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Literature summary for 3.5.1.104 extracted from
- Characterization of the divalent metal binding site of bacterial polysaccharide deacetylase using crystallography and quantum chemical calculations (2014), Proteins, 82, 1311-1318.
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| gene hp0310, expression as N-terminally His6-tagged enzyme | Helicobacter pylori |
| gene hp0310, sequence comparison, recombinant expression of N-terminally His6-tagged enzyme | Helicobacter pylori |
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| purified recombinant N-terminally His6-tagged enzyme, vapor diffusion technique, mixing of 18 mg/ml protein solution with 0.2 M ammonium sulfate, 0.1 M tris sodium citrate, pH 5.6, and 15% w/v PEG 4000, 20°C, X-ray diffraction structure determination and analysis at 2.2 A resolution | Helicobacter pylori |
| purified recombinant N-terminally His6-tagged enzyme, vapor diffusion technique, mixing of 18 mg/ml protein solution with precipitant solution containing 0.2 M ammonium sulfate, 0.1 M tris sodium citrate, pH 5.6, and 15% w/v PEG 4000, 20°C, X-ray diffraction structure determination and analysis at 2.2 A resolution, molecular replacement and modeling | Helicobacter pylori |
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| EDTA | complete inhibition | Helicobacter pylori |  |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| additional information | metal site models show an intrinsic preference for zinc, but also significant flexibility of the site so that binding of other ions can eventually occur, e.g. Fe2+, Co2+, Cu2+, Mg2+, quantum chemical calculations, overview | Helicobacter pylori | |
| Zn2+ | the zinc ion of the metalloenzyme is coordinated by a conserved binding triad of amino acids consisting of one aspartate and two histidine residues, determination of the metal-binding site, which is essential for the enzyme's catalytic activity, one metal site per monomer, structure and quantum chemical calculations of models, overview. The metal ion occupies a tetrahedral environment with binding to one of the carboxylic oxygen of Asp14, His86, His90 and a water molecule | Helicobacter pylori | |
| Zn2+ | divalent metal binding site, one site per enzyme monomer, essential for the enzyme's catalytic activity, structure analysis, detailed overview | Helicobacter pylori | |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| peptidoglycan-N-acetyl-D-glucosamine + H2O | Helicobacter pylori | - |
peptidoglycan-D-glucosamine + acetate | - |
? | |
| peptidoglycan-N-acetyl-D-glucosamine + H2O | Helicobacter pylori | the enzyme catalyzes the removal of the acetyl group from the C2 atom of N-acetylglucosamine, which is a constituent of the peptidoglycan found in the cell walls of many bacteria | peptidoglycan-D-glucosamine + acetate | - |
? | |
| peptidoglycan-N-acetyl-D-glucosamine + H2O | Helicobacter pylori G27 | - |
peptidoglycan-D-glucosamine + acetate | - |
? | |
| peptidoglycan-N-acetyl-D-glucosamine + H2O | Helicobacter pylori G27 | the enzyme catalyzes the removal of the acetyl group from the C2 atom of N-acetylglucosamine, which is a constituent of the peptidoglycan found in the cell walls of many bacteria | peptidoglycan-D-glucosamine + acetate | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Helicobacter pylori | B5ZA76 | gene pgdA or hp0310 | - |
| Helicobacter pylori | B5ZA76 | gene hp0310 | - |
| Helicobacter pylori G27 | B5ZA76 | gene hp0310 | - |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant N-terminally His6-tagged enzyme | Helicobacter pylori |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| peptidoglycan-N-acetyl-D-glucosamine + H2O | - |
Helicobacter pylori | peptidoglycan-D-glucosamine + acetate | - |
? | |
| peptidoglycan-N-acetyl-D-glucosamine + H2O | the enzyme catalyzes the removal of the acetyl group from the C2 atom of N-acetylglucosamine, which is a constituent of the peptidoglycan found in the cell walls of many bacteria | Helicobacter pylori | peptidoglycan-D-glucosamine + acetate | - |
? | |
| peptidoglycan-N-acetyl-D-glucosamine + H2O | - |
Helicobacter pylori G27 | peptidoglycan-D-glucosamine + acetate | - |
? | |
| peptidoglycan-N-acetyl-D-glucosamine + H2O | the enzyme catalyzes the removal of the acetyl group from the C2 atom of N-acetylglucosamine, which is a constituent of the peptidoglycan found in the cell walls of many bacteria | Helicobacter pylori G27 | peptidoglycan-D-glucosamine + acetate | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| homotetramer | - |
Helicobacter pylori |
| tetramer | - |
Helicobacter pylori |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| HP0310 | - |
Helicobacter pylori |
| HpPgdA | - |
Helicobacter pylori |
| peptidoglycan deacetlyase | - |
Helicobacter pylori |
| pgdA | - |
Helicobacter pylori |
| polysaccharide deacetylase | - |
Helicobacter pylori |
General Information
| General Information | Comment | Organism |
|---|---|---|
| physiological function | the enzyme is responsible for a peptidoglycan modification that counteracts the host immune response | Helicobacter pylori |
| physiological function | peptidoglycan deacetylase is the enzyme responsible for a peptidoglycan modification that counteracts the host immune response | Helicobacter pylori |
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