
CHEBI:58207		consumes

5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine => tetrahydropteroyltri-L-glutamate + L-methionine
RHEA:21197
  • RHEA:21196

    Source assertion: Rhea RHEA:21197 lists CHEBI:58207 on its substrates side with coefficient 1.

    Source locationRHEA:21197/rh:substrates -> http://rdf.rhea-db.org/21196_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_21196_compound_3620/rh:compound -> http://rdf.rhea-db.org/Compound_3620/rh:accession
L-homocysteine zwitterion
CHEBI:58199		consumes

5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine => tetrahydropteroyltri-L-glutamate + L-methionine
RHEA:21197
  • RHEA:21196

    Source assertion: Rhea RHEA:21197 lists CHEBI:58199 on its substrates side with coefficient 1.

    Source locationRHEA:21197/rh:substrates -> http://rdf.rhea-db.org/21196_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_21196_compound_3869/rh:compound -> http://rdf.rhea-db.org/Compound_3869/rh:accession
5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine => tetrahydropteroyltri-L-glutamate + L-methionine
RHEA:21197		produces

tetrahydropteroyltri-L-glutamate(4-)
CHEBI:58140
  • RHEA:21196

    Source assertion: Rhea RHEA:21197 lists CHEBI:58140 on its products side with coefficient 1.

    Source locationRHEA:21197/rh:products -> http://rdf.rhea-db.org/21196_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_21196_compound_4911/rh:compound -> http://rdf.rhea-db.org/Compound_4911/rh:accession
5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine => tetrahydropteroyltri-L-glutamate + L-methionine
RHEA:21197		produces

L-methionine zwitterion
CHEBI:57844
  • RHEA:21196

    Source assertion: Rhea RHEA:21197 lists CHEBI:57844 on its products side with coefficient 1.

    Source locationRHEA:21197/rh:products -> http://rdf.rhea-db.org/21196_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_21196_compound_2530/rh:compound -> http://rdf.rhea-db.org/Compound_2530/rh:accession
(6S)-5-methyltetrahydrofolate(2-)
CHEBI:18608		consumes

(6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine => (6S)-5,6,7,8-tetrahydrofolate + L-methionine
RHEA:11173
  • RHEA:11172

    Source assertion: Rhea RHEA:11173 lists CHEBI:18608 on its substrates side with coefficient 1.

    Source locationRHEA:11173/rh:substrates -> http://rdf.rhea-db.org/11172_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_11172_compound_1195/rh:compound -> http://rdf.rhea-db.org/Compound_1195/rh:accession
L-homocysteine zwitterion
CHEBI:58199		consumes

(6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine => (6S)-5,6,7,8-tetrahydrofolate + L-methionine
RHEA:11173
  • RHEA:11172

    Source assertion: Rhea RHEA:11173 lists CHEBI:58199 on its substrates side with coefficient 1.

    Source locationRHEA:11173/rh:substrates -> http://rdf.rhea-db.org/11172_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_11172_compound_3869/rh:compound -> http://rdf.rhea-db.org/Compound_3869/rh:accession
(6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine => (6S)-5,6,7,8-tetrahydrofolate + L-methionine
RHEA:11173		produces

(6S)-5,6,7,8-tetrahydrofolate(2-)
CHEBI:57453
  • RHEA:11172

    Source assertion: Rhea RHEA:11173 lists CHEBI:57453 on its products side with coefficient 1.

    Source locationRHEA:11173/rh:products -> http://rdf.rhea-db.org/11172_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_11172_compound_4996/rh:compound -> http://rdf.rhea-db.org/Compound_4996/rh:accession
(6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine => (6S)-5,6,7,8-tetrahydrofolate + L-methionine
RHEA:11173		produces

L-methionine zwitterion
CHEBI:57844
  • RHEA:11172

    Source assertion: Rhea RHEA:11173 lists CHEBI:57844 on its products side with coefficient 1.

    Source locationRHEA:11173/rh:products -> http://rdf.rhea-db.org/11172_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_11172_compound_2530/rh:compound -> http://rdf.rhea-db.org/Compound_2530/rh:accession
S-adenosyl-L-methionine zwitterion
CHEBI:59789		consumes

S-adenosyl-L-methionine + a demethylated methyl donor -> S-adenosyl-L-homocysteine + a methylated methyl donor + H+
MetaCyc:RXN-7605
  • MetaCyc:RXN-7605

    Source assertion: RXN-7605 places S-ADENOSYLMETHIONINE on its left side with implicit coefficient 1; this is a generic methyl-transfer reaction, not a specified methylation target.

    Source locationReaction[@frameid='RXN-7605']/left/Compound[@frameid='S-ADENOSYLMETHIONINE']; comment; reaction-direction
  • MetaCyc:S-ADENOSYLMETHIONINE

    Source assertion: The native S-ADENOSYLMETHIONINE compound cross-references CHEBI:59789.

