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Literature summary for 3.2.1.3 extracted from
- Structural insight into industrially relevant glucoamylases flexible positions of starch-binding domains (2018), Acta Crystallogr. Sect. D, 74, 463-470 .
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| gene GAMP, recombinant expression of the enzyme in Aspergillus niger strain MBin118 | Amorphotheca resinae |
| gene GLAA, recombinant expression of the enzyme in Aspergillus niger strain MBin118 | Aspergillus niger |
| gene PDE_05527, recombinant expression of the enzyme in Aspergillus niger strain MBin118 | Penicillium oxalicum |
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| purified recombinant enzyme, sitting drop vapour diffusion method, mixing of 150 nl of 18 mg/ml protein in 25 mM piperazine, pH 5.0, and 150 mM NaCl, with 150 nl of reservoir solution containing 0.1 M HEPES, pH 7.5, and 25% PEG 3350, 20°C, X-ray diffraction structure determination and analysis at 2.3 A resolution, molecular replacement using the catalytic domain of Aspergillus awamori glucoamylase as a search model (PDB entry 1glm) | Aspergillus niger |
| purified recombinant enzyme, sitting drop vapour diffusion method, mixing of 150 nl of 37 mg/ml protein in 20 mM sodium acetate, pH 5.0, with 150 nl of reservoir solution containing 60% Tacsimate, pH 7.0, 20°C, X-ray diffraction structure determination and analysis at 3.6 A resolution, molecular replacement using the catalytic domain of Aspergillus awamori glucoamylase as a search model (PDB entry 1glm) | Amorphotheca resinae |
| purified recombinant enzyme, sitting drop vapour diffusion method, mixing of 200 nl of 10 mg/ml protein in 20 mM Tris-HCl, pH 7.5, 50 mM NaCl, with 150 nl of reservoir solution containing 100 nl of sodium propionate + sodium cacodylate, bis-tris-propane, pH 4.0, and 25% PEG 1500, and 50 nl of 0.2% thiodiglycolic acid, 0.2% adipic acid, 0.2% benzoic acid, 0.2% anhydrous oxalic acid, 0.2% terephthalic acid, and 20 mM HEPES, pH 6.8, and with 50 nl of a seeding stock solution containing 0.2 M sodium sulfate, and 20% PEG 3350, 20°C, X-ray diffraction structure determination and analysis at 2.0 A resolution, molecular replacement using the catalytic domain of Aspergillus awamori glucoamylase as a search model (PDB entry 1glm) | Penicillium oxalicum |
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| acarbose | binding structure, overview. Found in the active sites of both independent monomers. In both monomers an acarbose molecule is fitted and refined, assuming full occupancy | Amorphotheca resinae |  |
| acarviosine | the inhibitor occupies the active-site pocket with the cyclohexitol moiety of acarviosine populating the -1 subsite | Amorphotheca resinae | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Amorphotheca resinae | Q03045 | i.e. Hormoconis resinae | - |
| Aspergillus niger | P69328 | - |
- |
| Penicillium oxalicum | S7ZIW0 | i.e. Penicillium decumbens | - |
| Penicillium oxalicum 114-2 | S7ZIW0 | i.e. Penicillium decumbens | - |
| Penicillium oxalicum CGMCC 5302 | S7ZIW0 | i.e. Penicillium decumbens | - |
Posttranslational Modification
| Posttranslational Modification | Comment | Organism |
|---|---|---|
| glycoprotein | O-glycosylation is observed in enzyme AnGA, in particular in the linker domain, which connects to the carbohydrate-binding domain. Only two sites, at Ser483 and Ser484, can be modelled with confidence. The catalytic domain of AnGA has two resolved N-glycosylation sites at Asn195 and Asn419, with two GlcNAc residues visible at Asn195 and one at Asn419 | Aspergillus niger |
| glycoprotein | the enzyme is N-glycosylated. The purified recombinant enzyme is treated with enzyme Endo H to minimize N-glycosylation. The full-length structure of PoGA shows a greater degree of N-glycosylation, PoGA three glycosylation sites at Asn184, Asn410 and Asn514 are observed, most extensive at Asn184 | Penicillium oxalicum |
| glycoprotein | the model of enzyme HrGA with two molecules in the asymmetric unit includes residues 29-616 and up to seven N-glycosylation sites and has acarbose bound in the active site. The full-length structure of HrGA shows extensive N-glycosylation, where the resolved sites are at Asn99, Asn200, Asn427, Asn500, Asn514, Asn528 and Asn587. Asn200 is the only site that shows branching of the glycosylation chain | Amorphotheca resinae |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant enzyme from Aspergillus niger strain MBin118 by alpha-cyclodextrin affinity chromatography, elution with beta-cyclodextrin, followed by dialysis and ultrafiltration, to homogeneity | Penicillium oxalicum |
| recombinant enzyme from Aspergillus niger strain MBin118 by alpha-cyclodextrin affinity chromatography, elution with beta-cyclodextrin, followed by dialysis, to homogeneity | Aspergillus niger |
| recombinant enzyme from Aspergillus niger strain MBin118 by alpha-cyclodextrin affinity chromatography, elution with beta-cyclodextrin, followed by dialysis, to homogeneity | Amorphotheca resinae |
Reaction
| Reaction | Comment | Organism | Reaction ID |
|---|---|---|---|
| (alpha-D-glucopyranosyl-(1-4))n-alpha-D-glucopyranose + H2O = (alpha-D-glucopyranosyl-(1-4))n-1-alpha-D-glucopyranose + beta-D-glucopyranose | the enzyme catalyses the cleavage of alpha-1,4- and alpha-1,6-glycosidic bonds. Glucoamylases use a classical acid/base Koshland-type inverting mechanism, releasing alpha-glucose from the nonreducing end of an alpha-glucan chain | Aspergillus niger | |
