Tetrahydrofolic acid (YMDB00139)

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Identification

YMDB ID

YMDB00139

Name

Tetrahydrofolic acid

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

Tetrahydrofolic acid, also known as tetrahydrofolate, belongs to the class of organic compounds known as xanthines. These are purine derivatives with a ketone group conjugated at carbons 2 and 6 of the purine moiety. Tetrahydrofolic acid is a moderately basic compound (based on its pKa). Tetrahydrofolic acid exists in all eukaryotes, ranging from yeast to humans. Within yeast, tetrahydrofolic acid participates in a number of enzymatic reactions. In particular, L-serine and tetrahydrofolic acid can be converted into glycine and 5,10-methylene-THF; which is catalyzed by the enzyme serine hydroxymethyltransferase, mitochondrial. In addition, L-serine and tetrahydrofolic acid can be converted into glycine and 5,10-methylene-THF; which is catalyzed by the enzyme serine hydroxymethyltransferase. In yeast, tetrahydrofolic acid is involved in the metabolic pathway called the serine metabolism pathway.

Structure

MOL SDF PDB SMILES InChI

Synonyms

(6S)-Tetrahydrofolate
(6S)-Tetrahydrofolic acid
5,6,7,8-Tetrahydrofolate
5,6,7,8-tetrahydrofolic acid
tetra-H-folate
tetrahydrafolate
Tetrahydrofolate
tetrahydrofolic acid
tetrahydropteroyl mono-L-glutamate
tetrahydropteroylglutamate

CAS number

135-16-0

Weight

Average: 445.4292
Monoisotopic: 445.170981503

InChI Key

MSTNYGQPCMXVAQ-UHFFFAOYSA-N

InChI

InChI=1S/C19H23N7O6/c20-19-25-15-14(17(30)26-19)23-11(8-22-15)7-21-10-3-1-9(2-4-10)16(29)24-12(18(31)32)5-6-13(27)28/h1-4,11-12,21,23H,5-8H2,(H,24,29)(H,27,28)(H,31,32)(H4,20,22,25,26,30)

IUPAC Name

2-{[4-({[(6S)-4-hydroxy-2-imino-1,2,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]formamido}pentanedioic acid

Traditional IUPAC Name

2-{[4-({[(6S)-4-hydroxy-2-imino-5,6,7,8-tetrahydro-1H-pteridin-6-yl]methyl}amino)phenyl]formamido}pentanedioic acid

Chemical Formula

C₁₉H₂₃N₇O₆

SMILES

[H]OC(=O)C([H])([H])C([H])([H])C([H])(N([H])C(=O)C1=C([H])C([H])=C(N([H])C([H])([H])C2([H])N([H])C3=C(N([H])C(=N[H])N([H])C3=O)N([H])C2([H])[H])C([H])=C1[H])C(=O)O[H]

Chemical Taxonomy

Description

belongs to the class of organic compounds known as xanthines. These are purine derivatives with a ketone group conjugated at carbons 2 and 6 of the purine moiety.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Imidazopyrimidines

Sub Class

Purines and purine derivatives

Direct Parent

Xanthines

Alternative Parents

Substituents

Xanthine
Purinone
6-oxopurine
Alkaloid or derivatives
Pyrimidone
Pyrimidine
N-substituted imidazole
Heteroaromatic compound
Vinylogous amide
Imidazole
Azole
Urea
Lactam
Azacycle
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

purine alkaloid (CHEBI:27732 )
trimethylxanthine (CHEBI:27732 )
Purine alkaloids (C07481 )
a small molecule (1-3-7-TRIMETHYLXANTHINE )

Physical Properties

State

Solid

Charge

Melting point

250 °C

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	Not Available	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	0.27 g/L	ALOGPS
logP	-0.96	ALOGPS
logP	-3.6	ChemAxon
logS	-3.2	ALOGPS
pKa (Strongest Acidic)	2.04	ChemAxon
pKa (Strongest Basic)	5.76	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	208.26 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	132.4 m³·mol⁻¹	ChemAxon
Polarizability	44.57 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

Mitochondrion

Organoleptic Properties

Not Available

SMPDB Pathways

One Carbon Pool by Folate I	PW002468
Pantothenate and CoA biosynthesis	PW002463
glycine metabolism	PW002398
purine nucleotides de novo biosynthesis	PW002478
serine metabolism	PW002402