    Source locationCompound[@frameid='S-ADENOSYLMETHIONINE']/dblink[dblink-db='CHEBI']/dblink-oid
a demethylated methyl donor
MetaCyc:Demethylated-methyl-acceptors		consumes

A generic chemical class is retained without identifying a particular small molecule, protein, RNA or DNA substrate.

S-adenosyl-L-methionine + a demethylated methyl donor -> S-adenosyl-L-homocysteine + a methylated methyl donor + H+
MetaCyc:RXN-7605
  • MetaCyc:RXN-7605

    Source assertion: RXN-7605 places Demethylated-methyl-acceptors on its left side with implicit coefficient 1; this is a generic methyl-transfer reaction, not a specified methylation target.

    Source locationReaction[@frameid='RXN-7605']/left/Compound[@frameid='Demethylated-methyl-acceptors']; comment; reaction-direction
  • MetaCyc:Demethylated-methyl-acceptors

    Source assertion: The class leaves the methyl donor or acceptor identity undefined; the donor wording is its native label, while this reaction determines its acceptor role.

    Source locationCompound[@frameid='Demethylated-methyl-acceptors']/common-name, synonym, comment; cml/molecule
S-adenosyl-L-methionine + a demethylated methyl donor -> S-adenosyl-L-homocysteine + a methylated methyl donor + H+
MetaCyc:RXN-7605		produces

S-adenosyl-L-homocysteine zwitterion
CHEBI:57856
  • MetaCyc:RXN-7605

    Source assertion: RXN-7605 places ADENOSYL-HOMO-CYS on its right side with implicit coefficient 1; this is a generic methyl-transfer reaction, not a specified methylation target.

    Source locationReaction[@frameid='RXN-7605']/right/Compound[@frameid='ADENOSYL-HOMO-CYS']; comment; reaction-direction
  • MetaCyc:ADENOSYL-HOMO-CYS

    Source assertion: The native ADENOSYL-HOMO-CYS compound cross-references CHEBI:57856.

    Source locationCompound[@frameid='ADENOSYL-HOMO-CYS']/dblink[dblink-db='CHEBI']/dblink-oid
S-adenosyl-L-methionine + a demethylated methyl donor -> S-adenosyl-L-homocysteine + a methylated methyl donor + H+
MetaCyc:RXN-7605		produces

A generic chemical class is retained without identifying a particular small molecule, protein, RNA or DNA substrate.

a methylated methyl donor
MetaCyc:Methylated-methyl-acceptors
  • MetaCyc:RXN-7605

    Source assertion: RXN-7605 places Methylated-methyl-acceptors on its right side with implicit coefficient 1; this is a generic methyl-transfer reaction, not a specified methylation target.

    Source locationReaction[@frameid='RXN-7605']/right/Compound[@frameid='Methylated-methyl-acceptors']; comment; reaction-direction
  • MetaCyc:Methylated-methyl-acceptors

    Source assertion: The class leaves the methyl donor or acceptor identity undefined; the donor wording is its native label, while this reaction determines its acceptor role.

    Source locationCompound[@frameid='Methylated-methyl-acceptors']/common-name, synonym, comment; cml/molecule
S-adenosyl-L-methionine + a demethylated methyl donor -> S-adenosyl-L-homocysteine + a methylated methyl donor + H+
MetaCyc:RXN-7605		produces

hydron
CHEBI:15378
  • MetaCyc:RXN-7605

    Source assertion: RXN-7605 places PROTON on its right side with implicit coefficient 1; this is a generic methyl-transfer reaction, not a specified methylation target.

    Source locationReaction[@frameid='RXN-7605']/right/Compound[@frameid='PROTON']; comment; reaction-direction
  • MetaCyc:PROTON

    Source assertion: The native PROTON compound cross-references CHEBI:15378.

    Source locationCompound[@frameid='PROTON']/dblink[dblink-db='CHEBI']/dblink-oid
L-methionine + ATP + H2O => S-adenosyl-L-methionine + phosphate + diphosphate
RHEA:21081		part_of

MetaCyc:PWY-6151
  • MetaCyc:PWY-6151

    Source assertion: PWY-6151 includes child pathway SAM-PWY.

    Source locationPathway[@frameid='PWY-6151']/reaction-list/Pathway[@frameid='SAM-PWY']
  • MetaCyc:SAM-PWY

    Source assertion: SAM-PWY contains only S-ADENMETSYN-RXN, laid out left to right.

    Source locationPathway[@frameid='SAM-PWY']/reaction-list; reaction-layout
  • MetaCyc:S-ADENMETSYN-RXN

    Source assertion: S-ADENMETSYN-RXN explicitly cross-references RHEA:21081.

    Source locationReaction[@frameid='S-ADENMETSYN-RXN']/dblink[dblink-db='RHEA']; reaction-direction
  • RHEA:21080

    Source assertion: Rhea master 21080 has directed left-to-right reaction 21081.

