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Literature summary extracted from

  • Hattie, M.; Ito, T.; Debowski, A.W.; Arakawa, T.; Katayama, T.; Yamamoto, K.; Fushinobu, S.; Stubbs, K.A.
    Gaining insight into the catalysis by GH20 lacto-N-biosidase using small molecule inhibitors and structural analysis (2015), Chem. Commun. (Camb.), 51, 15008-15011 .
    View publication on PubMed

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.2.1.140 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

EC Number Inhibitors Comment Organism Structure
3.2.1.140 1,3-bis[4-(5,6-dimethyl-1H-benzimidazol-2-yl)phenyl]urea
-
 Bifidobacterium bifidum
3.2.1.140 2-acetamido-2-deoxy-3-O-(beta-D-galactopyranosyl)-D-gluconohydroxyimino-1,5-lactone
-
 Bifidobacterium bifidum
3.2.1.140 2-acetamido-3-O-(beta-D-galactopyranosyl)-1,5-imino-1,2,5-trideoxy-D-glucitol
-
 Bifidobacterium bifidum
3.2.1.140 6-acetamido-6-deoxy-7-O-(beta-D-galactopyranosyl)castanospermine
-
 Bifidobacterium bifidum
3.2.1.140 8-acetamido-8-deoxy-2-O-(beta-D-galactopyranosyl)australine
-
 Bifidobacterium bifidum
3.2.1.140 additional information small molecule inhibitors docking to enzyme LnbB, compound synthesis, structure analysis and inhibition mode, NMR spectrometrci analysis, overview Bifidobacterium bifidum
3.2.1.140 O-(2-acetamido-2-deoxy-3-O-(beta-D-galactopyranosyl)-D-glucopyranosylidene)amino N-phenyl carbamate
-
 Bifidobacterium bifidum

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.2.1.140 lacto-N-tetraose + H2O Bifidobacterium bifidum
-
 lacto-N-biose + lactose
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
3.2.1.140 Bifidobacterium bifidum B3TLD6
-
-

Reaction

EC Number Reaction Comment Organism Reaction ID
3.2.1.140 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
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.2.1.140 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
-
 ?
3.2.1.140 lacto-N-tetraose + H2O
-
 Bifidobacterium bifidum lacto-N-biose + lactose
-
 ?

Synonyms

EC Number Synonyms Comment Organism
3.2.1.140 BbLNBase
-
 Bifidobacterium bifidum
3.2.1.140 GH20 lacto-N-biosidase
-
 Bifidobacterium bifidum
3.2.1.140 LnbB
-
 Bifidobacterium bifidum

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
3.2.1.140 37
-
 assay at Bifidobacterium bifidum

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.2.1.140 4.5
-
 assay at Bifidobacterium bifidum

Ki Value [mM]

EC Number Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
3.2.1.140 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
3.2.1.140 0.000125
-
 1,3-bis[4-(5,6-dimethyl-1H-benzimidazol-2-yl)phenyl]urea pH 4.5, 37°C Bifidobacterium bifidum
3.2.1.140 0.00052
-
 6-acetamido-6-deoxy-7-O-(beta-D-galactopyranosyl)castanospermine pH 4.5, 37°C Bifidobacterium bifidum
3.2.1.140 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
3.2.1.140 0.0077
-
 2-acetamido-2-deoxy-3-O-(beta-D-galactopyranosyl)-D-gluconohydroxyimino-1,5-lactone pH 4.5, 37°C Bifidobacterium bifidum
3.2.1.140 0.052
-
 8-acetamido-8-deoxy-2-O-(beta-D-galactopyranosyl)australine pH 4.5, 37°C Bifidobacterium bifidum

General Information

EC Number General Information Comment Organism
3.2.1.140 evolution the enzyme belongs to the glycosyl hydrolase family 20, GH20 Bifidobacterium bifidum
3.2.1.140 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