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Literature summary for 3.1.1.58 extracted from

  • Pokrovskaya, V.; Poloczek, J.; Little, D.; Griffiths, H.; Howell, P.; Nitz, M.
    Functional characterization of Staphylococcus epidermidis IcaB, a de-N-acetylase important for biofilm formation (2013), Biochemistry, 52, 5463-5471.
    View publication on PubMed
Search for more literature for 3.1.1.58

Application

Application Comment Organism
medicine the enzyme is a potential therapeutic target for antibiofilm therapies Staphylococcus epidermidis

Cloned(Commentary)

Cloned (Comment) Organism
gene icaB, recombinant overexpression of N-terminally His10-tagged enzyme lacking the native N-terminal signal peptide in Escherichia coli strain BL21(DE3) Staphylococcus epidermidis

Protein Variants

Protein Variants Comment Organism
additional information enzyme deletion by transposon mutagenesis of gene icaB Staphylococcus epidermidis

Inhibitors

Inhibitors Comment Organism Structure
dipicolinic acid a metal chelator, complete inhibition Staphylococcus epidermidis
EDTA a metal chelator, complete inhibition Staphylococcus epidermidis
additional information metal chelation to the His-tag of the recombinant enzyme effects N-deacetylation activity Staphylococcus epidermidis

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
 additional information steady-state kinetics, overview Staphylococcus epidermidis
0.5
-
 3-carboxyumbelliferyl acetate recombinant enzyme, pH 7.5, 37°C Staphylococcus epidermidis
20
-
 beta-1,6-linked N-acetylglucosamine pentamer recombinant enzyme, pH 7.5, 37°C Staphylococcus epidermidis
30
-
 beta-1,6-linked N-acetylglucosamine trimer recombinant enzyme, pH 7.5, 37°C Staphylococcus epidermidis

Localization

Localization Comment Organism GeneOntology No. Textmining
extracellular
-
 Staphylococcus epidermidis
-
-

Metals/Ions

Metals/Ions Comment Organism Structure
Ca2+ slightly activating Staphylococcus epidermidis
Co2+ activating Staphylococcus epidermidis
Mg2+ slightly activating Staphylococcus epidermidis
Mn2+ slightly activating Staphylococcus epidermidis
Ni2+ slightly activating Staphylococcus epidermidis
Zn2+ required, best divalent metal ion Staphylococcus epidermidis

Molecular Weight [Da]

Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
33000
-
 recombinant enzyme, gel filtration Staphylococcus epidermidis
33113
-
 1 * 33113, recombinant His10-tagged enzyme, sequence calculation Staphylococcus epidermidis

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
beta-1,6-linked N-acetylglucosamine oligomers + H2O Staphylococcus epidermidis specific for the substrate partially de-N-acetylated beta-1,6-linked N-acetylglucosamine oligomer + acetate
-
 ?

Organism

Organism UniProt Comment Textmining
Staphylococcus epidermidis
-
 gene icaB
-

Purification (Commentary)

Purification (Comment) Organism
recombinant N-terminally His10-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, tag cleavage through Factor Xa protease, and ulrafiltration/dialysis Staphylococcus epidermidis

Storage Stability

Storage Stability Organism
4°C, purified recombinant detagged enzyme at about 5 mg/ml, in purification buffer containing 5% v/v glycerol, 10 days with no significant loss of activity Staphylococcus epidermidis

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3-carboxyumbelliferyl acetate + H2O
-
 Staphylococcus epidermidis 3-carboxyumbelliferol + acetate
-
 ?
beta-1,6-linked N-acetylglucosamine hexamer + H2O
-
 Staphylococcus epidermidis partially de-N-acetylated beta-1,6-linked N-acetylglucosamine hexamer + acetate
-
 ?
beta-1,6-linked N-acetylglucosamine oligomer + H2O the enzyme preferentially de-N-acetylates the second residue from the reducing terminus in the pentasaccharide and second and third residues from the reducing terminus in the hexasaccharide Staphylococcus epidermidis partially de-N-acetylated beta-1,6-linked N-acetylglucosamine oligomer + acetate
-
 ?
beta-1,6-linked N-acetylglucosamine oligomers + H2O specific for the substrate Staphylococcus epidermidis partially de-N-acetylated beta-1,6-linked N-acetylglucosamine oligomer + acetate
-
 ?
beta-1,6-linked N-acetylglucosamine pentamer + H2O
-
 Staphylococcus epidermidis partially de-N-acetylated beta-1,6-linked N-acetylglucosamine pentamer + acetate
-
 ?
beta-1,6-linked N-acetylglucosamine trimer + H2O
-
 Staphylococcus epidermidis partially de-N-acetylated beta-1,6-linked N-acetylglucosamine trimer + acetate
-
 ?
additional information the enzyme shows metal-dependent N-deacetylase activity on beta-1,6-linked N-acetylglucosamine oligomers with low catalytic efficiency toward the oligomeric substrates. While the enzyme displays similar rates of N-deacetylation with trisaccharide through hexasaccharide beta-1,6-linked N-acetylglucosamine oligomers, position specific de-N-acetylation is only observed with penta- and hexasaccharides Staphylococcus epidermidis ?
-
 ?

Subunits

Subunits Comment Organism
monomer 1 * 33113, recombinant His10-tagged enzyme, sequence calculation Staphylococcus epidermidis

Synonyms

Synonyms Comment Organism
beta-1,6-linked N-acetylglucosamine de-N-acetylase
-
 Staphylococcus epidermidis
de-N-acetylase
-
 Staphylococcus epidermidis
IcaB
-
 Staphylococcus epidermidis
PNAG de-N-acetylase
-
 Staphylococcus epidermidis

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
37
-
 assay at Staphylococcus epidermidis

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.0007
-
 beta-1,6-linked N-acetylglucosamine trimer recombinant enzyme, pH 7.5, 37°C Staphylococcus epidermidis
0.0007
-
 beta-1,6-linked N-acetylglucosamine pentamer recombinant enzyme, pH 7.5, 37°C Staphylococcus epidermidis
0.0013
-
 3-carboxyumbelliferyl acetate recombinant enzyme, pH 7.5, 37°C Staphylococcus epidermidis

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.5
-
 assay at Staphylococcus epidermidis

General Information

General Information Comment Organism
evolution the enzyme belongs to the family 4 carbohydrate esterases, CE4 Staphylococcus epidermidis
malfunction enzyme deletion causes dramatically reduced biofilm formation in vitro as well as reduced pathogenicity in animal models of biofilm infections Staphylococcus epidermidis
additional information the metal-dependent enzyme has a conserved His-His-Asp catalytic triad Staphylococcus epidermidis

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
0.000003
-
 partially de-N-acetylated beta-1,6-linked N-acetylglucosamine pentamer recombinant enzyme, pH 7.5, 37°C Staphylococcus epidermidis
0.00002
-
 partially de-N-acetylated beta-1,6-linked N-acetylglucosamine trimer recombinant enzyme, pH 7.5, 37°C Staphylococcus epidermidis
0.0025
-
 3-carboxyumbelliferyl acetate recombinant enzyme, pH 7.5, 37°C Staphylococcus epidermidis