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Literature summary extracted from
- A Clostridium difficile alanine racemase affects spore germination and accommodates serine as a substrate (2017), J. Biol. Chem., 292, 10735-10742 .
Cloned(Commentary)
| EC Number | Cloned (Comment) | Organism |
|---|---|---|
| 5.1.1.1 | gene alr2, recombinant expression of wild-type and mutant enzymes in Escherichia coli strain BL21(DE3) | Clostridioides difficile |
| 5.1.1.18 | gene alr2, recombinant expression of wild-type and mutant enzymes in Escherichia coli strain BL21(DE3) | Clostridioides difficile |
Protein Variants
| EC Number | Protein Variants | Comment | Organism |
|---|---|---|---|
| 5.1.1.1 | K39A | site-directed mutagenesis, kinetically inactive mutant, the mutation disrupts the binding of the cofactor that is essential for catalysis (pyridoxal 5'-phosphate), the mutant shows altered binding kinetics with L-alanine and D-alanine, weak binding to L- and D-serine | Clostridioides difficile |
| 5.1.1.1 | additional information | construction of a alr2 knockout mutant RS07 generated by retargeting the pJS107 TargeTron plasmid. Complementation by expression of plasmid pRS89 encoding gene alr2. The alr2 mutant spores more readily germinate in response to L-alanine as a co-germinant, D-alanine also functions as a co-germinant, no germination in presence of taurocholic acid | Clostridioides difficile |
| 5.1.1.18 | K39A | site-directed mutagenesis, kinetically inactive mutant, the mutation disrupts the binding of the co-factor that is essential for catalysis (pyridoxal 5'-phosphate), the mutant shows altered binding kinetics with L-alanine and D-alanine, weak binding to L- and D-serine | Clostridioides difficile |
KM Value [mM]
| EC Number | KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|---|
| 5.1.1.1 | 0.046 | - |
L-alanine | pH 7.5, 37°C, recombinant mutant K39A | Clostridioides difficile |  |
| 5.1.1.1 | 0.064 | - |
L-alanine | pH 7.5, 37°C, recombinant wild-type enzyme | Clostridioides difficile | |
| 5.1.1.18 | 14 | - |
L-serine | pH 7.5, 37°C, recombinant wild-type enzyme | Clostridioides difficile | |
| 5.1.1.18 | 17 | - |
L-serine | pH 7.5, 37°C, recombinant mutant K39A | Clostridioides difficile | |
Natural Substrates/ Products (Substrates)
| EC Number | Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 5.1.1.1 | L-alanine | Clostridioides difficile | - |
D-alanine | - |
r | |
| 5.1.1.1 | L-alanine | Clostridioides difficile 630 | - |
D-alanine | - |
r | |
| 5.1.1.1 | additional information | Clostridioides difficile | Alr2 can interconvert L- and D-serine and Alr2 binds to L- and D-serine with 2fold weaker affinity to that of L- and D-alanine, cf. EC 5.1.1.18 | ? | - |
? | |
| 5.1.1.1 | additional information | Clostridioides difficile 630 | Alr2 can interconvert L- and D-serine and Alr2 binds to L- and D-serine with 2fold weaker affinity to that of L- and D-alanine, cf. EC 5.1.1.18 | ? | - |
? | |
| 5.1.1.18 | L-serine | Clostridioides difficile | - |
D-serine | - |
r | |
| 5.1.1.18 | L-serine | Clostridioides difficile UK1 | - |
D-serine | - |
r | |
Organism
| EC Number | Organism | UniProt | Comment | Textmining |
|---|---|---|---|---|
| 5.1.1.1 | Clostridioides difficile | Q180W0 | i.e. Clostridium difficile strain UK1 | - |
| 5.1.1.1 | Clostridioides difficile 630 | Q180W0 | i.e. Clostridium difficile strain UK1 | - |
| 5.1.1.18 | Clostridioides difficile | - |
i.e. Peptoclostridium difficile | - |
| 5.1.1.18 | Clostridioides difficile UK1 | - |
i.e. Peptoclostridium difficile | - |
Purification (Commentary)
| EC Number | Purification (Comment) | Organism |
|---|---|---|
| 5.1.1.1 | recombinant wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, dialysis, and gel filtration | Clostridioides difficile |
| 5.1.1.18 | recombinant wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, dialysis, and gel filtration | Clostridioides difficile |
Source Tissue
| EC Number | Source Tissue | Comment | Organism | Textmining |
|---|
Substrates and Products (Substrate)
| EC Number | Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 5.1.1.1 | L-alanine | - |
Clostridioides difficile | D-alanine | - |
r | |
| 5.1.1.1 | L-alanine | - |
Clostridioides difficile 630 | D-alanine | - |
r | |
| 5.1.1.1 | additional information | Alr2 can interconvert L- and D-serine and Alr2 binds to L- and D-serine with 2fold weaker affinity to that of L- and D-alanine, cf. EC 5.1.1.18 | Clostridioides difficile | ? | - |
