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Literature summary extracted from

  • Kobayashi, K.; Sudiarta, I.P.; Kodama, T.; Fukushima, T.; Ara, K.; Ozaki, K.; Sekiguchi, J.
    Identification and characterization of a novel polysaccharide deacetylase C (PdaC) from Bacillus subtilis (2012), J. Biol. Chem., 287, 9765-9776.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
3.5.1.104 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

EC Number Protein Variants Comment Organism
3.5.1.104 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

EC Number Inhibitors Comment Organism Structure
3.5.1.104 EDTA
-
 Bacillus subtilis
3.5.1.104 additional information the enzyme mutant is sensitive to lysozyme, the growth rate is decreased Bacillus subtilis

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.5.1.104 4.8
-
 peptidoglycan-N-acetyl-D-glucosamine pH 7.0, 37°C Bacillus subtilis
3.5.1.104 12.3
-
 GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc pH 7.0, 37°C Bacillus subtilis

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining
3.5.1.104 membrane
-
 Bacillus subtilis 16020
-

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.5.1.104 Ca2+ activates Bacillus subtilis
3.5.1.104 Mg2+ activates Bacillus subtilis
3.5.1.104 Mn2+ best activating metal ion Bacillus subtilis
3.5.1.104 additional information the enzyme requires divalent cations Bacillus subtilis
3.5.1.104 Ni2+ activates Bacillus subtilis
3.5.1.104 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]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
3.5.1.104 53000
-
 x * 53000, recombinant truncated enzyme, SDS-PAGE Bacillus subtilis

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.5.1.104 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 ?
-
 ?
3.5.1.104 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

EC Number Organism UniProt Comment Textmining
3.5.1.104 Bacillus subtilis
-
 gene pdaC
-
3.5.1.104 Bacillus subtilis 168
-
 gene pdaC
-

Purification (Commentary)

EC Number Purification (Comment) Organism
3.5.1.104 recombinant His-tagged truncated enzyme from Escherichia coli strain JM109 by affinity chromatography and dialysis Bacillus subtilis

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.5.1.104 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
-
 ?
3.5.1.104 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
-
 ?
3.5.1.104 GlcNAc-Mur[-L-Ala-D-Glu]-GlcNAc-MurNAcr[-L-Ala-D-Glu] + H2O i.e. 4S2P, deacetylation Bacillus subtilis ?
-
 ?
3.5.1.104 GlcNAc-Mur[-L-Ala-D-Glu]-GlcNAc-MurNAcr[-L-Ala-D-Glu] + H2O i.e. 4S2P, deacetylation Bacillus subtilis 168 ?
-
 ?
3.5.1.104 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 ?
-
 ?
3.5.1.104 additional information the purified recombinant enzyme shows no nuclease activity with DNA Bacillus subtilis ?
-
 ?
3.5.1.104 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 ?
-
 ?
3.5.1.104 additional information the purified recombinant enzyme shows no nuclease activity with DNA Bacillus subtilis 168 ?
-
 ?
3.5.1.104 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
-
 ?
3.5.1.104 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

EC Number Subunits Comment Organism
3.5.1.104 ? x * 53000, recombinant truncated enzyme, SDS-PAGE Bacillus subtilis
3.5.1.104 More enzyme domain structure and structure comparisons, overview Bacillus subtilis

Synonyms

EC Number Synonyms Comment Organism
3.5.1.104 GlcNAc deacetylase
-
 Bacillus subtilis
3.5.1.104 MurNAc deacetylase
-
 Bacillus subtilis
3.5.1.104 PdaC
-
 Bacillus subtilis
3.5.1.104 polysaccharide deacetylase C
-
 Bacillus subtilis
3.5.1.104 YjeA
-
 Bacillus subtilis

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
3.5.1.104 37
-
 assay at Bacillus subtilis

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.5.1.104 0.24
-
 GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc pH 7.0, 37°C Bacillus subtilis
3.5.1.104 0.32
-
 peptidoglycan-N-acetyl-D-glucosamine pH 7.0, 37°C Bacillus subtilis

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.5.1.104 7
-
 assay at Bacillus subtilis

General Information

EC Number General Information Comment Organism
3.5.1.104 malfunction a pdaC deletion mutant is sensitive to lysozyme treatment Bacillus subtilis
3.5.1.104 physiological function gene pdcA is regulated by an essential two-component system, YycFG, which is associated with cell division Bacillus subtilis