You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.
Identification
YMDB IDYMDB00112
NameL-Serine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionSerine (abbreviated as Ser or S) is an alpha-amino acid. The L-isomer is one of the 22 proteinogenic amino acids, i.e., the building blocks of proteins. It is classified as a polar amino acid, because of the hydrophilic nature of the alcohol side chain. Together with threonine, serine is one of two proteinogenic amino acids bearing an alcohol group. Serine is important in metabolism in that it participates in the biosynthesis of purines and pyrimidines. It is the precursor to several amino acids including glycine and cysteine, and tryptophan. It is also the precursor to numerous other metabolites, including sphingolipids and folate, which is the principal donor of one-carbon fragments in biosynthesis. Serine catabolism involves serine being converted to glycine and then glycine oxidation to CO2 and NH3, with the production of two equivalents of N5,N10-methyleneTHF. Serine can be catabolized back to the glycolytic intermediate, 3-phosphoglycerate, by a pathway that is essentially a reversal of serine biosynthesis. Serine can also be converted to pyruvate through a deamination reaction catalyzed by serine/threonine dehydratase.
Structure
Thumb
Synonyms
  • (-)-Serine
  • (S)-2-amino-3-hydroxy-Propanoate
  • (S)-2-amino-3-hydroxy-Propanoic acid
  • (S)-2-Amino-3-hydroxypropanoate
  • (S)-2-Amino-3-hydroxypropanoic acid
  • (S)-a-Amino-b-hydroxypropionate
  • (S)-a-Amino-b-hydroxypropionic acid
  • (S)-alpha-Amino-beta-hydroxypropionate
  • (S)-alpha-Amino-beta-hydroxypropionic acid
  • (S)-b-Amino-3-hydroxypropionate
  • (S)-b-Amino-3-hydroxypropionic acid
  • (S)-beta-Amino-3-hydroxypropionate
  • (S)-beta-Amino-3-hydroxypropionic acid
  • (S)-Serine
  • 2-Amino-3-hydroxypropanoate
  • 2-Amino-3-hydroxypropanoic acid
  • 3-hydroxy-L-Alanine
  • b-Hydroxy-L-alanine
  • beta-Hydroxy-L-alanine
  • beta-Hydroxyalanine
  • L-(-)-Serine
  • L-3-Hydroxy-2-aminopropionate
  • L-3-Hydroxy-2-aminopropionic acid
  • L-3-Hydroxy-alanine
  • L-Ser
  • Serine
  • (2S)-2-Amino-3-hydroxypropanoic acid
  • (S)-(-)-Serine
  • L-2-Amino-3-hydroxypropionic acid
  • L-Serin
  • S
  • Ser
  • (2S)-2-Amino-3-hydroxypropanoate
  • (S)-Α-amino-β-hydroxypropionate
  • (S)-Α-amino-β-hydroxypropionic acid
  • Β-hydroxy-L-alanine
  • b-Hydroxyalanine
  • Β-hydroxyalanine
  • L-2-Amino-3-hydroxypropionate
  • L Serine
CAS number56-45-1
WeightAverage: 105.0926
Monoisotopic: 105.042593095
InChI KeyMTCFGRXMJLQNBG-REOHCLBHSA-N
InChIInChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m0/s1
IUPAC Name(2S)-2-amino-3-hydroxypropanoic acid
Traditional IUPAC NameL-serine
Chemical FormulaC3H7NO3
SMILES[H]OC(=O)[C@@]([H])(N([H])[H])C([H])([H])O[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as serine and derivatives. Serine and derivatives are compounds containing serine or a derivative thereof resulting from reaction of serine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentSerine and derivatives
Alternative Parents
Substituents
  • Serine or derivatives
  • Alpha-amino acid
  • L-alpha-amino acid
  • Beta-hydroxy acid
  • Hydroxy acid
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Alcohol
  • Primary amine
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Primary aliphatic amine
  • Organic oxide
  • Organopnictogen compound
  • Carbonyl group
  • Organic oxygen compound
  • Amine
  • Organic nitrogen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting point228 °C
Experimental Properties
PropertyValueReference
Water Solubility425 mg/mL at 25 oC [YALKOWSKY,SH & DANNENFELSER,RM (1992)]PhysProp