    Source locationhttp://rdf.rhea-db.org/21080/rh:directionalReaction
S-adenosyl-L-homocysteine + H2O => S-(5-deoxy-D-ribos-5-yl)-L-homocysteine + adenine
RHEA:17806		part_of

MetaCyc:PWY-6151
  • MetaCyc:PWY-6151

    Source assertion: PWY-6151 contains ADENOSYLHOMOCYSTEINE-NUCLEOSIDASE-RXN and selects its left-to-right pathway layout.

    Source locationPathway[@frameid='PWY-6151']/reaction-list/Reaction[@frameid='ADENOSYLHOMOCYSTEINE-NUCLEOSIDASE-RXN']; reaction-layout
  • MetaCyc:ADENOSYLHOMOCYSTEINE-NUCLEOSIDASE-RXN

    Source assertion: ADENOSYLHOMOCYSTEINE-NUCLEOSIDASE-RXN explicitly cross-references RHEA:17806.

    Source locationReaction[@frameid='ADENOSYLHOMOCYSTEINE-NUCLEOSIDASE-RXN']/dblink[dblink-db='RHEA']; reaction-direction
  • RHEA:17805

    Source assertion: Rhea master 17805 has directed left-to-right reaction 17806.

    Source locationhttp://rdf.rhea-db.org/17805/rh:directionalReaction
S-(5-deoxy-D-ribos-5-yl)-L-homocysteine => (S)-4,5-dihydroxypentane-2,3-dione + L-homocysteine
RHEA:17754		part_of

MetaCyc:PWY-6151
  • MetaCyc:PWY-6151

    Source assertion: PWY-6151 contains RIBOSYLHOMOCYSTEINASE-RXN and selects its left-to-right pathway layout.

    Source locationPathway[@frameid='PWY-6151']/reaction-list/Reaction[@frameid='RIBOSYLHOMOCYSTEINASE-RXN']; reaction-layout
  • MetaCyc:RIBOSYLHOMOCYSTEINASE-RXN

    Source assertion: RIBOSYLHOMOCYSTEINASE-RXN explicitly cross-references RHEA:17754.

    Source locationReaction[@frameid='RIBOSYLHOMOCYSTEINASE-RXN']/dblink[dblink-db='RHEA']; reaction-direction
  • RHEA:17753

    Source assertion: Rhea master 17753 has directed left-to-right reaction 17754.

    Source locationhttp://rdf.rhea-db.org/17753/rh:directionalReaction
5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine => tetrahydropteroyltri-L-glutamate + L-methionine
RHEA:21197		part_of

MetaCyc:PWY-6151
  • MetaCyc:PWY-6151

    Source assertion: PWY-6151 contains HOMOCYSMET-RXN and selects its left-to-right pathway layout.

    Source locationPathway[@frameid='PWY-6151']/reaction-list/Reaction[@frameid='HOMOCYSMET-RXN']; reaction-layout
  • MetaCyc:HOMOCYSMET-RXN

    Source assertion: HOMOCYSMET-RXN explicitly cross-references RHEA:21199; its standalone reaction direction is REVERSIBLE.

    Source locationReaction[@frameid='HOMOCYSMET-RXN']/dblink[dblink-db='RHEA']; reaction-direction
  • RHEA:21196

    Source assertion: Rhea master 21196 has directed left-to-right reaction 21197 and bidirectional reaction 21199.

    Source locationhttp://rdf.rhea-db.org/21196/rh:directionalReaction; rh:bidirectionalReaction
(6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine => (6S)-5,6,7,8-tetrahydrofolate + L-methionine
RHEA:11173		part_of

MetH alternative, represented by the current monoglutamate Rhea equation; native HOMOCYSMETB12-RXN permits an unspecified folate glutamate-chain length. This does not make monoglutamate the exclusive cellular substrate.

MetaCyc:PWY-6151
  • MetaCyc:PWY-6151

    Source assertion: The pathway comment explicitly permits cobalamin-dependent methionine synthase as an alternative to the independent enzyme and states that E. coli has both.

    Source locationPathway[@frameid='PWY-6151']/comment; paragraph beginning 'The cycle continues'
  • MetaCyc:HOMOCYSMETB12-RXN

    Source assertion: HOMOCYSMETB12-RXN explicitly cross-references RHEA:11173.

    Source locationReaction[@frameid='HOMOCYSMETB12-RXN']/dblink[dblink-db='RHEA']; reaction-direction
  • RHEA:11172

    Source assertion: Rhea master 11172 has directed left-to-right reaction 11173.

