5-Methylthioribulose 1-phosphate (YMDB00129)

Identification

YMDB ID

YMDB00129

Name

5-Methylthioribulose 1-phosphate

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

5-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

MOL SDF PDB SMILES InChI

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 number

86316-83-8

Weight

Average: 260.202
Monoisotopic: 260.011959972

InChI Key

CNSJRYUMVMWNMC-RITPCOANSA-N

InChI

InChI=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 Name

methylthioribulose-1-phosphate

Chemical Formula

C₆H₁₃O₇PS

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.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Glycerone 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 Framework

Aliphatic acyclic compounds

External Descriptors

deoxyribulose phosphate (CHEBI:28096 )

Physical Properties

State

Solid

Charge

Melting point

Not Available

Experimental Properties

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

Predicted Properties

Property	Value	Source
Water Solubility	19.3 g/L	ALOGPS
logP	-0.43	ALOGPS
logP	-1.3	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	1.18	ChemAxon
pKa (Strongest Basic)	-3.4	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	124.29 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	53.31 m³·mol⁻¹	ChemAxon
Polarizability	22.59 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

cytoplasm

Organoleptic Properties

Not Available

SMPDB Pathways

Methionine metabolism and salvage

PW002384

KEGG Pathways

Cysteine and methionine metabolism

ec00270

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 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	splash10-01w1-9710000000-da3fc8534da2cd8957f4	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-03di-7973000000-51639c96fd3e70d14bf8	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03dl-3590000000-48a371cabc865281cedb	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-01pc-3920000000-0f483ba04442297b4622	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000g-9300000000-6e02d97a8ab3c704f801	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-9310000000-4f7b1426b6d9f8a88ffa	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004j-9100000000-1e987229b4853fb45072	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-fe6a484561738ead9cd1	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-1590000000-1113571c4892aa6f836e	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03ka-9400000000-da5dcbcf9b27c541867d	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0002-9000000000-fec7f320592a6e9bc867	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a4r-3490000000-1b9248527c15132ff9ee	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004j-9000000000-f420c16db721baadbf7c	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-06c27ade5d32e8e9acda	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
1D NMR	1H 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
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:

Resource	Link
CHEBI ID	28096
HMDB ID	HMDB01299
Pubchem Compound ID	329
Kegg ID	C04582
ChemSpider ID	152225
FOODB ID	FDB022541
Wikipedia ID	Not Available
BioCyc ID	CPD-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.

5-Methylthioribulose 1-phosphate (YMDB00129)

Structure for #<Compound:0xae81d464>

Enzymes

Reactions

Reactions