LogP-3.07 [HANSCH,C ET AL. (1995)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility480 g/LALOGPS
logP-3.4ALOGPS
logP-3.9ChemAxon
logS0.66ALOGPS
pKa (Strongest Acidic)2.03ChemAxon
pKa (Strongest Basic)8.93ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area83.55 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity22.04 m³·mol⁻¹ChemAxon
Polarizability9.39 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • extracellular
  • mitochondrion
  • endoplasmic reticulum
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
glycine metabolismPW002398 ThumbThumb?image type=greyscaleThumb?image type=simple
serine metabolismPW002402 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Biosynthesis of unsaturated fatty acidsec01040 Map01040
Cyanoamino acid metabolismec00460 Map00460
Cysteine and methionine metabolismec00270 Map00270
Glycine, serine and threonine metabolismec00260 Map00260
Methane metabolismec00680 Map00680
SMPDB Reactions
Homocysteine + L-Serinewater + L-Cystathionine
DL-O-Phosphoserine + waterphosphate + L-Serine
L-Serine + Tetrahydrofolic acidwater + Glycine + 5,10-Methylene-THF
L-Serine + Tetrahydrofolic acidwater + Glycine + 5,10-Methylene-THF
L-Serinewater + hydron + 2-aminoprop-2-enoate
KEGG Reactions
L-Homocysteine + L-SerineL-Cystathionine + water
L-Serine + 5,6,7,8-Tetrahydrofolic acidGlycine + water + 5,10-Methylene-THF
L-SerinePyruvic acid + Ammonium
NADP + L-SerineNADPH + hydron + L-3-Oxoalanine
L-Serine + CDP-diacylglycerol ↔ Cytidine monophosphate + PC(14:0/16:0) + hydron
Concentrations
Intracellular Concentrations
Intracellular ConcentrationSubstrateGrowth ConditionsStrainCitation
3123 ± 62 µM YPD mediaaerobicBaker's yeastPMID: 7654310
1073 ± 21 µM YPG mediaaerobicBaker's yeastPMID: 7654310
488 ± 10 µM SD mediaaerobicBaker's yeastPMID: 7654310
293 ± 6 µM SG mediaaerobicBaker's yeastPMID: 7654310
1952 ± 39 µM M (molasses)aerobicBaker's yeastPMID: 7654310
5758 ± 115 µM MA (molasses)aerobicBaker's yeastPMID: 7654310
2147 ± 43 µM MB (molasses)aerobicBaker's yeastPMID: 7654310
5172 ± 104 µM MAB (molasses)aerobicBaker's yeastPMID: 7654310
1828 ± 91 µM YEB media with 0.5 mM glucoseaerobicBaker's yeastExperimentally Determined
Not Available
2290 ± 577 µM Synthetic medium with 20 g/L glucoseaerobicBaker's yeastPMID: 12584756
Conversion Details Here
Extracellular ConcentrationsNot Available
Spectra
Spectra
References
References:
  • Martinez-Force, E., Benitez, T. (1995). "Effects of varying media, temperature, and growth rates on the intracellular concentrations of yeast amino acids." Biotechnol Prog 11:386-392.7654310
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Wiebers, J. L., Garner, H. R. (1967). "Acyl derivatives of homoserine as substrates for homocysteine synthesis in Neurospora crassa, yeast, and Escherichia coli." J Biol Chem 242:5644-5649.12325384
  • Cherest, H., Eichler, F., Robichon-Szulmajster, H. (1969). "Genetic and regulatory aspects of methionine biosynthesis in Saccharomyces cerevisiae." J Bacteriol 97:328-336.5764336
  • Takada, Y., Noguchi, T. (1985). "Characteristics of alanine: glyoxylate aminotransferase from Saccharomyces cerevisiae, a regulatory enzyme in the glyoxylate pathway of glycine and serine biosynthesis from tricarboxylic acid-cycle intermediates." Biochem J 231:157-163.3933486
  • Hans, M. A., Heinzle, E., Wittmann, C. (2003). "Free intracellular amino acid pools during autonomous oscillations in Saccharomyces cerevisiae." Biotechnol Bioeng 82:143-151.12584756
  • Nookaew, I., Jewett, M. C., Meechai, A., Thammarongtham, C., Laoteng, K., Cheevadhanarak, S., Nielsen, J., Bhumiratana, S. (2008). "The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism." BMC Syst Biol 2:71.18687109