    Source locationhttp://rdf.rhea-db.org/11172/rh:directionalReaction
S-adenosyl-L-methionine + a demethylated methyl donor -> S-adenosyl-L-homocysteine + a methylated methyl donor + H+
MetaCyc:RXN-7605		part_of

MetaCyc:PWY-6151
  • MetaCyc:PWY-6151

    Source assertion: PWY-6151 contains the generic methyl-transfer reaction RXN-7605, laid out left to right.

    Source locationPathway[@frameid='PWY-6151']/reaction-list/Reaction[@frameid='RXN-7605']; reaction-layout
5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine => tetrahydropteroyltri-L-glutamate + L-methionine
RHEA:21197		precedes

The source-defined cycle closes through CHEBI:57844; ordering does not assert an irreversible thermodynamic constraint.

L-methionine + ATP + H2O => S-adenosyl-L-methionine + phosphate + diphosphate
RHEA:21081
  • MetaCyc:PWY-6151

    Source assertion: Native pathway ordering places HOMOCYSMET-RXN before S-ADENMETSYN-RXN.

    Source locationPathway/reaction-ordering[Reaction/@frameid='S-ADENMETSYN-RXN']/predecessor-reactions/Reaction[@frameid='HOMOCYSMET-RXN']
  • RHEA:21196

    Source assertion: Rhea RHEA:21197 lists CHEBI:57844 on its products side with coefficient 1.

    Source locationRHEA:21197/rh:products -> http://rdf.rhea-db.org/21196_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_21196_compound_2530/rh:compound -> http://rdf.rhea-db.org/Compound_2530/rh:accession
  • RHEA:21080

    Source assertion: Rhea RHEA:21081 lists CHEBI:57844 on its substrates side with coefficient 1.

    Source locationRHEA:21081/rh:substrates -> http://rdf.rhea-db.org/21080_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_21080_compound_2530/rh:compound -> http://rdf.rhea-db.org/Compound_2530/rh:accession
L-methionine + ATP + H2O => S-adenosyl-L-methionine + phosphate + diphosphate
RHEA:21081		precedes

The source-defined cycle closes through CHEBI:59789; ordering does not assert an irreversible thermodynamic constraint.

S-adenosyl-L-methionine + a demethylated methyl donor -> S-adenosyl-L-homocysteine + a methylated methyl donor + H+
MetaCyc:RXN-7605
  • MetaCyc:PWY-6151

    Source assertion: Native pathway ordering places S-ADENMETSYN-RXN before RXN-7605.

    Source locationPathway/reaction-ordering[Reaction/@frameid='RXN-7605']/predecessor-reactions/Reaction[@frameid='S-ADENMETSYN-RXN']
  • RHEA:21080

    Source assertion: Rhea RHEA:21081 lists CHEBI:59789 on its products side with coefficient 1.

    Source locationRHEA:21081/rh:products -> http://rdf.rhea-db.org/21080_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_21080_compound_6127/rh:compound -> http://rdf.rhea-db.org/Compound_6127/rh:accession
  • MetaCyc:RXN-7605

    Source assertion: RXN-7605 places S-ADENOSYLMETHIONINE on its left side with implicit coefficient 1; this is a generic methyl-transfer reaction, not a specified methylation target.

    Source locationReaction[@frameid='RXN-7605']/left/Compound[@frameid='S-ADENOSYLMETHIONINE']; comment; reaction-direction
S-adenosyl-L-methionine + a demethylated methyl donor -> S-adenosyl-L-homocysteine + a methylated methyl donor + H+
MetaCyc:RXN-7605		precedes

The source-defined cycle closes through CHEBI:57856; ordering does not assert an irreversible thermodynamic constraint.

S-adenosyl-L-homocysteine + H2O => S-(5-deoxy-D-ribos-5-yl)-L-homocysteine + adenine
RHEA:17806
  • MetaCyc:PWY-6151

    Source assertion: Native pathway ordering places RXN-7605 before ADENOSYLHOMOCYSTEINE-NUCLEOSIDASE-RXN.

    Source locationPathway/reaction-ordering[Reaction/@frameid='ADENOSYLHOMOCYSTEINE-NUCLEOSIDASE-RXN']/predecessor-reactions/Reaction[@frameid='RXN-7605']
  • MetaCyc:RXN-7605

    Source assertion: RXN-7605 places ADENOSYL-HOMO-CYS on its right side with implicit coefficient 1; this is a generic methyl-transfer reaction, not a specified methylation target.

    Source locationReaction[@frameid='RXN-7605']/right/Compound[@frameid='ADENOSYL-HOMO-CYS']; comment; reaction-direction
  • RHEA:17805

    Source assertion: Rhea RHEA:17806 lists CHEBI:57856 on its substrates side with coefficient 1.

    Source locationRHEA:17806/rh:substrates -> http://rdf.rhea-db.org/17805_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_17805_compound_4281/rh:compound -> http://rdf.rhea-db.org/Compound_4281/rh:accession
S-adenosyl-L-homocysteine + H2O => S-(5-deoxy-D-ribos-5-yl)-L-homocysteine + adenine
RHEA:17806		precedes

The source-defined cycle closes through CHEBI:58195; ordering does not assert an irreversible thermodynamic constraint.

