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Literature summary for 2.1.2.1 extracted from
- Serine hydroxymethyltransferase: a model enzyme for mechanistic, structural, and evolutionary studies (2011), Biochim. Biophys. Acta, 1814, 1489-1496.
Activating Compound
| Activating Compound | Comment | Organism | Structure |
|---|---|---|---|
| L-serine | stabilizes the dimeric form of the enzyme | Escherichia coli |  |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| L276A | site-directed mutagenesis, mutation in the third hydrophobic cluster. The decrease of hydrophobic contact area in the mutant causes a shift of the equilibrium between dimeric and monomeric forms in favor of the latter, pyridoxal 5'-phosphate binding stabilizes the dimeric form of the mutant | Escherichia coli |
| L85A | site-directed mutagenesis, mutation in the third hydrophobic cluster. The decrease of hydrophobic contact area in the mutant causes a shift of the equilibrium between dimeric and monomeric forms in favor of the latter, pyridoxal 5'-phosphate binding stabilizes the dimeric form of the mutant | Escherichia coli |
| L85A/L276A | site-directed mutagenesis, mutation in the third hydrophobic cluster. The decrease of hydrophobic contact area in the mutant causes a shift of the equilibrium between dimeric and monomeric forms in favor of the latter, pyridoxal 5'-phosphate binding stabilizes the dimeric form of the mutant | Escherichia coli |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.3 | - |
L-serine | wild-type enzyme, pH and temperature not specified in the publication | Escherichia coli | |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| L-serine + tetrahydropteroylglutamate | Bacillus subtilis | - |
glycine + 5,10-methylene-tetrahydropteroylglutamate + H2O | - |
r | |
| L-serine + tetrahydropteroylglutamate | Escherichia coli | - |
glycine + 5,10-methylene-tetrahydropteroylglutamate + H2O | - |
r | |
| additional information | Bacillus subtilis | SHMT also catalyzes the hydrolysis of 5,10-methenyl-tetrahydropteroylglutamate to 5-formyl-tetrahydropteroylglutamate | ? | - |
? | |
| additional information | Escherichia coli | SHMT also catalyzes the hydrolysis of 5,10-methenyl-tetrahydropteroylglutamate to 5-formyl-tetrahydropteroylglutamate | ? | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Bacillus subtilis | - |
- |
- |
| Escherichia coli | - |
- |
- |
Reaction
| Reaction | Comment | Organism | Reaction ID |
|---|---|---|---|
| 5,10-methylenetetrahydrofolate + glycine + H2O = tetrahydrofolate + L-serine | general mechanism of pyridoxal 5'-phosphate-catalyzed aldolic cleavage, racemisation, and transamination reactions, and catalytic mechanism of the transaldimination reaction involving Tyr55, His228, and Arg235, overview. Tyr55 is contributed by the symmetry-related monomer, with respect to the pyridoxal 5'-phosphate-binding subunit, and functions as the general acid-base catalyst in this proton transfer | Bacillus subtilis | |
| 5,10-methylenetetrahydrofolate + glycine + H2O = tetrahydrofolate + L-serine | general mechanism of pyridoxal 5'-phosphate-catalyzed aldolic cleavage, racemisation, and transamination reactions, and catalytic mechanism of the transaldimination reaction involving Tyr55, His228, and Arg235, overview. Tyr55 is contributed by the symmetry-related monomer, with respect to the pyridoxal 5'-phosphate-binding subunit, and functions as the general acid-base catalyst in this proton transfer | Escherichia coli |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| L-serine + tetrahydropteroylglutamate | - |
Bacillus subtilis | glycine + 5,10-methylene-tetrahydropteroylglutamate + H2O | - |
r | |
| L-serine + tetrahydropteroylglutamate | - |
Escherichia coli | glycine + 5,10-methylene-tetrahydropteroylglutamate + H2O | - |
r | |
| additional information | SHMT also catalyzes the hydrolysis of 5,10-methenyl-tetrahydropteroylglutamate to 5-formyl-tetrahydropteroylglutamate | Bacillus subtilis | ? | - |
? | |
| additional information | SHMT also catalyzes the hydrolysis of 5,10-methenyl-tetrahydropteroylglutamate to 5-formyl-tetrahydropteroylglutamate | Escherichia coli | ? | - |
? | |
| additional information | broad substrate and reaction specificity | Bacillus subtilis | ? | - |
? | |
| additional information | broad substrate and reaction specificity, overview | Escherichia coli | ? | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| dimer | - |
Bacillus subtilis |
| dimer | wild-type eSHMT is a dimer in both apo- and holo-enzyme forms | Escherichia coli |
