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Literature summary for 3.5.1.104 extracted from
- Identification and characterization of a novel polysaccharide deacetylase C (PdaC) from Bacillus subtilis (2012), J. Biol. Chem., 287, 9765-9776.
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| gene pdcA, overexpression of His-tagged truncated enzyme, lacking the transmembrane region, in Escherichia coli strain JM109, subcloning in Escherichia coli strain C600 | Bacillus subtilis |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| additional information | construction of a conditional null mutant of pdaC: the concatenated pM4SD-PdaC is derived from Escherichia coli strain C600 and Bacillus subtilis strain 168 is transformed with the plasmid by single crossing over recombination, resulting in the PdaCp strain | Bacillus subtilis |
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| EDTA | - |
Bacillus subtilis |  |
| additional information | the enzyme mutant is sensitive to lysozyme, the growth rate is decreased | Bacillus subtilis |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 4.8 | - |
peptidoglycan-N-acetyl-D-glucosamine | pH 7.0, 37°C | Bacillus subtilis | |
| 12.3 | - |
GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc | pH 7.0, 37°C | Bacillus subtilis | |
Localization
| Localization | Comment | Organism | GeneOntology No. | Textmining |
|---|---|---|---|---|
| membrane | - |
Bacillus subtilis | 16020 | - |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Ca2+ | activates | Bacillus subtilis | |
| Mg2+ | activates | Bacillus subtilis | |
| Mn2+ | best activating metal ion | Bacillus subtilis | |
| additional information | the enzyme requires divalent cations | Bacillus subtilis | |
| Ni2+ | activates | Bacillus subtilis | |
| Zn2+ | lower dependence on zinc or nickel ions for deacetylation of peptidoglycan by the enzyme than other metal ions, Mn2+, Mg2+, and Ca2+ | Bacillus subtilis | |
Molecular Weight [Da]
| Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
|---|---|---|---|
| 53000 | - |
x * 53000, recombinant truncated enzyme, SDS-PAGE | Bacillus subtilis |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| additional information | Bacillus subtilis | PdaC acts as a GlcNAc deacetylase toward chitin oligomers and as a MurNAc deacetylase toward Bacillus subtilis peptidoglycan, activity toward MurNAc is higher than toward GlcNAc | ? | - |
? | |
| additional information | Bacillus subtilis 168 | PdaC acts as a GlcNAc deacetylase toward chitin oligomers and as a MurNAc deacetylase toward Bacillus subtilis peptidoglycan, activity toward MurNAc is higher than toward GlcNAc | ? | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Bacillus subtilis | - |
gene pdaC | - |
| Bacillus subtilis 168 | - |
gene pdaC | - |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant His-tagged truncated enzyme from Escherichia coli strain JM109 by affinity chromatography and dialysis | Bacillus subtilis |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc + H2O | deacetylation of the chitin oligomer at position 3 | Bacillus subtilis | GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcN-beta-1,4-GlcNAc + acetate | - |
? | |
| GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc + H2O | deacetylation of the chitin oligomer at position 3 | Bacillus subtilis 168 | GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcN-beta-1,4-GlcNAc + acetate | - |
? | |
| GlcNAc-Mur[-L-Ala-D-Glu]-GlcNAc-MurNAcr[-L-Ala-D-Glu] + H2O | i.e. 4S2P, deacetylation | Bacillus subtilis | ? | - |
? | |
| GlcNAc-Mur[-L-Ala-D-Glu]-GlcNAc-MurNAcr[-L-Ala-D-Glu] + H2O | i.e. 4S2P, deacetylation | Bacillus subtilis 168 | ? | - |
? | |
| additional information | PdaC acts as a GlcNAc deacetylase toward chitin oligomers and as a MurNAc deacetylase toward Bacillus subtilis peptidoglycan, activity toward MurNAc is higher than toward GlcNAc | Bacillus subtilis | ? | - |
? | |
| additional information | the purified recombinant enzyme shows no nuclease activity with DNA | Bacillus subtilis | ? | - |
? | |
| additional information | PdaC acts as a GlcNAc deacetylase toward chitin oligomers and as a MurNAc deacetylase toward Bacillus subtilis peptidoglycan, activity toward MurNAc is higher than toward GlcNAc | Bacillus subtilis 168 | ? | - |
? | |
| additional information | the purified recombinant enzyme shows no nuclease activity with DNA | Bacillus subtilis 168 | ? | - |
? | |
| peptidoglycan-N-acetyl-D-glucosamine + H2O | substrates: peptidoglycans digested by DL-endopeptidase, or by LD-endopeptidase, or by L-alanine amidase, the latter is a very poor substrate. Purified recombinant and truncated enzyme, expressed in Escherichia coli, deacetylates Bacillus subtilis peptidoglycan and its polymer, (-GlcNAc-MurNAc[-L-Ala-D-Glu]-)n. The enzyme deacetylates N-acetylmuramic acid not N-acetyl-D-glucosamine from the polymer. The enzyme PdaC is a unique enzyme exhibiting two different deacetylase activities. The enzyme works as a MurNAc deacetylase toward glycan strands containing L-Ala-D-Glu | Bacillus subtilis | peptidoglycan-D-glucosamine + acetate | - |
? | |
| peptidoglycan-N-acetyl-D-glucosamine + H2O | substrates: peptidoglycans digested by DL-endopeptidase, or by LD-endopeptidase, or by L-alanine amidase, the latter is a very poor substrate. Purified recombinant and truncated enzyme, expressed in Escherichia coli, deacetylates Bacillus subtilis peptidoglycan and its polymer, (-GlcNAc-MurNAc[-L-Ala-D-Glu]-)n. The enzyme deacetylates N-acetylmuramic acid not N-acetyl-D-glucosamine from the polymer. The enzyme PdaC is a unique enzyme exhibiting two different deacetylase activities. The enzyme works as a MurNAc deacetylase toward glycan strands containing L-Ala-D-Glu | Bacillus subtilis 168 | peptidoglycan-D-glucosamine + acetate | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| ? | x * 53000, recombinant truncated enzyme, SDS-PAGE | Bacillus subtilis |
| More | enzyme domain structure and structure comparisons, overview | Bacillus subtilis |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| GlcNAc deacetylase | - |
Bacillus subtilis |
| MurNAc deacetylase | - |
Bacillus subtilis |
| PdaC | - |
Bacillus subtilis |
| polysaccharide deacetylase C | - |
Bacillus subtilis |
| YjeA | - |
Bacillus subtilis |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 37 | - |
assay at | Bacillus subtilis |
Turnover Number [1/s]
| Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.24 | - |
GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc | pH 7.0, 37°C | Bacillus subtilis | |
| 0.32 | - |
peptidoglycan-N-acetyl-D-glucosamine | pH 7.0, 37°C | Bacillus subtilis | |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 7 | - |
assay at | Bacillus subtilis |
General Information
| General Information | Comment | Organism |
|---|---|---|
| malfunction | a pdaC deletion mutant is sensitive to lysozyme treatment | Bacillus subtilis |
| physiological function | gene pdcA is regulated by an essential two-component system, YycFG, which is associated with cell division | Bacillus subtilis |
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