S-(5-deoxy-D-ribos-5-yl)-L-homocysteine => (S)-4,5-dihydroxypentane-2,3-dione + L-homocysteine
RHEA:17754
  • MetaCyc:PWY-6151

    Source assertion: Native pathway ordering places ADENOSYLHOMOCYSTEINE-NUCLEOSIDASE-RXN before RIBOSYLHOMOCYSTEINASE-RXN.

    Source locationPathway/reaction-ordering[Reaction/@frameid='RIBOSYLHOMOCYSTEINASE-RXN']/predecessor-reactions/Reaction[@frameid='ADENOSYLHOMOCYSTEINE-NUCLEOSIDASE-RXN']
  • RHEA:17805

    Source assertion: Rhea RHEA:17806 lists CHEBI:58195 on its products side with coefficient 1.

    Source locationRHEA:17806/rh:products -> http://rdf.rhea-db.org/17805_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_17805_compound_5411/rh:compound -> http://rdf.rhea-db.org/Compound_5411/rh:accession
  • RHEA:17753

    Source assertion: Rhea RHEA:17754 lists CHEBI:58195 on its substrates side with coefficient 1.

    Source locationRHEA:17754/rh:substrates -> http://rdf.rhea-db.org/17753_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_17753_compound_5411/rh:compound -> http://rdf.rhea-db.org/Compound_5411/rh:accession
S-(5-deoxy-D-ribos-5-yl)-L-homocysteine => (S)-4,5-dihydroxypentane-2,3-dione + L-homocysteine
RHEA:17754		precedes

The source-defined cycle closes through CHEBI:58199; ordering does not assert an irreversible thermodynamic constraint.

5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine => tetrahydropteroyltri-L-glutamate + L-methionine
RHEA:21197
  • MetaCyc:PWY-6151

    Source assertion: Native pathway ordering places RIBOSYLHOMOCYSTEINASE-RXN before HOMOCYSMET-RXN.

    Source locationPathway/reaction-ordering[Reaction/@frameid='HOMOCYSMET-RXN']/predecessor-reactions/Reaction[@frameid='RIBOSYLHOMOCYSTEINASE-RXN']
  • RHEA:17753

    Source assertion: Rhea RHEA:17754 lists CHEBI:58199 on its products side with coefficient 1.

    Source locationRHEA:17754/rh:products -> http://rdf.rhea-db.org/17753_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_17753_compound_3869/rh:compound -> http://rdf.rhea-db.org/Compound_3869/rh:accession
  • RHEA:21196

    Source assertion: Rhea RHEA:21197 lists CHEBI:58199 on its substrates side with coefficient 1.

    Source locationRHEA:21197/rh:substrates -> http://rdf.rhea-db.org/21196_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_21196_compound_3869/rh:compound -> http://rdf.rhea-db.org/Compound_3869/rh:accession
S-(5-deoxy-D-ribos-5-yl)-L-homocysteine => (S)-4,5-dihydroxypentane-2,3-dione + L-homocysteine
RHEA:17754		provides_input_for

Material continuity for the documented MetH alternative, not an additional native reaction-ordering triple.

(6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine => (6S)-5,6,7,8-tetrahydrofolate + L-methionine
RHEA:11173
  • MetaCyc:PWY-6151

    Source assertion: The pathway comment permits MetH as an alternative methionine-regenerating enzyme in E. coli.

    Source locationPathway[@frameid='PWY-6151']/comment; methionine synthase alternatives
  • RHEA:17753

    Source assertion: Rhea RHEA:17754 lists CHEBI:58199 on its products side with coefficient 1.

    Source locationRHEA:17754/rh:products -> http://rdf.rhea-db.org/17753_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_17753_compound_3869/rh:compound -> http://rdf.rhea-db.org/Compound_3869/rh:accession
  • RHEA:11172

    Source assertion: Rhea RHEA:11173 lists CHEBI:58199 on its substrates side with coefficient 1.

    Source locationRHEA:11173/rh:substrates -> http://rdf.rhea-db.org/11172_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_11172_compound_3869/rh:compound -> http://rdf.rhea-db.org/Compound_3869/rh:accession
(6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine => (6S)-5,6,7,8-tetrahydrofolate + L-methionine
RHEA:11173		provides_input_for

Material continuity for the documented MetH alternative, not an additional native reaction-ordering triple.

L-methionine + ATP + H2O => S-adenosyl-L-methionine + phosphate + diphosphate
RHEA:21081
  • MetaCyc:PWY-6151

    Source assertion: The pathway comment permits MetH as an alternative methionine-regenerating enzyme in E. coli.

