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5,10-Methylene-THF (YMDB00260)

Identification
YMDB IDYMDB00260
Name5,10-Methylene-THF
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description5,10-Methylene-THF, also known as CH2H4folate, belongs to the class of organic compounds known as tetrahydrofolic acids. These are heterocyclic compounds based on the 5,6,7,8-tetrahydropteroic acid skeleton conjugated with at least one L-glutamic acid unit. 5,10-Methylene-THF is a strong basic compound (based on its pKa). 5,10-Methylene-THF exists in all eukaryotes, ranging from yeast to humans. Within yeast, 5,10-methylene-THF participates in a number of enzymatic reactions. In particular, glycine and 5,10-methylene-THF can be biosynthesized from L-serine and tetrahydrofolic acid through the action of the enzyme serine hydroxymethyltransferase, mitochondrial. In addition, glycine and 5,10-methylene-THF can be biosynthesized from L-serine and tetrahydrofolic acid through the action of the enzyme serine hydroxymethyltransferase. In yeast, 5,10-methylene-THF is involved in the metabolic pathway called the serine metabolism pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • (6R)-5,10-methylenetetrahydrofolate
  • 5,10-Methenyltetrahydropteroylglutamate
  • 5,10-Methylene-6-Hydrofolate
  • 5,10-Methylene-6-Hydrofolic acid
  • 5,10-methylene-THF
  • 5,10-Methylenetetrahydrofolate
  • 5,10-Methylenetetrahydrofolic acid
  • N5>,N10-methylenetetrahydrofolate
  • (6R)-5,10-Methylenetetrahydrofolic acid
  • 5,10-Methylene-5,6,7,8-tetrahydrofolate
  • Tetrahydromethylenefolate
  • 5,10-Methylenetetrahydrofolate, (D-glu)-isomer
  • CH2H4Folate
  • 5,10-Methylenetetrahydrofolate monohydrochloride, (L-glu)-isomer
  • 5,10-Methylenetetrahydrofolate, (L-glu)-(S)-isomer
CAS number31690-11-6
WeightAverage: 457.4399
Monoisotopic: 457.170981503
InChI KeyQYNUQALWYRSVHF-PZORYLMUSA-N
InChIInChI=1S/C20H23N7O6/c21-20-24-16-15(18(31)25-20)27-9-26(8-12(27)7-22-16)11-3-1-10(2-4-11)17(30)23-13(19(32)33)5-6-14(28)29/h1-4,12-13H,5-9H2,(H,23,30)(H,28,29)(H,32,33)(H4,21,22,24,25,31)/t12-,13?/m1/s1
IUPAC Name2-({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
Traditional IUPAC Name2-({4-[(6aR)-1-hydroxy-3-imino-4H,5H,6H,6aH,7H,9H-imidazo[1,5-f]pteridin-8-yl]phenyl}formamido)pentanedioic acid
Chemical FormulaC20H23N7O6
SMILES[H]OC(=O)C([H])([H])C([H])([H])C([H])(N([H])C(=O)C1=C([H])C([H])=C(C([H])=C1[H])N1C([H])([H])N2C3=C(N=C(N([H])[H])N([H])C3=O)N([H])C([H])([H])[C@]2([H])C1([H])[H])C(=O)O[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as tetrahydrofolic acids. These are heterocyclic compounds based on the 5,6,7,8-tetrahydropteroic acid skeleton conjugated with at least one L-glutamic acid unit.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPteridines and derivatives
Sub ClassPterins and derivatives
Direct ParentTetrahydrofolic acids
Alternative Parents
Substituents
  • Tetrahydrofolic acid
  • Glutamic acid or derivatives
  • N-acyl-alpha amino acid or derivatives
  • N-acyl-alpha-amino acid
  • Hippuric acid
  • Hippuric acid or derivatives
  • Phenylimidazolidine
  • Alpha-amino acid or derivatives
  • Benzamide
  • Benzoic acid or derivatives
  • Imidazopyrazine
  • Benzoyl
  • Dialkylarylamine
  • Aniline or substituted anilines
  • Pyrimidone
  • Aminopyrimidine
  • Secondary aliphatic/aromatic amine
  • Benzenoid
  • Pyrimidine
  • Monocyclic benzene moiety
  • Dicarboxylic acid or derivatives
  • Heteroaromatic compound
  • Vinylogous amide
  • Imidazolidine
  • Secondary carboxylic acid amide
  • Amino acid or derivatives
  • Amino acid
  • Carboxamide group
  • Secondary amine
  • Azacycle
  • Carboxylic acid
  • Carboxylic acid derivative
  • Primary amine
  • Organic nitrogen compound
  • Carbonyl group
  • Hydrocarbon derivative
  • Amine
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.82 g/LALOGPS
logP-0.94ALOGPS
logP-2.6ChemAxon
logS-2.8ALOGPS
pKa (Strongest Acidic)3.01ChemAxon
pKa (Strongest Basic)5.61ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area190.68 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity134.77 m³·mol⁻¹ChemAxon
Polarizability46.12 ųChemAxon
Number of Rings4ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • mitochondrion
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
One Carbon Pool by Folate IPW002468 ThumbThumb?image type=greyscaleThumb?image type=simple
Pantothenate and CoA biosynthesisPW002463 ThumbThumb?image type=greyscaleThumb?image type=simple
glycine metabolismPW002398 ThumbThumb?image type=greyscaleThumb?image type=simple
serine metabolismPW002402 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Glycine, serine and threonine metabolismec00260 Map00260
Methane metabolismec00680 Map00680
One carbon pool by folateec00670 Map00670
Pantothenate and CoA biosynthesisec00770 Map00770
SMPDB Reactions
L-Serine + Tetrahydrofolic acid → water + Glycine + 5,10-Methylene-THF
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
5,10-Methylene-THF + NADP → 5,10-Methenyltetrahydrofolic acid + NADPH
KEGG Reactions
Alpha-Ketoisovaleric acid + water + 5,10-Methylene-THF → 2-Dehydropantoic acid + 5,6,7,8-Tetrahydrofolic acid
5,10-Methylene-THF + NADPH + hydron → NADP + 5-Methyltetrahydrofolic acid
NAD + Glycine + 5,6,7,8-Tetrahydrofolic acid → NADH + Carbon dioxide + 5,10-Methylene-THF + Ammonium
L-Serine + 5,6,7,8-Tetrahydrofolic acid ↔ Glycine + water + 5,10-Methylene-THF
5,6,7,8-Tetrahydrofolic acid + hydron + S(8)-aminomethyldihydrolipoylprotein → dihydrolipoylprotein + 5,10-Methylene-THF + Ammonium
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-03di-1635900000-4b2ed6618451a7e931b1JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-001i-2129050000-80e96fb3203322200945JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-08fu-0003900000-ce1f75a98c0216d169e2JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-0229400000-c8c29bf14ef80a73f864JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-02u3-1192000000-ab556f50884c7b4fdcbeJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0001900000-6ba3ddeb1f652fdc6b6bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-08fr-1225900000-82b75909f87dfeb54211JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9553000000-5aca24c246430955de51JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0bt9-0006900000-dd6e195db40930799024JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-0109200000-aa6336e6c1c41c98d390JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-01q9-1695000000-8b9546bbad524392a35bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000f-0009800000-1ef964ba403eb61f6bf0JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01w3-1407900000-f4b4d0db119b458049fbJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0udl-5935200000-5fa8390660d5a558ac8bJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • 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
  • 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
Synthesis Reference:Agrawal, Nitish; Mihai, Cornelia; Kohen, Amnon. Microscale synthesis of isotopically labeled R-[6-xH]N5,N10-methylene-5,6,7,8-tetrahydrofolate as a cofactor for thymidylate synthase. Analytical Biochemistry (2004), 328(1), 44-50.
External Links:
ResourceLink
CHEBI ID15636
HMDB IDHMDB01533
Pubchem Compound ID439175
Kegg IDC00143
ChemSpider ID388320
FOODB IDFDB022675
Wikipedia5,10-methylenetetrahydrofolate
BioCyc IDMETHYLENE-THF

