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Literature summary extracted from
- Kinetic characterization and quaternary structure of glutamate racemase from the periodontal anaerobe Fusobacterium nucleatum (2009), Arch. Biochem. Biophys., 491, 16-24.
Application
| EC Number | Application | Comment | Organism |
|---|---|---|---|
| 5.1.1.3 | drug development | enzyme is an attractive target for the development of antibacterial agents | Bacillus subtilis |
| 5.1.1.3 | drug development | enzyme is an attractive target for the development of antibacterial agents | Fusobacterium nucleatum subsp. nucleatum |
Cloned(Commentary)
| EC Number | Cloned (Comment) | Organism |
|---|---|---|
| 5.1.1.3 | overexpression in BL21(DE3) Escherichia coli as fusion protein bearing an N-terminal hexahistidine tag | Bacillus subtilis |
| 5.1.1.3 | overexpression in BL21(DE3) Escherichia coli as fusion protein bearing an N-terminal hexahistidine tag | Fusobacterium nucleatum subsp. nucleatum |
Protein Variants
| EC Number | Protein Variants | Comment | Organism |
|---|---|---|---|
| 5.1.1.3 | A151V | production by site-directed mutagenesis, alanine ist essential for activity, mutation of residue 151 located at the entryway to the active site reveals that FnGR is very sensitive to increased steric bulk at this position | Fusobacterium nucleatum subsp. nucleatum |
| 5.1.1.3 | V149A | while V149A BsGR exhibits a 3- and 6fold increase in the value of Km for L- and D-glutamate relative to wild-type BsGR, respectively, the values of kcat are slightly increased relative to the wild-type enzyme | Bacillus subtilis |
Inhibitors
| EC Number | Inhibitors | Comment | Organism | Structure |
|---|---|---|---|---|
| 5.1.1.3 | additional information | although Tris-HCl isthe buffer most commonly employed when assaying glutamate racemases from various microbial sources, FnGR is slightly inhibited in this buffer, kcat values are reduced 14% and 25% in the L-D and D-L reaction directions at pH 8.0, respectively relative to the corresponding values observed using the phosphate assay buffer | Fusobacterium nucleatum subsp. nucleatum |
KM Value [mM]
| EC Number | KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|---|
| 5.1.1.3 | 0.9 | - |
L-glutamate | His-tagged recombinant FnGR, in potassium phosphate buffer (10 mM, pH 8.0) | Fusobacterium nucleatum subsp. nucleatum |  |
| 5.1.1.3 | 1.04 | - |
L-glutamate | recombinant FnGR, in potassium phosphate buffer (10 mM, pH 8.0) | Fusobacterium nucleatum subsp. nucleatum | |
| 5.1.1.3 | 1.5 | - |
D-glutamate | His-tagged recombinant FnGR, in potassium phosphate buffer (10 mM, pH 8.0) | Fusobacterium nucleatum subsp. nucleatum | |
| 5.1.1.3 | 1.7 | - |
D-glutamate | His-tagged recombinant BsGR, in potassium phosphate buffer (10 mM, pH 8.0) | Bacillus subtilis | |
| 5.1.1.3 | 1.7 | - |
D-glutamate | recombinant FnGR, in potassium phosphate buffer (10 mM, pH 8.0) | Fusobacterium nucleatum subsp. nucleatum | |
| 5.1.1.3 | 10 | - |
D-glutamate | His-tagged recombinant BsGR mutant V149A, in potassium phosphate buffer (10 mM, pH 8.0) | Bacillus subtilis | |
| 5.1.1.3 | 14 | - |
L-glutamate | His-tagged recombinant BsGR, in potassium phosphate buffer (10 mM, pH 8.0) | Bacillus subtilis | |
| 5.1.1.3 | 26 | - |
L-2-aminoadipic acid | His-tagged recombinant FnGR, in potassium phosphate buffer (10 mM, pH 8.0) | Fusobacterium nucleatum subsp. nucleatum | |
| 5.1.1.3 | 47 | - |
L-glutamate | His-tagged recombinant BsGR mutant V149A, in potassium phosphate buffer (10 mM, pH 8.0) | Bacillus subtilis | |
Molecular Weight [Da]
| EC Number | Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
|---|---|---|---|---|
| 5.1.1.3 | 32050 | - |
calculated His-tagged FnGR | Fusobacterium nucleatum subsp. nucleatum |
| 5.1.1.3 | 32130 | - |
calculated His-BsGR V149A | Bacillus subtilis |
| 5.1.1.3 | 32160 | - |
calculated His-tagged BsGR | Bacillus subtilis |
| 5.1.1.3 | 34000 | - |