KEGG Pathways

Folate biosynthesis	ec00790
Glycine, serine and threonine metabolism	ec00260
Methane metabolism	ec00680
One carbon pool by folate	ec00670
Pantothenate and CoA biosynthesis	ec00770

SMPDB Reactions

L-Serine + Tetrahydrofolic acid → water + Glycine + 5,10-Methylene-THF

Glycine + Tetrahydrofolic acid → Ammonium + 5,10-Methylene-THF

S-Aminomethyldihydrolipoylprotein; + Tetrahydrofolic acid ↔ 5,10-Methylene-THF + Ammonia + dihydrolipoylprotein

N10-Formyl-THF + ADP + phosphate → Adenosine triphosphate + Formic acid + Tetrahydrofolic acid

KEGG Reactions

Not Available

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0uka-4676900000-780e78301e85c240ab73	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-006x-1311190000-af98cc8be4da08f9b782	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0002-7796610000-0937514a7f23431b726e	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-0nor-3269210000-20105ed6a7a6e24e2441	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-00kr-1935200000-a9449c19c1ae3b0d70da	JSpectraViewer \| MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0032-0431900000-ff1f3948e47561161293	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001i-0952300000-ed9d84bc39d490f6210e	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-001i-0920000000-0d0efcb6c323340d20b9	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0006-0001900000-abb4cec0eb79b0bd2de1	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0v4l-2356900000-2fd17d2f587bbd5e882c	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9441000000-8c630c7a3633467d6bb3	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0002-0080900000-73480c24ce118e5e02f3	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-0491100000-0b5df4d0f168f8f15275	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0089-0962000000-9a988cf519f340f5d7cf	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-005c-0002900000-9587282a39f915386f95	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0zi3-2807900000-28355749389d1e225f7b	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0udi-3911000000-e7b1ccb0c9f2d7c8269a	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
2D NMR	[1H,1H] 2D NMR Spectrum	Not Available	JSpectraViewer
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	JSpectraViewer

References

References:

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
RAMASASTRI, B. V., BLAKLEY, R. L. (1964). "5,10-METHYLENETETRAHYDROFOLIC DEHYDROGENASE FROM BAKERS' YEAST. II. USE IN ASSAY OF TETRAHYDROFOLIC ACID." J Biol Chem 239:106-111.14114828
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

Synthesis Reference:

Not Available

External Links:

Resource	Link
CHEBI ID	15635
HMDB ID	HMDB01846
Pubchem Compound ID	1129
Kegg ID	C00101
ChemSpider ID	1097
FOODB ID	FDB022705
Wikipedia	Tetrahydrofolic_acid
BioCyc ID	THF

Enzymes

Protein Details

1. Phosphoribosylglycinamide formyltransferase

General function:: Involved in hydroxymethyl-, formyl- and related transferase activity
Specific function:: 10-formyltetrahydrofolate + N(1)-(5-phospho-D- ribosyl)glycinamide = tetrahydrofolate + N(2)-formyl-N(1)-(5- phospho-D-ribosyl)glycinamide
Gene Name:: ADE8
Uniprot ID:: P04161
Molecular weight:: 23540.0

Reactions

10-formyltetrahydrofolate + N(1)-(5-phospho-D-ribosyl)glycinamide → tetrahydrofolate + N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide.

Protein Details

2. Serine hydroxymethyltransferase, cytosolic

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.

Protein Details

3. Serine hydroxymethyltransferase, mitochondrial

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.

Protein Details

4. Phosphoribosylaminoimidazole carboxylase

General function:: Involved in phosphoribosylaminoimidazole carboxylase activity
Specific function:: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4- carboxylate = 5-amino-1-(5-phospho-D-ribosyl)imidazole + CO(2)
Gene Name:: ADE2
Uniprot ID:: P21264
Molecular weight:: 62338.69922

Reactions

5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate → 5-amino-1-(5-phospho-D-ribosyl)imidazole + CO(2).

Protein Details

5. Dihydrofolate reductase

General function:: Involved in dihydrofolate reductase activity
Specific function:: Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis
Gene Name:: DFR1
Uniprot ID:: P07807
Molecular weight:: 24260.80078

Reactions

5,6,7,8-tetrahydrofolate + NADP(+) → 7,8-dihydrofolate + NADPH.

