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Glycine (YMDB00016)
Identification | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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YMDB ID | YMDB00016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Name | Glycine | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Species | Saccharomyces cerevisiae | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Strain | Baker's yeast | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Description | Glycine (abbreviated as Gly or G) is an alpha-amino acid. It is one of the 22 proteinogenic amino acids, i.e., the building blocks of proteins. It is the smallest, simplest amino acid as it lacks any side chain or chirality. It is generally considered a polar amino acid. Glycine is a colourless, sweet-tasting crystalline solid. The principal function of glycine is as a precursor to proteins. It is also a building block to numerous natural products. Glycine is classified as a glucogenic amino acid, since it can be converted to serine by serine hydroxymethyltransferase, and serine can be converted back to the glycolytic intermediate, 3-phosphoglycerate or to pyruvate by serine/threonine dehydratase. Glycine is degraded via three pathways. The predominant pathway involves the catalysis of glycine cleavage enzyme, the same enzyme also involved in the biosynthesis of glycine. In the second pathway, glycine is degraded in two steps. The first step is the reverse of glycine biosynthesis from serine with serine hydroxymethyl transferase. Serine is then converted to pyruvate by serine dehydratase. In the third pathway, glycine is converted to glyoxylate by D-amino acid oxidase. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Synonyms |
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CAS number | 56-40-6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Weight | Average: 75.0666 Monoisotopic: 75.032028409 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
InChI Key | DHMQDGOQFOQNFH-UHFFFAOYSA-N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
InChI | InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IUPAC Name | 2-aminoacetic acid | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Traditional IUPAC Name | glycine | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Chemical Formula | C2H5NO2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SMILES | [H]OC(=O)C([H])([H])N([H])[H] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Chemical Taxonomy | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Description | belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Kingdom | Organic compounds | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Super Class | Organic acids and derivatives | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Class | Carboxylic acids and derivatives | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sub Class | Amino acids, peptides, and analogues | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Direct Parent | Alpha amino acids | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Alternative Parents | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Substituents |
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Molecular Framework | Aliphatic acyclic compounds | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
External Descriptors |
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Physical Properties | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
State | Solid | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Charge | 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Melting point | 262.2 °C | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Experimental Properties |
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Predicted Properties |
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Biological Properties | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Cellular Locations |
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Organoleptic Properties |
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SMPDB Pathways |
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KEGG Pathways |
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SMPDB Reactions | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
KEGG Reactions | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Concentrations | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Intracellular Concentrations |
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Extracellular Concentrations |
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Spectra | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Spectra | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
References | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
References: |
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Synthesis Reference: | Anslow, Winston K.; King, Harold. Synthesis of glycine. Journal of the Chemical Society (1929), 2163-6. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
External Links: |
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Enzymes
- General function:
- Involved in glycine dehydrogenase (decarboxylating) activity
- Specific function:
- The glycine cleavage system (glycine decarboxylase complex) catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein
- Gene Name:
- GCV2
- Uniprot ID:
- P49095
- Molecular weight:
- 114450.0
Reactions
Glycine + H-protein-lipoyllysine → H-protein-S-aminomethyldihydrolipoyllysine + CO(2). |
- General function:
- Involved in ATP binding
- Specific function:
- ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione
- Gene Name:
- GSH2
- Uniprot ID:
- Q08220
- Molecular weight:
- 55814.69922
Reactions
ATP + gamma-L-glutamyl-L-cysteine + glycine → ADP + phosphate + glutathione. |
- 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. |
- 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. |
- General function:
- Involved in lyase activity
- Specific function:
- Catalyzes the cleavage of L-allo-threonine and L- threonine to glycine and acetaldehyde
- Gene Name:
- GLY1
- Uniprot ID:
- P37303
- Molecular weight:
- 42814.60156
Reactions
L-threonine → glycine + acetaldehyde. |
L-allo-threonine → glycine + acetaldehyde. |
- General function:
- Involved in 5-aminolevulinate synthase activity
- Specific function:
- Succinyl-CoA + glycine = 5-aminolevulinate + CoA + CO(2)
- Gene Name:
- HEM1
- Uniprot ID:
- P09950
- Molecular weight:
- 59361.69922
Reactions
Succinyl-CoA + glycine → 5-aminolevulinate + CoA + CO(2). |
- General function:
- Involved in metabolic process
- Specific function:
- Has alanine:glyoxylate aminotransferase activity
- Gene Name:
- AGX1
- Uniprot ID:
- P43567
- Molecular weight:
- 41906.80078
Reactions
L-alanine + glyoxylate → pyruvate + glycine. |
- General function:
- Involved in nucleotide binding
- Specific function:
- Catalyzes the attachment of glycine to tRNA(Gly). Is also able produce diadenosine tetraphosphate (Ap4A), a universal pleiotropic signaling molecule needed for cell regulation pathways, by direct condensation of 2 ATPs
- Gene Name:
- GRS1
- Uniprot ID:
- P38088
- Molecular weight:
- 75410.20313
Reactions
ATP + glycine + tRNA(Gly) → AMP + diphosphate + glycyl-tRNA(Gly). |
- General function:
- Involved in catalytic activity
- Specific function:
- ATP + 5-phospho-D-ribosylamine + glycine = ADP + phosphate + N(1)-(5-phospho-D-ribosyl)glycinamide
- Gene Name:
- ADE5
- Uniprot ID:
- P07244
- Molecular weight:
- 86067.39844
Reactions
ATP + 5-phospho-D-ribosylamine + glycine → ADP + phosphate + N(1)-(5-phospho-D-ribosyl)glycinamide. |
ATP + 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine → ADP + phosphate + 5-amino-1-(5-phospho-D-ribosyl)imidazole. |
- General function:
- Involved in nucleotide binding
- Specific function:
- Catalyzes the attachment of glycine to tRNA(Gly). Is also able produce diadenosine tetraphosphate (Ap4A), a universal pleiotropic signaling molecule needed for cell regulation pathways, by direct condensation of 2 ATPs
- Gene Name:
- GRS2
- Uniprot ID:
- Q06817
- Molecular weight:
- 71017.89844
Reactions
ATP + glycine + tRNA(Gly) → AMP + diphosphate + glycyl-tRNA(Gly). |
- General function:
- Involved in oxidoreductase activity
- Specific function:
- Lipoamide dehydrogenase is a component of the alpha- ketoacid dehydrogenase complexes. This includes the pyruvate dehydrogenase complex, which catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2). Acts also as component of the glycine cleavage system (glycine decarboxylase complex), which catalyzes the degradation of glycine
- Gene Name:
- LPD1
- Uniprot ID:
- P09624
- Molecular weight:
- 54009.69922
Reactions
Protein N(6)-(dihydrolipoyl)lysine + NAD(+) → protein N(6)-(lipoyl)lysine + NADH. |
- General function:
- Involved in transferase activity, transferring nitrogenous groups
- Specific function:
- Component of serine palmitoyltransferase (SPT), which catalyzes the committed step in the synthesis of sphingolipids, the condensation of serine with palmitoyl CoA to form the long chain base 3-ketosphinganine
- Gene Name:
- LCB1
- Uniprot ID:
- P25045
- Molecular weight:
- 62206.60156
Reactions
Palmitoyl-CoA + L-serine → CoA + 3-dehydro-D-sphinganine + CO(2). |
- 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). |
Transporters
- General function:
- Involved in transport
- Specific function:
- Permease for various amino acids as well as for GABA. Can also transport L-cysteine and beta-alanine
- Gene Name:
- GAP1
- Uniprot ID:
- P19145
- Molecular weight:
- 65654.89844
- General function:
- Involved in transport
- Specific function:
- Can transport glutamate, aspartate, glutamine, asparagine, serine, alanine and glycine
- Gene Name:
- DIP5
- Uniprot ID:
- P53388
- Molecular weight:
- 68096.70313
- General function:
- Involved in transport
- Specific function:
- Required for high-affinity proline transport. May be responsible for proline recognition and probably also for proline translocation across the plasma membrane. Also function as non- specific GABA permease. Can also transport alanine and glycine
- Gene Name:
- PUT4
- Uniprot ID:
- P15380
- Molecular weight:
- 68786.79688
- General function:
- Involved in transport
- Specific function:
- Required for high-affinity tryptophan transport. Also transports cysteine, phenyalanine and tyrosine
- Gene Name:
- TAT2
- Uniprot ID:
- P38967
- Molecular weight:
- 65403.80078
- General function:
- Involved in transport
- Specific function:
- Broad substrate range permease which transports asparagine and glutamine with intermediate specificity. Also transports Ala, Cys, Gly, Ile, Leu, Met, Phe, Ser, Thr, Tyr and Val. Important for the utilization of amino acids as a nitrogen source
- Gene Name:
- AGP1
- Uniprot ID:
- P25376
- Molecular weight:
- 69670.70313