    Source locationPathway[@frameid='PWY-6151']/comment; methionine synthase alternatives
  • RHEA:11172

    Source assertion: Rhea RHEA:11173 lists CHEBI:57844 on its products side with coefficient 1.

    Source locationRHEA:11173/rh:products -> http://rdf.rhea-db.org/11172_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_11172_compound_2530/rh:compound -> http://rdf.rhea-db.org/Compound_2530/rh:accession
  • RHEA:21080

    Source assertion: Rhea RHEA:21081 lists CHEBI:57844 on its substrates side with coefficient 1.

    Source locationRHEA:21081/rh:substrates -> http://rdf.rhea-db.org/21080_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_21080_compound_2530/rh:compound -> http://rdf.rhea-db.org/Compound_2530/rh:accession
methionine adenosyltransferase
MetaCyc:S-ADENMETSYN-CPLX		has_part

Source subunit coefficient 4; the protein component is not asserted to independently catalyze the overall reaction.

S-adenosylmethionine synthase
UniProtKB:P0A817
  • MetaCyc:S-ADENMETSYN-CPLX

    Source assertion: The native complex contains 4 copies of S-ADENMETSYN-MONOMER.

    Source locationProtein[@frameid='S-ADENMETSYN-CPLX']/component/Protein; component/coefficient
  • MetaCyc:S-ADENMETSYN-MONOMER

    Source assertion: S-ADENMETSYN-MONOMER is unified with UniProtKB:P0A817.

    Source locationProtein[@frameid='S-ADENMETSYN-MONOMER']/dblink[dblink-db='UNIPROT']
  • UniProtKB:P0A817

    Source assertion: The reviewed SUBUNIT annotation describes a homotetramer (dimer of dimers), with experimental ECO:0000269 evidence.

    Source locationcomments[commentType='SUBUNIT']
  • PMID:14967023

    Source assertion: The E. coli crystal structure is a dimer of dimers.

    Source locationEurope PMC resultList.result[0].abstractText; structural Results
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
MetaCyc:CPLX0-1541		has_part

Source subunit coefficient 2; the protein component is not asserted to independently catalyze the overall reaction.

5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
UniProtKB:P0AF12
  • MetaCyc:CPLX0-1541

    Source assertion: The native complex contains 2 copies of EG11090-MONOMER.

    Source locationProtein[@frameid='CPLX0-1541']/component/Protein; component/coefficient
  • MetaCyc:EG11090-MONOMER

    Source assertion: EG11090-MONOMER is unified with UniProtKB:P0AF12.

    Source locationProtein[@frameid='EG11090-MONOMER']/dblink[dblink-db='UNIPROT']
  • UniProtKB:P0AF12

    Source assertion: The reviewed SUBUNIT annotation describes a homodimer, including ECO:0000269 structural evidence.

    Source locationcomments[commentType='SUBUNIT']
  • PMID:11591349

    Source assertion: The E. coli nucleosidase structure supports a functional dimer; contacts join the two monomers.

    Source locationEurope PMC resultList.result[0].abstractText; structural Results
methionine adenosyltransferase
MetaCyc:S-ADENMETSYN-CPLX		catalyzes

L-methionine + ATP + H2O => S-adenosyl-L-methionine + phosphate + diphosphate
RHEA:21081
  • MetaCyc:S-ADENMETSYN-CPLX

    Source assertion: The native complex catalyzes S-ADENMETSYN-RXN.

    Source locationProtein[@frameid='S-ADENMETSYN-CPLX']/catalyzes/Enzymatic-Reaction/reaction
  • UniProtKB:P0A817

    Source assertion: The reviewed E. coli K-12 protein has catalytic annotation RHEA:21080; evidence: ECO:0000269 experimental and ECO:0000255 HAMAP.

    Source locationorganism.taxonId; comments[commentType='CATALYTIC ACTIVITY'].reaction
  • RHEA:21080

    Source assertion: Rhea master 21080 has directed left-to-right reaction 21081.

    Source locationhttp://rdf.rhea-db.org/21080/rh:directionalReaction
  • PMID:6251075

    Source assertion: Purified E. coli adenosylmethionine synthetase performs synthesis and a stimulated tripolyphosphatase reaction.

    Source locationEurope PMC resultList.result[0].abstractText
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
MetaCyc:CPLX0-1541		catalyzes

S-adenosyl-L-homocysteine + H2O => S-(5-deoxy-D-ribos-5-yl)-L-homocysteine + adenine
RHEA:17806
  • MetaCyc:CPLX0-1541

    Source assertion: The native complex catalyzes ADENOSYLHOMOCYSTEINE-NUCLEOSIDASE-RXN.

    Source locationProtein[@frameid='CPLX0-1541']/catalyzes/Enzymatic-Reaction/reaction
  • UniProtKB:P0AF12

    Source assertion: The reviewed E. coli K-12 protein has catalytic annotation RHEA:17805; evidence: ECO:0000269 experimental and ECO:0000255 HAMAP.