BsGR, determined by gel filtration | Bacillus subtilis |
| 5.1.1.3 | 35000 | - |
FnGR, determined by SDS-PAGE | Fusobacterium nucleatum subsp. nucleatum |
Natural Substrates/ Products (Substrates)
| EC Number | Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 5.1.1.3 | D-glutamate | Fusobacterium nucleatum subsp. nucleatum | enzyme catalyzes the formation of D-glutamate from L-glutamate through a 1,1-proton transfer mechanism which reversibly inverts the stereochemistry at the alpha-carbon of glutamate | L-glutamate | - |
r | |
| 5.1.1.3 | L-2-aminoadipic acid | Bacillus subtilis | - |
D-2-aminoadipic acid | - |
? | |
| 5.1.1.3 | L-2-aminoadipic acid | Fusobacterium nucleatum subsp. nucleatum | - |
D-2-aminoadipic acid | - |
? | |
| 5.1.1.3 | L-glutamate | Bacillus subtilis | enzyme catalyzes the formation of D-glutamate from L-glutamate through a 1,1-proton transfer mechanism which reversibly inverts the stereochemistry at the alpha-carbon of glutamate | D-glutamate | - |
r | |
| 5.1.1.3 | L-glutamate | Fusobacterium nucleatum subsp. nucleatum | enzyme catalyzes the formation of D-glutamate from L-glutamate through a 1,1-proton transfer mechanism which reversibly inverts the stereochemistry at the alpha-carbon of glutamate | D-glutamate | - |
r | |
Organism
| EC Number | Organism | UniProt | Comment | Textmining |
|---|---|---|---|---|
| 5.1.1.3 | Bacillus subtilis | P94556 | - |
- |
| 5.1.1.3 | Fusobacterium nucleatum subsp. nucleatum | Q8REE6 | - |
- |
Purification (Commentary)
| EC Number | Purification (Comment) | Organism |
|---|---|---|
| 5.1.1.3 | by using of nickel ion affinity chromatography at 4°C | Bacillus subtilis |
| 5.1.1.3 | by using of nickel ion affinity chromatography at 4°C | Fusobacterium nucleatum subsp. nucleatum |
Storage Stability
| EC Number | Storage Stability | Organism |
|---|---|---|
| 5.1.1.3 | no loss of activity is noted after the enzyme is stored at 80°C for more than 8 months, at least 80% of enzyme activity is retained after incubation for 8 h at 4°C | Fusobacterium nucleatum subsp. nucleatum |
Substrates and Products (Substrate)
| EC Number | Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 5.1.1.3 | D-glutamate | enzyme catalyzes the formation of D-glutamate from L-glutamate through a 1,1-proton transfer mechanism which reversibly inverts the stereochemistry at the alpha-carbon of glutamate | Fusobacterium nucleatum subsp. nucleatum | L-glutamate | - |
r | |
| 5.1.1.3 | L-2-aminoadipic acid | - |
Bacillus subtilis | D-2-aminoadipic acid | - |
? | |
| 5.1.1.3 | L-2-aminoadipic acid | - |
Fusobacterium nucleatum subsp. nucleatum | D-2-aminoadipic acid | - |
? | |
| 5.1.1.3 | L-glutamate | enzyme catalyzes the formation of D-glutamate from L-glutamate through a 1,1-proton transfer mechanism which reversibly inverts the stereochemistry at the alpha-carbon of glutamate | Bacillus subtilis | D-glutamate | - |
r | |
| 5.1.1.3 | L-glutamate | enzyme catalyzes the formation of D-glutamate from L-glutamate through a 1,1-proton transfer mechanism which reversibly inverts the stereochemistry at the alpha-carbon of glutamate | Fusobacterium nucleatum subsp. nucleatum | D-glutamate | - |
r | |
Subunits
| EC Number | Subunits | Comment | Organism |
|---|---|---|---|
| 5.1.1.3 | dimer | determined by blue native PAGE, FnGR is a pseudosymmetric enzyme, the presence of glutamate does not significantly alter the position of the monomer-dimer equilibrium of the enzyme | Fusobacterium nucleatum subsp. nucleatum |
| 5.1.1.3 | monomer | determined by gel filtration, BsGR is a monomeric enzyme, which dimerizes in the presence of either 10 mM D- or L-glutamate | Bacillus subtilis |
Synonyms
| EC Number | Synonyms | Comment | Organism |
|---|---|---|---|
| 5.1.1.3 | BsGR | - |
Bacillus subtilis |
| 5.1.1.3 | FnGR | - |
Fusobacterium nucleatum subsp. nucleatum |
| 5.1.1.3 | glutamate racemase | - |
Bacillus subtilis |
| 5.1.1.3 | glutamate racemase | - |
