Glycine, serine and threonine metabolism

Source	ID	Pathway
KEGG	00260

Pathway Metabolites

YMDB ID	Name CAS Number	IUPAC Name	Formula Weight
YMDB00016	Glycine 56-40-6	2-aminoacetic acid	C₂H₅NO₂ 75.0666
YMDB00033	Glyoxylic acid 298-12-4	2-oxoacetic acid	C₂H₂O₃ 74.0355
YMDB00034	L-aspartic 4-semialdehyde 15106-57-7	(2S)-2-amino-4-oxobutanoic acid	C₄H₇NO₃ 117.1033
YMDB00042	1,3-Diaminopropane 109-76-2	propane-1,3-diamine	C₃H₁₀N₂ 74.1249
YMDB00046	L-Cysteine 52-90-4	(2R)-2-amino-3-sulfanylpropanoic acid	C₃H₇NO₂S 121.158
YMDB00071	2-Ketobutyric acid 600-18-0	2-oxobutanoic acid	C₄H₆O₃ 102.0886
YMDB00076	DL-O-Phosphoserine 17885-08-4	2-amino-3-(phosphonooxy)propanoic acid	C₃H₈NO₆P 185.0725
YMDB00083	5-Aminolevulinic acid 106-60-5	5-amino-4-oxopentanoic acid	C₅H₉NO₃ 131.1299
YMDB00091	Ammonia 7664-41-7	ammonia	H₃N 17.0305
YMDB00104	L-Homoserine 672-15-1	(2S)-2-amino-4-hydroxybutanoic acid	C₄H₉NO₃ 119.1192
YMDB00112	L-Serine 56-45-1	(2S)-2-amino-3-hydroxypropanoic acid	C₃H₇NO₃ 105.0926
YMDB00113	4-Phospho-L-aspartic acid 22138-53-0	(2S)-2-amino-4-oxo-4-(phosphonooxy)butanoic acid	C₄H₈NO₇P 213.0826
YMDB00126	L-Tryptophan 73-22-3	(2S)-2-amino-3-(1H-indol-3-yl)propanoic acid	C₁₁H₁₂N₂O₂ 204.2252
YMDB00139	Tetrahydrofolic acid 135-16-0	2-{[4-({[(6S)-4-hydroxy-2-imino-1,2,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]formamido}pentanedioic acid	C₁₉H₂₃N₇O₆ 445.4292
YMDB00170	Pyruvaldehyde 78-98-8	2-oxopropanal	C₃H₄O₂ 72.0627
YMDB00175	Pyruvic acid 127-17-3	2-oxopropanoic acid	C₃H₄O₃ 88.0621
YMDB00214	L-Threonine 72-19-5	(2S,3R)-2-amino-3-hydroxybutanoic acid	C₄H₉NO₃ 119.1192
YMDB00227	Choline 62-49-7	(2-hydroxyethyl)trimethylazanium	C₅H₁₄NO 104.1708
YMDB00245	L-Cystathionine 56-88-2	(2S)-2-amino-4-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}butanoic acid	C₇H₁₄N₂O₄S 222.262
YMDB00258	O-Phosphohomoserine 4210-66-6	(2S)-2-amino-4-(phosphonooxy)butanoic acid	C₄H₁₀NO₆P 199.0991
YMDB00260	5,10-Methylene-THF 31690-11-6	2-({4-[(6aR)-1-hydroxy-3-imino-3H,4H,5H,6H,6aH,7H,8H,9H-imidazo[1,5-f]pteridin-8-yl]phenyl}formamido)pentanedioic acid	C₂₀H₂₃N₇O₆ 457.4399
YMDB00284	D-Serine 312-84-5	(2R)-2-amino-3-hydroxypropanoic acid	C₃H₇NO₃ 105.0926
YMDB00295	L-Allothreonine 24830-94-2	(2S,3S)-2-amino-3-hydroxybutanoic acid	C₄H₉NO₃ 119.1192
YMDB00393	Phosphohydroxypyruvic acid 3913-50-6	2-oxo-3-(phosphonooxy)propanoic acid	C₃H₅O₇P 184.0414
YMDB00483	5,6,7,8-Tetrahydrofolic acid 135-16-0	(2S)-2-[(4-{[(2-amino-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl)methyl]amino}phenyl)formamido]pentanedioic acid	C₁₉H₂₃N₇O₆ 445.4292
YMDB00695	L-2-amino-3-oxobutanoic acid	(2S)-2-amino-3-oxobutanoic acid	C₄H₇NO₃ 117.1033
YMDB00756	3-phospho-D-glyceric acid 820-11-1	(2R)-2-hydroxy-3-(phosphonooxy)propanoic acid	C₃H₇O₇P 186.0572
YMDB00761	O-Phospho-L-serine 407-41-0	(2S)-2-amino-3-(phosphonooxy)propanoic acid	C₃H₈NO₆P 185.0725
YMDB00848	(6R)-5,10-methylenetetrahydrofolic acid 3432-99-3	(2S)-2-({4-[(6aR)-3-amino-1-oxo-1H,2H,5H,6H,6aH,7H,8H,9H-imidazolidino[1,5-f]pteridin-8-yl]phenyl}formamido)pentanedioic acid	C₂₀H₂₃N₇O₆ 457.4399
YMDB00892	Aminoacetone 298-08-8	1-aminopropan-2-one	C₃H₇NO 73.0938
YMDB00896	L-Aspartic acid 56-84-8	(2S)-2-aminobutanedioic acid	C₄H₇NO₄ 133.1027
YMDB00912	Carbon dioxide 124-38-9	methanedione	CO₂ 44.0095
YMDB01011	2-oxobutanoate 600-18-0		C₄H₅O₃ 101.0807
YMDB01022	L-aspartate 4-semialdehyde 15106-57-7		C₄H₆NO₃ 116.0953
YMDB01027	L-2-amino-3-oxobutanoate		C₄H₆NO₃ 116.0953
YMDB01033	Glyoxylate 298-12-4		C₂HO₃ 73.0275
YMDB01053	pyruvate 127-17-3		C₃H₃O₃ 87.0541
YMDB01067	4-phospho-L-aspartate 22138-53-0		C₄H₅NO₇P 210.0588
YMDB01068	5-aminolevulinate 106-60-5		C₅H₈NO₃ 130.1219
YMDB01251	PS(16:0/16:0) 3036-82-6	(2S)-2-amino-3-({[(2R)-2,3-bis(hexadecanoyloxy)propoxy](hydroxy)phosphoryl}oxy)propanoic acid	C₃₈H₇₄NO₁₀P 735.981
YMDB01257	PS(18:0/18:1(9Z))	(2S)-2-amino-3-({hydroxy[(2R)-2-[(9Z)-octadec-9-enoyloxy]-3-(octadecanoyloxy)propoxy]phosphoryl}oxy)propanoic acid	C₄₂H₈₀NO₁₀P 790.073

