3-phospho-D-glyceric acid (YMDB00756)

Identification

YMDB ID

YMDB00756

Name

3-phospho-D-glyceric acid

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

D-Glycerate 3-phosphate, also known as 3-phosphoglyceric acid or 3-phospho-(R)-glycerate, belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group. D-Glycerate 3-phosphate is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms

3-(dihydrogen phosphate)Glycerate
3-(dihydrogen phosphate)Glyceric acid
3-Glycerophosphorate
3-Glycerophosphoric acid
3-P-D-glycerate
3-P-glycerate
3-PGA
3-phospho-(R)-glycerate
3-phospho-D-glycerate
3-phospho-glycerate
3-phospho-glyceric acid
3-phosphoglycerate
3-phosphoglyceric acid
D-(-)-3-Phosphoglyceric acid
d-glycerate 3-phosphate
D-glycerate-3-P
Glycerate 3-phosphate
glycerate-3-P
Glyceric acid 3-phosphate
Phosphoglycerate
3-Phospho-(R)-glyceric acid
3-Phospho-D-glyceric acid
D-Glyceric acid 3-phosphoric acid
(2R)-2-Hydroxy-3-(phosphonatooxy)propanoic acid
(2R)-2-Hydroxy-3-(phosphonooxy)propanoic acid
2-Hydroxy-3-(phosphonatooxy)propanoate
D-3-Phosphoglyceric acid
D-Glyceric acid 3-phosphate
3-Phosphoglycerate, trisodium salt
3-Phosphoglycerate, monosodium salt
3-Phosphoglycerate, (R)-isomer

CAS number

820-11-1

Weight

Average: 186.0572
Monoisotopic: 185.99293909

InChI Key

OSJPPGNTCRNQQC-UWTATZPHSA-N

InChI

InChI=1S/C3H7O7P/c4-2(3(5)6)1-10-11(7,8)9/h2,4H,1H2,(H,5,6)(H2,7,8,9)/t2-/m1/s1

IUPAC Name

(2R)-2-hydroxy-3-(phosphonooxy)propanoic acid

Traditional IUPAC Name

D-glycerate 3-phosphate

Chemical Formula

C₃H₇O₇P

SMILES

O[C@H](COP(O)(O)=O)C(O)=O

Chemical Taxonomy

Description

belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Sugar acids and derivatives

Alternative Parents

Substituents

Glyceric_acid
Monoalkyl phosphate
Alpha-hydroxy acid
Hydroxy acid
Monosaccharide
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Carboxylic acid
Alcohol
Carbonyl group
Organic oxide
Hydrocarbon derivative
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

3-phosphoglyceric acid (CHEBI:17794 )

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	21 g/L	ALOGPS
logP	-2.3	ALOGPS
logP	-1.6	ChemAxon
logS	-0.95	ALOGPS
pKa (Strongest Acidic)	1.3	ChemAxon
pKa (Strongest Basic)	-4.2	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	124.29 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	31.26 m³·mol⁻¹	ChemAxon
Polarizability	13.54 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

Ethanol fermentation	PW002448
Glycerol metabolism	PW002407
Glycolysis I	PW002386
Starch and sucrose metabolism	PW002481
glycine metabolism	PW002398

KEGG Pathways

Glycerolipid metabolism	ec00561
Glycine, serine and threonine metabolism	ec00260
Glycolysis / Gluconeogenesis	ec00010
Glyoxylate and dicarboxylate metabolism	ec00630
Methane metabolism	ec00680

SMPDB Reactions

Not Available

KEGG Reactions

NAD + 3-phospho-D-glyceric acid → NADH + Phosphohydroxypyruvic acid + hydron

Adenosine triphosphate + 3-phospho-D-glyceric acid ↔ 3-phospho-D-glyceroyl dihydrogen phosphate + ADP

2-phospho-D-glyceric acid ↔ 3-phospho-D-glyceric acid

Concentrations

Intracellular Concentrations

Intracellular Concentration	Substrate	Growth Conditions	Strain	Citation
120 ± 10 µM	Synthetic medium with 2% glucose	aerobic;resting cells	Baker's yeast	PMID: 6229402
630 ± 100 µM	Synthetic medium with 2% galactose	aerobic;resting cells	Baker's yeast	PMID: 6229402
Conversion Details Here

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9200000000-2d6f0050126bbc72d771	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-03dj-9150000000-ebe296689ddfcee96d61	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , negative	splash10-00kb-9500000000-3a504199c8820dbd44a1	JSpectraViewer \| MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00kr-2900000000-97a3da464b710b2684a9	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00kv-8900000000-f897e638356fb29020cb	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0006-9100000000-655876160dc523273c42	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-003r-5900000000-b5d234c9dd7df3920489	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9100000000-6b06c4977ed320e922a2	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-69afa1a98654e3a171ea	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0002-9000000000-e64736ac1f9d1f7dd9ef	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-9000000000-b24e251f42140de98ced	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-001i-9000000000-7c1557a43a172be0e63d	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004j-9000000000-0b41dc890757740bbb51	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	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
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer

References

References:

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
Faller, L. D., Johnson, A. M. (1974). "Calorimetric studies of the role of magnesium ions in yeast enolase catalysis." Proc Natl Acad Sci U S A 71:1083-1087.4598292
Melcher, K., Entian, K. D. (1992). "Genetic analysis of serine biosynthesis and glucose repression in yeast." Curr Genet 21:295-300.1326413
Albers, E., Laize, V., Blomberg, A., Hohmann, S., Gustafsson, L. (2003). "Ser3p (Yer081wp) and Ser33p (Yil074cp) are phosphoglycerate dehydrogenases in Saccharomyces cerevisiae." J Biol Chem 278:10264-10272.12525494
Rodicio, R., Heinisch, J. (1987). "Isolation of the yeast phosphoglyceromutase gene and construction of deletion mutants." Mol Gen Genet 206:133-140.3033435
Lagunas, R., Gancedo, C. (1983). "Role of phosphate in the regulation of the Pasteur effect in Saccharomyces cerevisiae." Eur J Biochem 137:479-483.6229402

Synthesis Reference:

Not Available

External Links:

Resource	Link
CHEBI ID	17794
HMDB ID	HMDB00807
Pubchem Compound ID	25245548
Kegg ID	C00197
ChemSpider ID	388326
FOODB ID	FDB030460
Wikipedia	3-Phosphoglyceric_acid
BioCyc ID	G3P

Enzymes

Protein Details

1. D-3-phosphoglycerate dehydrogenase 2

General function:: Involved in oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
Specific function:: 3-phospho-D-glycerate + NAD(+) = 3- phosphonooxypyruvate + NADH
Gene Name:: SER33
Uniprot ID:: P40510
Molecular weight:: 51187.80078

Reactions

3-phospho-D-glycerate + NAD(+) → 3-phosphonooxypyruvate + NADH.
2-hydroxyglutarate + NAD(+) → 2-oxoglutarate + NADH.

Protein Details

2. Phosphoglycerate kinase

General function:: Involved in phosphoglycerate kinase activity
Specific function:: ATP + 3-phospho-D-glycerate = ADP + 3-phospho- D-glyceroyl phosphate
Gene Name:: PGK1
Uniprot ID:: P00560
Molecular weight:: 44738.0

Reactions

ATP + 3-phospho-D-glycerate → ADP + 3-phospho-D-glyceroyl phosphate.

Protein Details

3. Phosphoglycerate mutase 1

General function:: Involved in catalytic activity
Specific function:: Interconversion of 3- and 2-phosphoglycerate with 2,3- bisphosphoglycerate as the primer of the reaction. Can also Catalyze the reaction of EC 5.4.2.4 (synthase) and EC 3.1.3.13 (phosphatase), but with a reduced activity
Gene Name:: GPM1
Uniprot ID:: P00950
Molecular weight:: 27608.30078

Reactions

2-phospho-D-glycerate → 3-phospho-D-glycerate.

Protein Details

4. Putative phosphoglycerate mutase DET1

General function:: Involved in catalytic activity
Specific function:: Involved, either directly or indirectly, in the bidirectional transport of sterols between the endoplasmic reticulum and the plasma membrane
Gene Name:: DET1
Uniprot ID:: Q99288
Molecular weight:: 39171.80078

Reactions

2-phospho-D-glycerate → 3-phospho-D-glycerate.

Protein Details

5. Probable phosphoglycerate mutase YOR283W

General function:: Involved in catalytic activity
Specific function:: Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
Gene Name:: Not Available
Uniprot ID:: Q12040
Molecular weight:: 26176.5

Reactions

2-phospho-D-glycerate → 3-phospho-D-glycerate.

Protein Details

6. Phosphoglycerate mutase 3

General function:: Involved in catalytic activity
Specific function:: Could be non-functional
Gene Name:: GPM3
Uniprot ID:: Q12326
Molecular weight:: 34863.19922

Reactions

2-phospho-D-glycerate → 3-phospho-D-glycerate.

Protein Details

7. Phosphoglycerate mutase 2

General function:: Involved in catalytic activity
Specific function:: Could be non-functional
Gene Name:: GPM2
Uniprot ID:: Q12008
Molecular weight:: 36072.80078

Reactions

2-phospho-D-glycerate → 3-phospho-D-glycerate.

Protein Details

8. D-3-phosphoglycerate dehydrogenase 1

General function:: Involved in oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
Specific function:: 3-phospho-D-glycerate + NAD(+) = 3- phosphonooxypyruvate + NADH
Gene Name:: SER3
Uniprot ID:: P40054
Molecular weight:: 51192.80078

Reactions

3-phospho-D-glycerate + NAD(+) → 3-phosphonooxypyruvate + NADH.
2-hydroxyglutarate + NAD(+) → 2-oxoglutarate + NADH.

Structure for #<Compound:0xaa2c5998>

Enzymes

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