  • Jhee, K. H., McPhie, P., Miles, E. W. (2000). "Yeast cystathionine beta-synthase is a pyridoxal phosphate enzyme but, unlike the human enzyme, is not a heme protein." J Biol Chem 275:11541-11544.10766767
  • McNeil, J. B., Bognar, A. L., Pearlman, R. E. (1996). "In vivo analysis of folate coenzymes and their compartmentation in Saccharomyces cerevisiae." Genetics 142:371-381.8852837
  • Fujisawa, H., Nagata, S., Misono, H. (2003). "Characterization of short-chain dehydrogenase/reductase homologues of Escherichia coli (YdfG) and Saccharomyces cerevisiae (YMR226C)." Biochim Biophys Acta 1645:89-94.12535615
  • Melcher, K., Entian, K. D. (1992). "Genetic analysis of serine biosynthesis and glucose repression in yeast." Curr Genet 21:295-300.1326413
  • Yamashita, S., Nikawa, J. (1997). "Phosphatidylserine synthase from yeast." Biochim Biophys Acta 1348:228-235.9370337
  • Cowart, L. A., Hannun, Y. A. (2005). "Using genomic and lipidomic strategies to investigate sphingolipid function in the yeast heat-stress response." Biochem Soc Trans 33:1166-1169.16246073
  • Obeid, L. M., Okamoto, Y., Mao, C. (2002). "Yeast sphingolipids: metabolism and biology." Biochim Biophys Acta 1585:163-171.12531550
  • Castrillo, J. I., Zeef, L. A., Hoyle, D. C., Zhang, N., Hayes, A., Gardner, D. C., Cornell, M. J., Petty, J., Hakes, L., Wardleworth, L., Rash, B., Brown, M., Dunn, W. B., Broadhurst, D., O'Donoghue, K., Hester, S. S., Dunkley, T. P., Hart, S. R., Swainston, N., Li, P., Gaskell, S. J., Paton, N. W., Lilley, K. S., Kell, D. B., Oliver, S. G. (2007). "Growth control of the eukaryote cell: a systems biology study in yeast." J Biol 6:4.17439666
Synthesis Reference:Qin, Wei-min; Cao, Fei; Zhou, Hua; Li, Zhen-jiang; Wei, Ping. Asymmetric synthesis of D- and L-serine with "Glycine equivalent" method. Huaxue Shiji (2005), 27(11), 643-644, 670.
External Links:
ResourceLink
CHEBI ID17115
HMDB IDHMDB00187
Pubchem Compound ID5951
Kegg IDC00065
ChemSpider ID5736
FOODB IDFDB012739
WikipediaSerine
BioCyc IDSER

Enzymes

General function:
Involved in catalytic activity
Specific function:
Interconversion of serine and glycine
Gene Name:
SHM2
Uniprot ID:
P37291
Molecular weight:
52218.0
Reactions
5,10-methylenetetrahydrofolate + glycine + H(2)O → tetrahydrofolate + L-serine.
General function:
Involved in catalytic activity
Specific function:
Interconversion of serine and glycine
Gene Name:
SHM1
Uniprot ID:
P37292
Molecular weight:
53686.0
Reactions
5,10-methylenetetrahydrofolate + glycine + H(2)O → tetrahydrofolate + L-serine.
General function:
Involved in transferase activity, transferring nitrogenous groups
Specific function:
Component of serine palmitoyltransferase (SPT), which catalyzes the committed step in the synthesis of sphingolipids, the condensation of serine with palmitoyl CoA to form the long chain base 3-ketosphinganine
Gene Name:
LCB1
Uniprot ID:
P25045
Molecular weight:
62206.60156
Reactions
Palmitoyl-CoA + L-serine → CoA + 3-dehydro-D-sphinganine + CO(2).
General function:
Involved in transferase activity
Specific function:
Catalytic subunit of serine palmitoyltransferase (SPT), which catalyzes the committed step in the synthesis of sphingolipids, the condensation of serine with palmitoyl CoA to form the long chain base 3-ketosphinganine
Gene Name:
LCB2
Uniprot ID:
P40970
Molecular weight:
63110.19922
Reactions
Palmitoyl-CoA + L-serine → CoA + 3-dehydro-D-sphinganine + CO(2).
General function:
Involved in catalytic activity
Specific function:
L-serine = pyruvate + NH(3)
Gene Name:
CHA1
Uniprot ID:
P25379
Molecular weight:
39301.0
Reactions
L-serine → pyruvate + NH(3).