Pathway Proteins

Uniprot ID	Gene Name Locus	Name	Type	Metabolites
P49095	GCV2 YMR189W	Glycine dehydrogenase [decarboxylating], mitochondrial	Enzyme	Glycine Carbon dioxide
P37291	SHM2 YLR058C	Serine hydroxymethyltransferase, cytosolic	Enzyme	Glycine L-Serine Tetrahydrofolic acid 5,10-Methylene-THF 5,6,7,8-Tetrahydrofolic acid (6R)-5,10-methylenetetrahydrofolic acid water
P37292	SHM1 YBR263W	Serine hydroxymethyltransferase, mitochondrial	Enzyme	Glycine L-Serine Tetrahydrofolic acid 5,10-Methylene-THF 5,6,7,8-Tetrahydrofolic acid (6R)-5,10-methylenetetrahydrofolic acid water
P37303	GLY1 YEL046C	Low specificity L-threonine aldolase	Enzyme	Glycine Acetaldehyde L-Threonine L-Allothreonine
P09950	HEM1 YDR232W	5-aminolevulinate synthase, mitochondrial	Enzyme	Glycine Coenzyme A 5-Aminolevulinic acid Succinyl-CoA hydron Carbon dioxide
P43567	AGX1 YFL030W	Alanine--glyoxylate aminotransferase 1	Enzyme	Glycine Glyoxylic acid L-Alanine Pyruvic acid
P09624	LPD1 YFL018C	Dihydrolipoyl dehydrogenase, mitochondrial	Enzyme	Glycine Coenzyme A NAD NADH Oxoglutaric acid Pyruvic acid Acetyl-CoA NAD(+) Ammonium 5,6,7,8-Tetrahydrofolic acid Succinyl-CoA S(8)-aminomethyldihydrolipoamide lipoamide S(8)-succinyldihydrolipoamide (6R)-5,10-methylenetetrahydrofolic acid hydron Dihydrolipoamide Carbon dioxide
P07246	ADH3 YMR083W	Alcohol dehydrogenase 3, mitochondrial	Enzyme	Acetaldehyde NAD Phenylacetaldehyde NADH Indoleacetaldehyde NAD(+) isobutyraldehyde 2-Methylbutanal 3-methylbutanal 2-methylbutan-1-ol isoamylol isobutanol tryptophol hydron Ethanol
P00330	ADH1 YOL086C	Alcohol dehydrogenase 1	Enzyme	Acetaldehyde NAD Phenylacetaldehyde NADH Indoleacetaldehyde NAD(+) isobutyraldehyde 2-Methylbutanal 3-methylbutanal 2-methylbutan-1-ol isoamylol isobutanol tryptophol hydron Ethanol
P10127	ADH4 YGL256W	Alcohol dehydrogenase 4	Enzyme	Acetaldehyde NAD Phenylacetaldehyde NADH Indoleacetaldehyde NAD(+) isobutyraldehyde 2-Methylbutanal 3-methylbutanal 2-methylbutan-1-ol isoamylol isobutanol tryptophol hydron Ethanol
P38113	ADH5 YBR145W	Alcohol dehydrogenase 5	Enzyme	Acetaldehyde NAD Phenylacetaldehyde NADH Indoleacetaldehyde NAD(+) isobutyraldehyde 2-Methylbutanal 3-methylbutanal 2-methylbutan-1-ol isoamylol isobutanol tryptophol hydron Ethanol
P00331	ADH2 YMR303C	Alcohol dehydrogenase 2	Enzyme	Acetaldehyde NAD Phenylacetaldehyde NADH Indoleacetaldehyde NAD(+) isobutyraldehyde 2-Methylbutanal 3-methylbutanal 2-methylbutan-1-ol isoamylol isobutanol tryptophol hydron Ethanol
P13663	HOM2 YDR158W	Aspartate-semialdehyde dehydrogenase	Enzyme	L-aspartic 4-semialdehyde 4-Phospho-L-aspartic acid NADPH NADP hydron phosphate