Fusobacterium nucleatum subsp. nucleatum |
Turnover Number [1/s]
| EC Number | Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|---|
| 5.1.1.3 | 2.4 | - |
L-2-aminoadipic acid | His-tagged recombinant FnGR, in potassium phosphate buffer (10 mM, pH 8.0) | Fusobacterium nucleatum subsp. nucleatum | |
| 5.1.1.3 | 8.3 | - |
D-glutamate | His-tagged recombinant BsGR, in potassium phosphate buffer (10 mM, pH 8.0) | Bacillus subtilis | |
| 5.1.1.3 | 13.8 | - |
L-glutamate | His-tagged recombinant FnGR, in potassium phosphate buffer (10 mM, pH 8.0) | Fusobacterium nucleatum subsp. nucleatum | |
| 5.1.1.3 | 15 | - |
D-glutamate | His-tagged recombinant BsGR mutant V149A, in potassium phosphate buffer (10 mM, pH 8.0) | Bacillus subtilis | |
| 5.1.1.3 | 17.4 | - |
L-glutamate | recombinant FnGR, in potassium phosphate buffer (10 mM, pH 8.0) | Fusobacterium nucleatum subsp. nucleatum | |
| 5.1.1.3 | 22 | - |
D-glutamate | His-tagged recombinant FnGR, in potassium phosphate buffer (10 mM, pH 8.0) | Fusobacterium nucleatum subsp. nucleatum | |
| 5.1.1.3 | 26 | - |
D-glutamate | recombinant FnGR, in potassium phosphate buffer (10 mM, pH 8.0) | Fusobacterium nucleatum subsp. nucleatum | |
| 5.1.1.3 | 63 | - |
L-glutamate | His-tagged recombinant BsGR, in potassium phosphate buffer (10 mM, pH 8.0) | Bacillus subtilis | |
| 5.1.1.3 | 76 | - |
L-glutamate | His-tagged recombinant BsGR mutant V149A, in potassium phosphate buffer (10 mM, pH 8.0) | Bacillus subtilis | |
pH Optimum
| EC Number | pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|---|
| 5.1.1.3 | 8.5 | - |
5 mM Tris-HCl | Bacillus subtilis |
| 5.1.1.3 | 8.5 | - |
5 mM Tris-HCl | Fusobacterium nucleatum subsp. nucleatum |
pH Range
| EC Number | pH Minimum | pH Maximum | Comment | Organism |
|---|---|---|---|---|
| 5.1.1.3 | 8 | 8.5 | FnGR is active over a broad pH range, with the maximum of activity between pH 8.0 and 8.5 for the reaction in the L-D direction | Fusobacterium nucleatum subsp. nucleatum |
| 5.1.1.3 | 8.5 | 9 | FnGR is active over a broad pH range, with the maximum of activity between pH 8.0 and 8.5 for the reaction in the D-L direction | Fusobacterium nucleatum subsp. nucleatum |
General Information
| EC Number | General Information | Comment | Organism |
|---|---|---|---|
| 5.1.1.3 | physiological function | peptidoglycan synthesis | Bacillus subtilis |
| 5.1.1.3 | physiological function | peptidoglycan synthesis | Fusobacterium nucleatum subsp. nucleatum |
kcat/KM [mM/s]
| EC Number | kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|---|
| 5.1.1.3 | 0.09 | - |
L-2-aminoadipic acid | His-tagged recombinant FnGR, in potassium phosphate buffer (10 mM, pH 8.0) | Fusobacterium nucleatum subsp. nucleatum | |
| 5.1.1.3 | 1.5 | - |
D-glutamate | His-tagged recombinant BsGR mutant V149A, in potassium phosphate buffer (10 mM, pH 8.0) | Bacillus subtilis | |
| 5.1.1.3 | 1.8 | - |
L-glutamate | His-tagged recombinant BsGR mutant V149A, in potassium phosphate buffer (10 mM, pH 8.0) | Bacillus subtilis | |
| 5.1.1.3 | 4 | - |
D-glutamate | His-tagged recombinant FnGR, in potassium phosphate buffer (10 mM, pH 8.0) | Fusobacterium nucleatum subsp. nucleatum | |
| 5.1.1.3 | 4.6 | - |
L-glutamate | His-tagged recombinant BsGR, in potassium phosphate buffer (10 mM, pH 8.0) | Bacillus subtilis | |
| 5.1.1.3 | 5 | - |
D-glutamate | His-tagged recombinant BsGR, in potassium phosphate buffer (10 mM, pH 8.0) | Bacillus subtilis | |
| 5.1.1.3 | 15 | - |
L-glutamate | His-tagged recombinant FnGR, in potassium phosphate buffer (10 mM, pH 8.0) | Fusobacterium nucleatum subsp. nucleatum | |
| 5.1.1.3 | 15 | - |
D-glutamate | recombinant FnGR, in potassium phosphate buffer (10 mM, pH 8.0) | Fusobacterium nucleatum subsp. nucleatum | |
| 5.1.1.3 | 17 | - |
L-glutamate | recombinant FnGR, in potassium phosphate buffer (10 mM, pH 8.0) | Fusobacterium nucleatum subsp. nucleatum | |
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