You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.

5-Methylthioribulose 1-phosphate (YMDB00129)

Identification
YMDB IDYMDB00129
Name5-Methylthioribulose 1-phosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description5-Methylthioribulose 1-phosphate, also known as 1PMT-ribulose or 1-phospho-5-S-methylthioribulose, belongs to the class of organic compounds known as glycerone phosphates. These are organic compounds containing a glycerone moiety that carries a phosphate group at the O-1 or O-2 position. 5-Methylthioribulose 1-phosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). 5-Methylthioribulose 1-phosphate exists in all living species, ranging from bacteria to humans. Within yeast, 5-methylthioribulose 1-phosphate participates in a number of enzymatic reactions. In particular, 5-methylthioribulose 1-phosphate can be converted into 5-(methylthio)-2,3-dioxopentyl phosphate through the action of the enzyme methylthioribulose-1-phosphate dehydratase. In addition, 5-methylthioribulose 1-phosphate can be biosynthesized from 5-methylthioribose 1-phosphate through the action of the enzyme methylthioribose-1-phosphate isomerase. In yeast, 5-methylthioribulose 1-phosphate is involved in the metabolic pathway called the methionine metabolism and salvage pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 1-phospho-5-S-methylthioribulose
  • 1-phosphomethylthioribulose
  • 1PMT-ribulose
  • 5-methylthio-2-ribulose-1-phosphate
  • 5-Methylthio-5-deoxy-D-ribulose 1-phosphate
  • 5-methylthio-5-deoxy-D-ribulose-1-phosphate
  • 5-Methylthioribulose 1-phosphate
  • 5-Methylthioribulose 1-phosphic acid
  • 5-methylthioribulose-1-phosphate
  • 5-S-methyl-1-O-phosphono-5-thio-D-ribulose
  • 5-S-methyl-5-thio-D-erythro-pent-2-ulose 1-(dihydrogen phosphate)
  • 5-S-methyl-5-thio-D-ribulose 1-(dihydrogen phosphate)
  • methylthioribulose-1-phosphate
  • MTRu-1-P
  • S-Methyl-5-thio-D-ribulose 1-phosphate
  • 5-(Methylsulfanyl)-D-ribulose 1-phosphate
  • 5-(Methylsulfanyl)-D-ribulose 1-phosphoric acid
  • 5-(Methylsulphanyl)-D-ribulose 1-phosphate
  • 5-(Methylsulphanyl)-D-ribulose 1-phosphoric acid
  • 5-Methylthioribulose 1-phosphoric acid
  • 1-PMT-Ribulose
  • Methylthioribulose 1-phosphate
  • 5-(Methylthio)ribulose 1-phosphate
CAS number86316-83-8
WeightAverage: 260.202
Monoisotopic: 260.011959972
InChI KeyCNSJRYUMVMWNMC-RITPCOANSA-N
InChIInChI=1S/C6H13O7PS/c1-15-3-5(8)6(9)4(7)2-13-14(10,11)12/h5-6,8-9H,2-3H2,1H3,(H2,10,11,12)/t5-,6+/m1/s1
IUPAC Name{[(3R,4S)-3,4-dihydroxy-5-(methylsulfanyl)-2-oxopentyl]oxy}phosphonic acid
Traditional IUPAC Namemethylthioribulose-1-phosphate
Chemical FormulaC6H13O7PS
SMILES[H]O[C@@]([H])(C(=O)C([H])([H])OP(=O)(O[H])O[H])[C@]([H])(O[H])C([H])([H])SC([H])([H])[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as glycerone phosphates. These are organic compounds containing a glycerone moiety that carries a phosphate group at the O-1 or O-2 position.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbonyl compounds
Direct ParentGlycerone phosphates
Alternative Parents
Substituents
  • Glycerone phosphate
  • Monoalkyl phosphate
  • Acyloin
  • Beta-hydroxy ketone
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Alpha-hydroxy ketone
  • Secondary alcohol
  • 1,2-diol
  • Thioether
  • Sulfenyl compound
  • Dialkylthioether
  • Organosulfur compound
  • Alcohol
  • Organic oxide
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility19.3 g/LALOGPS
logP-0.43ALOGPS
logP-1.3ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)1.18ChemAxon
pKa (Strongest Basic)-3.4ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area124.29 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity53.31 m³·mol⁻¹ChemAxon
Polarizability22.59 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Methionine metabolism and salvagePW002384 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Cysteine and methionine metabolismec00270 Map00270
SMPDB Reactions
5-Methylthioribulose 1-phosphate → 5-(methylsulfanyl)-2,3-dioxopentyl phosphate + water
5-Methylthioribose 1-phosphate → 5-Methylthioribulose 1-phosphate
KEGG Reactions
5-Methylthioribulose 1-phosphate → 5-(methylsulfanyl)-2,3-dioxopentyl phosphate + water
S-Methyl-5-thio-alpha-D-ribose 1-phosphate ↔ 5-Methylthioribulose 1-phosphate
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-01w1-9710000000-da3fc8534da2cd8957f4JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-03di-7973000000-51639c96fd3e70d14bf8JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03dl-3590000000-48a371cabc865281cedbJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-01pc-3920000000-0f483ba04442297b4622JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000g-9300000000-6e02d97a8ab3c704f801JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-9310000000-4f7b1426b6d9f8a88ffaJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004j-9100000000-1e987229b4853fb45072JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-fe6a484561738ead9cd1JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-1590000000-1113571c4892aa6f836eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03ka-9400000000-da5dcbcf9b27c541867dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0002-9000000000-fec7f320592a6e9bc867JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4r-3490000000-1b9248527c15132ff9eeJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004j-9000000000-f420c16db721baadbf7cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-06c27ade5d32e8e9acdaJSpectraViewer
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
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
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
  • 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
  • Pirkov, I., Norbeck, J., Gustafsson, L., Albers, E. (2008). "A complete inventory of all enzymes in the eukaryotic methionine salvage pathway." FEBS J 275:4111-4120.18625006
Synthesis Reference:Imker, Heidi J.; Fedorov, Alexander A.; Fedorov, Elena V.; Almo, Steven C.; Gerlt, John A. Mechanistic Diversity in the RuBisCO Superfamily: The "Enolase" in the Methionine Salvage Pathway in Geobacillus kaustophilus. Biochemistry (2007), 46(13), 4
External Links:
ResourceLink
CHEBI ID28096
HMDB IDHMDB01299
Pubchem Compound ID329
Kegg IDC04582
ChemSpider ID152225
FOODB IDFDB022541
Wikipedia IDNot Available
BioCyc IDCPD-1063

Enzymes

Protein Details
1. Methylthioribulose-1-phosphate dehydratase
General function:
Involved in metal ion binding
Specific function:
Catalyzes the dehydration of methylthioribulose-1- phosphate (MTRu-1-P) into 2,3-diketo-5-methylthiopentyl-1- phosphate (DK-MTP-1-P)
Gene Name:
MDE1
Uniprot ID:
P47095
Molecular weight:
27426.59961
Reactions
S-methyl-5-thio-D-ribulose 1-phosphate → 5-(methylthio)-2,3-dioxopentyl phosphate + H(2)O.
Protein Details
2. Methylthioribose-1-phosphate isomerase
General function:
Involved in cellular metabolic process
Specific function:
Catalyzes the interconversion of methylthioribose-1- phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1- P)
Gene Name:
MRI1
Uniprot ID:
Q06489
Molecular weight:
45019.89844
Reactions
S-methyl-5-thio-alpha-D-ribose 1-phosphate → S-methyl-5-thio-D-ribulose 1-phosphate.