    Source locationorganism.taxonId; comments[commentType='CATALYTIC ACTIVITY'].reaction
  • RHEA:17805

    Source assertion: Rhea master 17805 has directed left-to-right reaction 17806.

    Source locationhttp://rdf.rhea-db.org/17805/rh:directionalReaction
  • PMID:11489131

    Source assertion: Purified GST-Pfs from MG1655 removes adenine from SAH, producing SRH before the LuxS step; sequential filtration and mass spectra test this order.

    Source locationPDF pp467-468, Table 1 and Fig.4B; p473, Overexpression and purification of LuxS and Pfs
S-ribosylhomocysteine lyase
UniProtKB:P45578		enables

Functional LuxS contribution; its homodimer annotation is by similarity (ECO:0000250). No independently verified E. coli assembly identifier or monomer sufficiency is asserted.

S-(5-deoxy-D-ribos-5-yl)-L-homocysteine => (S)-4,5-dihydroxypentane-2,3-dione + L-homocysteine
RHEA:17754
  • UniProtKB:P45578

    Source assertion: The reviewed E. coli K-12 protein has catalytic annotation RHEA:17753; evidence: curated catalytic annotation without a per-reaction evidence tag.

    Source locationorganism.taxonId; comments[commentType='CATALYTIC ACTIVITY'].reaction
  • RHEA:17753

    Source assertion: Rhea master 17753 has directed left-to-right reaction 17754.

    Source locationhttp://rdf.rhea-db.org/17753/rh:directionalReaction
  • PMID:11489131

    Source assertion: Purified GST-LuxS from MG1655 acts on SRH after Pfs, with homocysteine detected. DPD was inferred to cyclize; this study did not absolutely identify the AI-2 structure.

    Source locationPDF pp467-468, Table 1; pp470-471, Discussion; p473, Overexpression and purification
5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
UniProtKB:P25665		enables

MetE is annotated monomeric; this edge preserves its gene-product activity and separately inspected experimental support without upgrading HAMAP evidence.

5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine => tetrahydropteroyltri-L-glutamate + L-methionine
RHEA:21197
  • UniProtKB:P25665

    Source assertion: The reviewed E. coli K-12 protein has catalytic annotation RHEA:21196; evidence: ECO:0000255 HAMAP.

    Source locationorganism.taxonId; comments[commentType='CATALYTIC ACTIVITY'].reaction
  • RHEA:21196

    Source assertion: Rhea master 21196 has directed left-to-right reaction 21197 and bidirectional reaction 21199.

    Source locationhttp://rdf.rhea-db.org/21196/rh:directionalReaction; rh:bidirectionalReaction
  • MetaCyc:HOMOCYSMET-MONOMER

    Source assertion: The E. coli MetE entry states that it uses triglutamate folate, whereas MetH uses mono- or triglutamate forms; purified K-12 enzyme was characterized.

    Source locationProtein[@frameid='HOMOCYSMET-MONOMER']/comment, first three paragraphs
  • PMID:16618098

    Source assertion: MetE transfers a methyl group from methyltetrahydropteroyltriglutamate to homocysteine; substrate-dependent absorbance studies address methyl-donor activation.

    Source locationEurope PMC resultList.result[0].abstractText
Methionine synthase
UniProtKB:P13009		enables

(6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine => (6S)-5,6,7,8-tetrahydrofolate + L-methionine
RHEA:11173
  • UniProtKB:P13009

    Source assertion: The reviewed E. coli K-12 protein has catalytic annotation RHEA:11172; evidence: ECO:0000269 experimental.

    Source locationorganism.taxonId; comments[commentType='CATALYTIC ACTIVITY'].reaction
  • RHEA:11172

    Source assertion: Rhea master 11172 has directed left-to-right reaction 11173.

    Source locationhttp://rdf.rhea-db.org/11172/rh:directionalReaction
  • PMID:9201956

    Source assertion: MetH transfers methyl from bound methylcobalamin to homocysteine and remethylates the cofactor with methyltetrahydrofolate; purified holoenzyme and fragments were investigated.

    Source locationEurope PMC resultList.result[0].abstractText
S-adenosylmethionine synthase
UniProtKB:P0A817		has_cofactor

Mn2+ and Co2+ are tested alternatives to Mg2+, not a requirement that all three divalent metals bind simultaneously; potassium is a separate monovalent cofactor.

magnesium(2+)
CHEBI:18420
  • UniProtKB:P0A817

    Source assertion: The reviewed COFACTOR annotation lists Mg(2+) (CHEBI:18420) with ECO:0000269 evidence; it distinguishes two divalent sites and one potassium site per subunit.

    Source locationcomments[commentType='COFACTOR'].cofactors; note
  • PMID:6251075

    Source assertion: Enzymatic activities require a divalent metal; phosphorothioate ATP studies used Mg2+, Mn2+ or Co2+ and indicate metal-nucleotide binding.