| More | the folding mechanism of SHMT is divided in two phases and terminates with pyridoxal 5'-phosphate binding. In the first one, the large and small domains rapidly assume their native state, forming a folding intermediate that is not able to bind pyridoxal 5'-phosphate. In the second, slower phase, the enzyme folds into the native structure, acquiring the capability to bind the cofactor. Importance of the third hydrophobic cluster, highly conserved in type I fold enzyme, as key structural determinant of the assembly of eSHMT active site and overall native fold. This cluster plays a fundamental role in the transition from the first to the second phase of SHMT folding process | Escherichia coli |
| More | the folding mechanism of SHMT is divided in two phases and terminates with pyridoxal 5'-phosphate binding. In the first one, the large and small domains rapidly assume their native state, forming a folding intermediate that is not able to bind pyridoxal 5'-phosphate. In the second, slower phase, the enzyme folds into the native structure, acquiring the capability to bind the cofactor. Importance of the third hydrophobic cluster, highly conserved in typr I fold enzymes, as key structural determinant of the assembly of eSHMT active site and overall native fold. This cluster plays a fundamental role in the transition from the first to the second phase of SHMT folding process | Bacillus subtilis |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| serine hydroxymethyltransferase | - |
Bacillus subtilis |
| serine hydroxymethyltransferase | - |
Escherichia coli |
| SHMT | - |
Bacillus subtilis |
| SHMT | - |
Escherichia coli |
Turnover Number [1/s]
| Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 640 | - |
L-serine | wild-type enzyme, pH and temperature not specified in the publication | Escherichia coli | |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| pyridoxal 5'-phosphate | dependent on | Bacillus subtilis | |
| pyridoxal 5'-phosphate | dependent on, stabilizes the dimeric form of the enzyme | Escherichia coli | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | serine hydroxymethyltransferase is a ubiquitous representative of the family of fold type I pyridoxal 5'-phosphate-dependent enzymes, structural determinants, overview | Bacillus subtilis |
| evolution | serine hydroxymethyltransferase is a ubiquitous representative of the family of fold type I pyridoxal 5'-phosphate-dependent enzymes, structural determinants, overview | Escherichia coli |
| metabolism | the reaction catalyzed by this enzyme, the reversible transfer of the Cbeta of serine to tetrahydropteroylglutamate, represents a link between amino acid and folates metabolism and operates as a major source of one-carbon units for several essential biosynthetic processes | Bacillus subtilis |
| metabolism | the reaction catalyzed by this enzyme, the reversible transfer of the Cbeta of serine to tetrahydropteroylglutamate, represents a link between amino acid and folates metabolism and operates as a major source of one-carbon units for several essential biosynthetic processes | Escherichia coli |
| physiological function | the reaction catalyzed by this enzyme, the reversible transfer of the Cbeta of serine to tetrahydropteroylglutamate, represents a link between amino acid and folates metabolism and operates as a major source of one-carbon units for several essential biosynthetic processes, e.g. as a primary source of the one carbon units required for the synthesis of thymidylate, purines, and methionine. SHMT also catalyzes the hydrolysis of 5,10-methenyl-tetrahydropteroylglutamate to 5-formyl-tetrahydropteroylglutamate, which serves as a storage form of reduced folates and one-carbon groups in cells in a dormant stage | Bacillus subtilis |
| physiological function | the reaction catalyzed by this enzyme, the reversible transfer of the Cbeta of serine to tetrahydropteroylglutamate, represents a link between amino acid and folates metabolism and operates as a major source of one-carbon units for several essential biosynthetic processes, e.g. as a primary source of the one carbon units required for the synthesis of thymidylate, purines, and methionine. SHMT also catalyzes the hydrolysis of 5,10-methenyl-tetrahydropteroylglutamate to 5-formyl-tetrahydropteroylglutamate,which serves as a storage formof reduced folates and onecarbon groups in cells in a dormant stage | Escherichia coli |
kcat/KM [mM/s]
| kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 35.5 | - |
L-serine | wild-type enzyme, pH and temperature not specified in the publication | Escherichia coli | |
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