Literature summary for 3.2.1.140 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 .

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Crystallization (Commentary)

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

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

Inhibitors	Comment	Organism
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/ Products (Substrates)

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

Organism

Organism	UniProt	Comment	Textmining
Bifidobacterium bifidum	B3TLD6	-	-

Reaction

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	a

Substrates and Products (Substrate)

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

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

Temperature Optimum [°C]

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

pH Optimum

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

Ki Value [mM]

Ki Value [mM]	Ki Value maximum [mM]	Inhibitor	Comment	Organism
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

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