P31373	CYS3 YAL012W	Cystathionine gamma-lyase	Enzyme	L-Cysteine 2-Ketobutyric acid Ammonia Pyruvic acid L-Cystathionine Ammonium Hydrogen sulfide hydron water Selenomethionine Se-Methylselenocysteine 2-aminoprop-2-enoate methylselenol
P40510	SER33 YIL074C	D-3-phosphoglycerate dehydrogenase 2	Enzyme	2-hydroxyglutaric acid NAD NADH Oxoglutaric acid 3-Phosphoglyceric acid Phosphohydroxypyruvic acid NAD(+) 3-phospho-D-glyceric acid hydron
P00927	ILV1 YER086W	Threonine dehydratase, mitochondrial	Enzyme	2-Ketobutyric acid Ammonia L-Threonine Ammonium
P25379	CHA1 YCL064C	Catabolic L-serine/threonine dehydratase	Enzyme	2-Ketobutyric acid Ammonia L-Serine Pyruvic acid L-Threonine Ammonium hydron water 2-aminoprop-2-enoate
P33330	SER1 YOR184W	Phosphoserine aminotransferase	Enzyme	DL-O-Phosphoserine Oxoglutaric acid L-Glutamic acid O-Phospho-4-hydroxy-L-threonine 2-Oxo-3-hydroxy-4-phosphobutanoic acid Phosphohydroxypyruvic acid O-Phospho-L-serine
P48015	GCV1 YDR019C	Aminomethyltransferase, mitochondrial	Enzyme	Glycine Ammonia Tetrahydrofolic acid 5,10-Methenyltetrahydrofolic acid 5,10-Methylene-THF N5-Formyl-THF Ammonium water
P0CF21	SDL1 YIL167W	L-serine dehydratase	Enzyme	Ammonia L-Serine Pyruvic acid
P17423	THR1 YHR025W	Homoserine kinase	Enzyme	L-Homoserine Adenosine triphosphate O-Phosphohomoserine hydron ADP
P10869	HOM3 YER052C	Aspartokinase	Enzyme	L-aspartic 4-semialdehyde L-Homoserine Adenosine triphosphate 4-Phospho-L-aspartic acid NADPH NADP hydron L-Aspartic acid ADP
P08456	CHO1 YER026C	CDP-diacylglycerol--serine O-phosphatidyltransferase	Enzyme	L-Serine Cytidine monophosphate hydron
P42941	SER2 YGR208W	Phosphoserine phosphatase	Enzyme	DL-O-Phosphoserine L-Serine O-Phospho-L-serine water phosphate
P32582	CYS4 YGR155W	Cystathionine beta-synthase	Enzyme	L-Serine L-Cystathionine Homocysteine L-Homocysteine water
P00931	TRP5 YGL026C	Tryptophan synthase	Enzyme	L-Serine D-Glyceraldehyde 3-phosphate L-Tryptophan (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate 1-C-(indol-3-yl)glycerol 3-phosphate water Indole 1-C-(3-indolyl)-glycerol 3-phosphate
P16120	THR4 YCR053W	Threonine synthase	Enzyme	L-Threonine O-Phosphohomoserine O-Phospho-4-hydroxy-L-threonine 4-Hydroxy-L-threonine water phosphate
P31116	HOM6 YJR139C	Homoserine dehydrogenase	Enzyme	L-aspartic 4-semialdehyde L-Homoserine NAD NADH NAD(+) NADPH NADP hydron
P40054	SER3 YER081W	D-3-phosphoglycerate dehydrogenase 1	Enzyme	2-hydroxyglutaric acid NAD NADH Oxoglutaric acid 3-Phosphoglyceric acid Phosphohydroxypyruvic acid NAD(+) 3-phospho-D-glyceric acid hydron
P53095	DSD1 YGL196W	D-serine dehydratase	Enzyme	Ammonia Pyruvic acid D-Serine