Protein Details

6. C-1-tetrahydrofolate synthase, mitochondrial

General function:: Involved in formate-tetrahydrofolate ligase activity
Specific function:: 5,10-methylenetetrahydrofolate + NADP(+) = 5,10-methenyltetrahydrofolate + NADPH
Gene Name:: MIS1
Uniprot ID:: P09440
Molecular weight:: 106216.0

Reactions

5,10-methylenetetrahydrofolate + NADP(+) → 5,10-methenyltetrahydrofolate + NADPH.
5,10-methenyltetrahydrofolate + H(2)O → 10-formyltetrahydrofolate.
ATP + formate + tetrahydrofolate → ADP + phosphate + 10-formyltetrahydrofolate.

Protein Details

7. Bifunctional purine biosynthesis protein ADE17

General function:: Involved in IMP cyclohydrolase activity
Specific function:: 10-formyltetrahydrofolate + 5-amino-1-(5- phospho-D-ribosyl)imidazole-4-carboxamide = tetrahydrofolate + 5- formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide
Gene Name:: ADE17
Uniprot ID:: P38009
Molecular weight:: 65262.60156

Reactions

10-formyltetrahydrofolate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide → tetrahydrofolate + 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide.
IMP + H(2)O → 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide.

Protein Details

8. Bifunctional purine biosynthesis protein ADE16

General function:: Involved in IMP cyclohydrolase activity
Specific function:: 10-formyltetrahydrofolate + 5-amino-1-(5- phospho-D-ribosyl)imidazole-4-carboxamide = tetrahydrofolate + 5- formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide
Gene Name:: ADE16
Uniprot ID:: P54113
Molecular weight:: 65281.80078

Reactions

10-formyltetrahydrofolate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide → tetrahydrofolate + 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide.
IMP + H(2)O → 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide.

Protein Details

9. Methionyl-tRNA formyltransferase, mitochondrial

General function:: Involved in methionyl-tRNA formyltransferase activity
Specific function:: Formylates methionyl-tRNA in mitochondria
Gene Name:: FMT1
Uniprot ID:: P32785
Molecular weight:: 44616.19922

Reactions

10-formyltetrahydrofolate + L-methionyl-tRNA(fMet) + H(2)O → tetrahydrofolate + N-formylmethionyl-tRNA(fMet).

Protein Details

10. C-1-tetrahydrofolate synthase, cytoplasmic

General function:: Involved in formate-tetrahydrofolate ligase activity
Specific function:: 5,10-methylenetetrahydrofolate + NADP(+) = 5,10-methenyltetrahydrofolate + NADPH
Gene Name:: ADE3
Uniprot ID:: P07245
Molecular weight:: 102204.0

Reactions

5,10-methylenetetrahydrofolate + NADP(+) → 5,10-methenyltetrahydrofolate + NADPH.
5,10-methenyltetrahydrofolate + H(2)O → 10-formyltetrahydrofolate.
ATP + formate + tetrahydrofolate → ADP + phosphate + 10-formyltetrahydrofolate.

Protein Details

11. Aminomethyltransferase, mitochondrial

General function:: Involved in aminomethyltransferase activity
Specific function:: The glycine cleavage system (glycine decarboxylase complex) catalyzes the degradation of glycine
Gene Name:: GCV1
Uniprot ID:: P48015
Molecular weight:: 44468.69922

Reactions

[Protein]-S(8)-aminomethyldihydrolipoyllysine + tetrahydrofolate → [protein]-dihydrolipoyllysine + 5,10-methylenetetrahydrofolate + NH(3).

Protein Details

12. 3-methyl-2-oxobutanoate hydroxymethyltransferase

General function:: Involved in 3-methyl-2-oxobutanoate hydroxymethyltransferase activity
Specific function:: 5,10-methylenetetrahydrofolate + 3-methyl-2- oxobutanoate + H(2)O = tetrahydrofolate + 2-dehydropantoate
Gene Name:: ECM31
Uniprot ID:: P38122
Molecular weight:: 34464.69922

Reactions

5,10-methylenetetrahydrofolate + 3-methyl-2-oxobutanoate + H(2)O → tetrahydrofolate + 2-dehydropantoate.

Structure for #<Compound:0xb18a6504>

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