? | |
| 5.1.1.1 | additional information | Alr2 converts L-serine to an approximately equal amount of D-serine. When tested with D-serine, Alr2 does not convert as much, and nearly 75% of the D-serine remains in the D-form | Clostridioides difficile | ? | - |
? | |
| 5.1.1.1 | additional information | Alr2 can interconvert L- and D-serine and Alr2 binds to L- and D-serine with 2fold weaker affinity to that of L- and D-alanine, cf. EC 5.1.1.18 | Clostridioides difficile 630 | ? | - |
? | |
| 5.1.1.1 | additional information | Alr2 converts L-serine to an approximately equal amount of D-serine. When tested with D-serine, Alr2 does not convert as much, and nearly 75% of the D-serine remains in the D-form | Clostridioides difficile 630 | ? | - |
? | |
| 5.1.1.18 | L-serine | - |
Clostridioides difficile | D-serine | - |
r | |
| 5.1.1.18 | L-serine | alanine racemase 2, Alr2, converts L-serine to an approximately equal amount of D-serine. When tested with D-serine, Alr2 does not convert as much, and nearly 75% of the D-serine remains in the D-form | Clostridioides difficile | D-serine | - |
r | |
| 5.1.1.18 | L-serine | - |
Clostridioides difficile UK1 | D-serine | - |
r | |
| 5.1.1.18 | L-serine | alanine racemase 2, Alr2, converts L-serine to an approximately equal amount of D-serine. When tested with D-serine, Alr2 does not convert as much, and nearly 75% of the D-serine remains in the D-form | Clostridioides difficile UK1 | D-serine | - |
r | |
Synonyms
| EC Number | Synonyms | Comment | Organism |
|---|---|---|---|
| 5.1.1.1 | ALR2 | - |
Clostridioides difficile |
| 5.1.1.1 | Alr2 racemase | - |
Clostridioides difficile |
Temperature Optimum [°C]
| EC Number | Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|---|
| 5.1.1.1 | 37 | - |
assay at | Clostridioides difficile |
| 5.1.1.18 | 37 | - |
assay at | Clostridioides difficile |
pH Optimum
| EC Number | pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|---|
| 5.1.1.1 | 7.5 | - |
assay at | Clostridioides difficile |
| 5.1.1.18 | 7.5 | - |
assay at | Clostridioides difficile |
Cofactor
| EC Number | Cofactor | Comment | Organism | Structure |
|---|---|---|---|---|
| 5.1.1.1 | pyridoxal 5'-phosphate | dependent on | Clostridioides difficile | |
| 5.1.1.18 | pyridoxal 5'-phosphate | dependent on | Clostridioides difficile | |
General Information
| EC Number | General Information | Comment | Organism |
|---|---|---|---|
| 5.1.1.1 | additional information | Alr2 racemase is the sixth most highly expressed gene during Clostridium difficile spore formation | Clostridioides difficile |
| 5.1.1.1 | physiological function | many endospore-forming bacteria embed alanine racemases into their spore coats, and these enzymes are thought to convert the L-alanine germinant into D-alanine, a spore germination inhibitor. Clostridium difficile spores can respond to a diverse set of amino acid co-germinants and Alr2 can accommodate serine as a substrate. L-alanine is a co-germinant, and D-alanine also functions as a co-germinant. L- and D-serine are also co-germinants for Clostridium difficile spores. Only the L-form of alanine can trigger spore germination when added with taurocholic acid. Gene alr2 is dispensable for germination in response to L-alanine but essential for germination in response to D-alanine | Clostridioides difficile |
| 5.1.1.18 | additional information | Alr2 racemase is the sixth most highly expressed gene during Clostridium difficile spore formation | Clostridioides difficile |
| 5.1.1.18 | physiological function | many endospore-forming bacteria embed alanine racemases into their spore coats, and these enzymes are thought to convert the L-alanine germinant into D-alanine, a spore germination inhibitor. Clostridium difficile spores can respond to a diverse set of amino acid co-germinants and alanine racemase 2, Alr2, EC 5.1.1.1, can accommodate serine as a substrate. L-alanine is a co-germinant, and D-alanine also functions as a co-germinant. L- and D-serine are also co-germinants for Clostridium difficile spores. Only the L-form of alanine can trigger spore germination when added with taurocholic acid. Gene alr2 is dispensable for germination in response to L-alanine but essential for germination in response to D-alanine | Clostridioides difficile |
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