| (alpha-D-glucopyranosyl-(1-4))n-alpha-D-glucopyranose + H2O = (alpha-D-glucopyranosyl-(1-4))n-1-alpha-D-glucopyranose + beta-D-glucopyranose | the enzyme catalyses the cleavage of alpha-1,4- and alpha-1,6-glycosidic bonds. Glucoamylases use a classical acid/base Koshland-type inverting mechanism, releasing alpha-glucose from the nonreducing end of an alpha-glucan chain | Penicillium oxalicum | |
| (alpha-D-glucopyranosyl-(1-4))n-alpha-D-glucopyranose + H2O = (alpha-D-glucopyranosyl-(1-4))n-1-alpha-D-glucopyranose + beta-D-glucopyranose | the enzyme catalyses the cleavage of alpha-1,4- and alpha-1,6-glycosidic bonds. Glucoamylases use a classical acid/base Koshland-type inverting mechanism, releasing alpha-glucose from the nonreducing end of an alpha-glucan chain | Amorphotheca resinae |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| More | glucoamylases consist of a catalytic domain and a carbohydrate-binding domain (CBM), with the latter being important for the interaction with the polymeric substrate. The relative orientation between the carbohydrate-binding domain (CBM) and the catalytic domain is flexible, as the domains can adopt different orientations independently of ligand binding, suggesting a role as an anchor to increase the contact time and the relative concentration of substrate near the active site. The C-terminal CBM adopts the well known beta-sandwich motif, which is a hallmark of carbohydrate-binding modules | Aspergillus niger |
| More | glucoamylases consist of a catalytic domain and a carbohydrate-binding domain (CBM), with the latter being important for the interaction with the polymeric substrate. The relative orientation between the carbohydrate-binding domain (CBM) and the catalytic domain is flexible, as the domains can adopt different orientations independently of ligand binding, suggesting a role as an anchor to increase the contact time and the relative concentration of substrate near the active site. The C-terminal CBM adopts the well known beta-sandwich motif, which is a hallmark of carbohydrate-binding modules | Penicillium oxalicum |
| More | glucoamylases consist of a catalytic domain and a carbohydrate-binding domain (CBM), with the latter being important for the interaction with the polymeric substrate. The relative orientation between the carbohydrate-binding domain (CBM) and the catalytic domain is flexible, as the domains can adopt different orientations independently of ligand binding, suggesting a role as an anchor to increase the contact time and the relative concentration of substrate near the active site. The model of enzyme HrGA with two molecules in the asymmetric unit includes residues 29-616 and up to seven N-glycosylation sites and has acarbose bound in the active site. The C-terminal CBM adopts the well known beta-sandwich motif, which is a hallmark of carbohydrate-binding modules | Amorphotheca resinae |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| AnGA | - |
Aspergillus niger |
| GAMP | - |
Amorphotheca resinae |
| GlaA | - |
Aspergillus niger |
| glucoamylase | - |
Aspergillus niger |
| glucoamylase | - |
Penicillium oxalicum |
| glucoamylase P | - |
Amorphotheca resinae |
| HrGA | - |
Amorphotheca resinae |
| PDE_05527 | - |
Penicillium oxalicum |
| PoGA | - |
Penicillium oxalicum |
pI Value
| Organism | Comment | pI Value Maximum | pI Value |
|---|---|---|---|
| Penicillium oxalicum | - |
- |
6 |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | the enzyme is a member of the glycoside hydrolase family 15 (GH15) | Aspergillus niger |
| evolution | the enzyme is a member of the glycoside hydrolase family 15 (GH15) | Penicillium oxalicum |
| evolution | the enzyme is a member of the glycoside hydrolase family 15 (GH15) | Amorphotheca resinae |
| additional information | the relative orientation between the carbohydrate-binding domain (CBM) and the catalytic domain is flexible, as the domains can adopt different orientations independently of ligand binding, suggesting a role as an anchor to increase the contact time and the relative concentration of substrate near the active site. The C-terminal CBM adopts the well known beta-sandwich motif, which is a hallmark of carbohydrate-binding modules | Aspergillus niger |
| additional information | the relative orientation between the carbohydrate-binding domain (CBM) and the catalytic domain is flexible, as the domains can adopt different orientations independently of ligand binding, suggesting a role as an anchor to increase the contact time and the relative concentration of substrate near the active site. The C-terminal CBM adopts the well known beta-sandwich motif, which is a hallmark of carbohydrate-binding modules | Penicillium oxalicum |
| additional information | the relative orientation between the carbohydrate-binding domain (CBM) and the catalytic domain is flexible, as the domains can adopt different orientations independently of ligand binding, suggesting a role as an anchor to increase the contact time and the relative concentration of substrate near the active site. The model of enzyme HrGA with two molecules in the asymmetric unit includes residues 29-616 and up to seven N-glycosylation sites and has acarbose bound in the active site. The C-terminal CBM adopts the well known beta-sandwich motif, which is a hallmark of carbohydrate-binding modules | Amorphotheca resinae |
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