Crystallization (Comment) | Organism |
---|---|
purified enzyme in complex with inhibitors 2-acetamido-2-deoxy-3-O-(beta-D-galactopyranosyl)-D-gluconohydroxyimino-1,5-lactone, 2-acetamido-3-O-(beta-D-galactopyranosyl)-1,5-imino-1,2,5-trideoxy-D-glucitol, 6-acetamido-6-deoxy-7-O-(beta-D-galactopyranosyl)castanospermine, and 8-acetamido-8-deoxy-2-O-(beta-D-galactopyranosyl)australine, sitting drop vapor diffusion method, mixing of 0.001 ml of 10 mg/ml protein solution containing 0.1 mM ligand, with an equal volume of a reservoir solution containing 0.2 M potassium sodium tartrate tetrahydrate, 0.1 M sodium citrate, pH 5.6, and 2.0 M ammonium sulfate, 20°C, X-ray diffraction structure determination and analysis at 1.6-2.2 A resolution, modeling | Bifidobacterium bifidum |
Inhibitors | Comment | Organism | Structure |
---|---|---|---|
1,3-bis[4-(5,6-dimethyl-1H-benzimidazol-2-yl)phenyl]urea | - |
Bifidobacterium bifidum | |
2-acetamido-2-deoxy-3-O-(beta-D-galactopyranosyl)-D-gluconohydroxyimino-1,5-lactone | - |
Bifidobacterium bifidum | |
2-acetamido-3-O-(beta-D-galactopyranosyl)-1,5-imino-1,2,5-trideoxy-D-glucitol | - |
Bifidobacterium bifidum | |
6-acetamido-6-deoxy-7-O-(beta-D-galactopyranosyl)castanospermine | - |
Bifidobacterium bifidum | |
8-acetamido-8-deoxy-2-O-(beta-D-galactopyranosyl)australine | - |
Bifidobacterium bifidum | |
additional information | small molecule inhibitors docking to enzyme LnbB, compound synthesis, structure analysis and inhibition mode, NMR spectrometrci analysis, overview | Bifidobacterium bifidum | |
O-(2-acetamido-2-deoxy-3-O-(beta-D-galactopyranosyl)-D-glucopyranosylidene)amino N-phenyl carbamate | - |
Bifidobacterium bifidum |
Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|
lacto-N-tetraose + H2O | Bifidobacterium bifidum | - |
lacto-N-biose + lactose | - |
? |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Bifidobacterium bifidum | B3TLD6 | - |
- |
Reaction | Comment | Organism | Reaction ID |
---|---|---|---|
beta-D-Gal-(1->3)-beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->4)-D-Glc + H2O = beta-D-Gal-(1->3)-D-GlcNAc + beta-D-Gal-(1->4)-D-Glc | the enzyme performs a two-step catalytic mechanism involving substrate-assisted catalysis that forms a transient oxazoline or oxazolinium ion intermediate, mechanism overview | Bifidobacterium bifidum |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
4-methylumbelliferyl 2-acetamido-2-deoxy-3-O-(beta-D-galactopyranosyl)-D-glucopyranoside + H2O | - |
Bifidobacterium bifidum | 4-methylumbelliferol + 2-acetamido-2-deoxy-3-O-(beta-D-galactopyranosyl)-D-glucopyranose | - |
? | |
lacto-N-tetraose + H2O | - |
Bifidobacterium bifidum | lacto-N-biose + lactose | - |
? |
Synonyms | Comment | Organism |
---|---|---|
BbLNBase | - |
Bifidobacterium bifidum |
GH20 lacto-N-biosidase | - |
Bifidobacterium bifidum |
LnbB | - |
Bifidobacterium bifidum |
Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
---|---|---|---|
37 | - |
assay at | Bifidobacterium bifidum |
pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
---|---|---|---|
4.5 | - |
assay at | Bifidobacterium bifidum |
Ki Value [mM] | Ki Value maximum [mM] | Inhibitor | Comment | Organism | Structure |
---|---|---|---|---|---|
0.000091 | - |
O-(2-acetamido-2-deoxy-3-O-(beta-D-galactopyranosyl)-D-glucopyranosylidene)amino N-phenyl carbamate | pH 4.5, 37°C | Bifidobacterium bifidum | |
0.000125 | - |
1,3-bis[4-(5,6-dimethyl-1H-benzimidazol-2-yl)phenyl]urea | pH 4.5, 37°C | Bifidobacterium bifidum | |
0.00052 | - |
6-acetamido-6-deoxy-7-O-(beta-D-galactopyranosyl)castanospermine | pH 4.5, 37°C | Bifidobacterium bifidum | |
0.00088 | - |
2-acetamido-3-O-(beta-D-galactopyranosyl)-1,5-imino-1,2,5-trideoxy-D-glucitol | pH 4.5, 37°C | Bifidobacterium bifidum | |
0.0077 | - |
2-acetamido-2-deoxy-3-O-(beta-D-galactopyranosyl)-D-gluconohydroxyimino-1,5-lactone | pH 4.5, 37°C | Bifidobacterium bifidum | |
0.052 | - |
8-acetamido-8-deoxy-2-O-(beta-D-galactopyranosyl)australine | pH 4.5, 37°C | Bifidobacterium bifidum |
General Information | Comment | Organism |
---|---|---|
evolution | the enzyme belongs to the glycosyl hydrolase family 20, GH20 | Bifidobacterium bifidum |
physiological function | lacto-N-biosidase (LNBase), a beta-N-acetyl-hexosaminidase that liberates lacto-N-biose (LNB) from human milk oligosaccharides (HMOs), is important to the LNB pathway | Bifidobacterium bifidum |