Enzymes

Protein Details
1. 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
2. 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
3. Thymidylate synthase
General function:
Involved in thymidylate synthase activity
Specific function:
Required for both nuclear and mitochondrial DNA synthesis
Gene Name:
TMP1
Uniprot ID:
P06785
Molecular weight:
35046.89844
Reactions
5,10-methylenetetrahydrofolate + dUMP → dihydrofolate + dTMP.
Protein Details
4. 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
5. 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
6. 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
7. 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.
Protein Details
8. Methylenetetrahydrofolate dehydrogenase [NAD+]
General function:
Involved in binding
Specific function:
Catalyzes oxidation of cytoplasmic one-carbon units for purine biosynthesis
Gene Name:
MTD1
Uniprot ID:
Q02046
Molecular weight:
36239.30078
Reactions
5,10-methylenetetrahydrofolate + NAD(+) → 5,10-methenyltetrahydrofolate + NADH.
Protein Details
9. Methylenetetrahydrofolate reductase 1
General function:
Involved in methylenetetrahydrofolate reductase (NADPH) activity
Specific function:
5-methyltetrahydrofolate + NAD(P)(+) = 5,10- methylenetetrahydrofolate + NAD(P)H
Gene Name:
MET12
Uniprot ID:
P46151
Molecular weight:
73940.79688
Reactions
5-methyltetrahydrofolate + NAD(P)(+) → 5,10-methylenetetrahydrofolate + NAD(P)H.
Protein Details
10. Methylenetetrahydrofolate reductase 2
General function:
Involved in methylenetetrahydrofolate reductase (NADPH) activity
Specific function:
5-methyltetrahydrofolate + NAD(P)(+) = 5,10- methylenetetrahydrofolate + NAD(P)H
Gene Name:
MET13
Uniprot ID:
P53128
Molecular weight:
68559.5
Reactions
5-methyltetrahydrofolate + NAD(P)(+) → 5,10-methylenetetrahydrofolate + NAD(P)H.