    Source locationEurope PMC resultList.result[0].abstractText
S-adenosylmethionine synthase
UniProtKB:P0A817		has_cofactor

Mn2+ and Co2+ are tested alternatives to Mg2+, not a requirement that all three divalent metals bind simultaneously; potassium is a separate monovalent cofactor.

manganese(2+)
CHEBI:29035
  • UniProtKB:P0A817

    Source assertion: The reviewed COFACTOR annotation lists Mn(2+) (CHEBI:29035) with ECO:0000269 evidence; it distinguishes two divalent sites and one potassium site per subunit.

    Source locationcomments[commentType='COFACTOR'].cofactors; note
  • PMID:6251075

    Source assertion: Enzymatic activities require a divalent metal; phosphorothioate ATP studies used Mg2+, Mn2+ or Co2+ and indicate metal-nucleotide binding.

    Source locationEurope PMC resultList.result[0].abstractText
S-adenosylmethionine synthase
UniProtKB:P0A817		has_cofactor

Mn2+ and Co2+ are tested alternatives to Mg2+, not a requirement that all three divalent metals bind simultaneously; potassium is a separate monovalent cofactor.

cobalt(2+)
CHEBI:48828
  • UniProtKB:P0A817

    Source assertion: The reviewed COFACTOR annotation lists Co(2+) (CHEBI:48828) with ECO:0000269 evidence; it distinguishes two divalent sites and one potassium site per subunit.

    Source locationcomments[commentType='COFACTOR'].cofactors; note
  • PMID:6251075

    Source assertion: Enzymatic activities require a divalent metal; phosphorothioate ATP studies used Mg2+, Mn2+ or Co2+ and indicate metal-nucleotide binding.

    Source locationEurope PMC resultList.result[0].abstractText
S-adenosylmethionine synthase
UniProtKB:P0A817		has_cofactor

Mn2+ and Co2+ are tested alternatives to Mg2+, not a requirement that all three divalent metals bind simultaneously; potassium is a separate monovalent cofactor.

potassium(1+)
CHEBI:29103
  • UniProtKB:P0A817

    Source assertion: The reviewed COFACTOR annotation lists K(+) (CHEBI:29103) with ECO:0000269 evidence; it distinguishes two divalent sites and one potassium site per subunit.

    Source locationcomments[commentType='COFACTOR'].cofactors; note
S-ribosylhomocysteine lyase
UniProtKB:P45578		has_cofactor

This is an inferred E. coli annotation at the generic iron-cation level. No exact oxidation state, direct E. coli metal measurement or zinc-independent activity is asserted.

iron cation
CHEBI:24875
  • UniProtKB:P45578

    Source assertion: UniProt annotates one iron cation per subunit as a cofactor, inferred by similarity (ECO:0000250).

    Source locationcomments[commentType='COFACTOR'].cofactors[0]; note
5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
UniProtKB:P25665		has_cofactor

zinc(2+)
CHEBI:29105
  • UniProtKB:P25665

    Source assertion: The COFACTOR annotation lists zinc(2+), one per subunit, with ECO:0000255 HAMAP evidence.

    Source locationcomments[commentType='COFACTOR']
  • PMID:11170420

    Source assertion: X-ray absorption studies of E. coli MetE demonstrate coordination of the homocysteine analogue to its zinc site.

    Source locationEurope PMC resultList.result[0].abstractText; MetE and L-selenohomocysteine
Methionine synthase
UniProtKB:P13009		has_cofactor

zinc(2+)
CHEBI:29105
  • UniProtKB:P13009

    Source assertion: The COFACTOR annotation lists zinc(2+), one per subunit, with ECO:0000269 evidence.

    Source locationcomments[commentType='COFACTOR'].cofactors; note
  • PMID:9398304

    Source assertion: E. coli MetH zinc removal abolished methyl transfer; reconstitution partly restored activity. Holoenzyme and a truncated protein contained about 0.9 equivalents of zinc.

    Source locationEurope PMC resultList.result[0].abstractText
Methionine synthase
UniProtKB:P13009		has_cofactor

Cobalamin cycling is internal to the net methionine-synthase equation. Reductive reactivation is not added as a second methyl-transfer step of the native cycle.

methylcobalamin
CHEBI:28115
  • UniProtKB:P13009

    Source assertion: UniProt lists methylcob(III)alamin as the cofactor with ECO:0000269 evidence.

    Source locationcomments[commentType='COFACTOR'].cofactors[cofactorCrossReference.id='CHEBI:28115']
  • PMID:9201956

    Source assertion: The bound methylcobalamin transfers methyl to homocysteine; methyltetrahydrofolate then remethylates the bound cob(I)alamin.

    Source locationEurope PMC resultList.result[0].abstractText

References

Curation history