L-threonine → 2-oxobutanoate + NH(3).
General function:
Involved in catalytic activity
Specific function:
L-serine = pyruvate + NH(3)
Gene Name:
SDL1
Uniprot ID:
P0CF21
Molecular weight:
13942.90039
Reactions
L-serine → pyruvate + NH(3).
General function:
Involved in nucleotide binding
Specific function:
Catalyzes the attachment of serine to tRNA(Ser). Is also probably able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec)
Gene Name:
SES1
Uniprot ID:
P07284
Molecular weight:
53309.19922
Reactions
ATP + L-serine + tRNA(Ser) → AMP + diphosphate + L-seryl-tRNA(Ser).
ATP + L-serine + tRNA(Sec) → AMP + diphosphate + L-seryl-tRNA(Sec).
General function:
Involved in nucleotide binding
Specific function:
Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec)
Gene Name:
DIA4
Uniprot ID:
P38705
Molecular weight:
50389.5
Reactions
ATP + L-serine + tRNA(Ser) → AMP + diphosphate + L-seryl-tRNA(Ser).
ATP + L-serine + tRNA(Sec) → AMP + diphosphate + L-seryl-tRNA(Sec).
General function:
Involved in oxidoreductase activity
Specific function:
Not Available
Gene Name:
Not Available
Uniprot ID:
Q05016
Molecular weight:
29158.09961
Reactions
L-serine + NADP+ → 2-ammoniomalonate semialdehyde + NADPH + H+
General function:
Involved in CDP-diacylglycerol-serine O-phosphatidyltransferase activity
Specific function:
CDP-diacylglycerol + L-serine = CMP + (3-sn- phosphatidyl)-L-serine
Gene Name:
CHO1
Uniprot ID:
P08456
Molecular weight:
30804.19922
Reactions
CDP-diacylglycerol + L-serine → CMP + (3-sn-phosphatidyl)-L-serine.
General function:
Involved in catalytic activity
Specific function:
O-phospho-L(or D)-serine + H(2)O = L(or D)- serine + phosphate
Gene Name:
SER2
Uniprot ID:
P42941
Molecular weight:
34207.0
Reactions
O-phospho-L(or D)-serine + H(2)O → L(or D)-serine + phosphate.
General function:
Involved in cysteine biosynthetic process from serine
Specific function:
L-serine + L-homocysteine = L-cystathionine + H(2)O
Gene Name:
CYS4
Uniprot ID:
P32582
Molecular weight:
56021.30078
Reactions
L-serine + L-homocysteine → L-cystathionine + H(2)O.
General function:
Involved in catalytic activity
Specific function:
L-serine + 1-C-(indol-3-yl)glycerol 3- phosphate = L-tryptophan + glyceraldehyde 3-phosphate + H(2)O
Gene Name:
TRP5
Uniprot ID:
P00931
Molecular weight:
76625.5
Reactions
L-serine + 1-C-(indol-3-yl)glycerol 3-phosphate → L-tryptophan + glyceraldehyde 3-phosphate + H(2)O.

Transporters

General function:
Involved in transport
Specific function:
Permease for various amino acids as well as for GABA. Can also transport L-cysteine and beta-alanine
Gene Name:
GAP1
Uniprot ID:
P19145
Molecular weight:
65654.89844
General function:
Involved in transport
Specific function:
High affinity transport of glutamine. Also transport Leu, Ser, Thr, Cys, Met and Asn
Gene Name:
GNP1
Uniprot ID:
P48813
Molecular weight:
73597.39844
General function:
Involved in transport
Specific function:
Can transport glutamate, aspartate, glutamine, asparagine, serine, alanine and glycine
Gene Name:
DIP5
Uniprot ID:
P53388
Molecular weight:
68096.70313
General function:
Involved in transport
Specific function:
Broad substrate range permease which transports asparagine and glutamine with intermediate specificity. Also transports Ala, Cys, Gly, Ile, Leu, Met, Phe, Ser, Thr, Tyr and Val. Important for the utilization of amino acids as a nitrogen source
Gene Name:
AGP1
Uniprot ID:
P25376
Molecular weight:
69670.70313
General function:
Involved in transport
Specific function:
General amino acid permease with broad substrate specificity
Gene Name:
AGP3
Uniprot ID:
P43548
Molecular weight:
61051.19922