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Literature summary extracted from

  • Fujita, K.; Sakamoto, A.; Kaneko, S.; Kotake, T.; Tsumuraya, Y.; Kitahara, K.
    Degradative enzymes for type II arabinogalactan side chains in Bifidobacterium longum subsp. longum (2019), Appl. Microbiol. Biotechnol., 103, 1299-1310 .
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
3.2.1.55 DNA and amino acid sequence determination and analysis, domain structure, phylogenetic analysis, recombinant expression of C-terminally His-tagged enzyme without the N-terminal signal peptide in Escherichia coli strain BL21(DE3) Bifidobacterium longum subsp. Longum
3.2.1.145 DNA and amino acid sequence determination and analysis, domain structure, phylogenetic analysis, recombinant expression of C-terminally His-tagged enzyme in Escherichia coli strain BL21(DE3) Bifidobacterium longum subsp. Longum
3.2.1.213 expression of C-terminal deletion mutant of Bl1,6Gal with a C-terminal His-tag (Bl1,6Gal-CDELTA248) Bifidobacterium longum subsp. Longum

Inhibitors

EC Number Inhibitors Comment Organism Structure
3.2.1.55 EDTA inhibits 47% at 1 mM Bifidobacterium longum subsp. Longum

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.2.1.55 additional information
-
additional information Km for larch type II arabinogalactan is 7.86 mg/ml for the recombinant enzyme Bifidobacterium longum subsp. Longum
3.2.1.213 0.549
-
beta-D-Gal(1->6)-beta-D-Gal-(1->6)-D-Gal pH 4.5, 40°C Bifidobacterium longum subsp. Longum

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.2.1.55 Ca2+ activates 24% at 1 mM Bifidobacterium longum subsp. Longum

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
3.2.1.213 133000
-
C-terminal deletion mutant of Bl1,6Gal with a C-terminal His-tag (Bl1,6Gal-CDELTA248), SDS-PAGE Bifidobacterium longum subsp. Longum

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.2.1.213 (1->6)-beta-D-galactooligosaccharide + H2O Bifidobacterium longum subsp. Longum degradative enzyme for type II arabinogalactan side chains in cooperation with exo-beta-1,3-galactanase. The enzyme, characterized from the bacterium Bifidobacterium longum, specifically hydrolyses (1->6)-beta-galactobiose from the non-reducing terminal of (1->6)-beta-D-galactooligosaccharides with a degree of polymerization of 3 or higher, using an exo mode of action. The enzyme cannot hydrolyse alpha-L-arabinofuranosylated (1->6)-beta-galactans (as found in arabinogalactans) and does not act on (1->3)-beta-D- or (1->4)-beta-D-galactans (1->6)-beta-D-galactobiose + ?
-
?

Organism

EC Number Organism UniProt Comment Textmining
3.2.1.55 Bifidobacterium longum subsp. Longum A0A401ETL2
-
-
3.2.1.145 Bifidobacterium longum subsp. Longum A0A401ETL2
-
-
3.2.1.213 Bifidobacterium longum subsp. Longum A0A401ETL2
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
3.2.1.55 recombinant C-terminally His-tagged enzyme without the N-terminal signal peptide from Escherichia coli strain BL21(DE3) Bifidobacterium longum subsp. Longum
3.2.1.145 recombinant C-terminally His-tagged enzyme from Escherichia coli strain BL21(DE3) Bifidobacterium longum subsp. Longum
3.2.1.213 C-terminal deletion mutant of Bl1,6Gal with a C-terminal His-tag (Bl1,6Gal-CDELTA248) Bifidobacterium longum subsp. Longum

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.2.1.55 4-nitrophenyl alpha-L-arabinofuranoside + H2O
-
Bifidobacterium longum subsp. Longum 4-nitrophenol + L-arabinofuranose
-
?
3.2.1.55 arabinan + H2O release of L-arabinofuranose Bifidobacterium longum subsp. Longum L-arabinofuranose + ?
-
?
3.2.1.55 beta-D-Galp-(1->6)-[alpha-L-Araf-(1->3)]-beta-D-Galp-(1->6)-beta-D-Galp + H2O recombinant BlArafA releases L-arabinose from the substrate, which is a beta-1,6-galactan side chain containing alpha-1,3-linked L-Araf Bifidobacterium longum subsp. Longum L-arabinofuranose + beta-D-Gal-(1->6)-beta-D-Gal-(1->6)-beta-D-Gal
-
?
3.2.1.55 gum arabic + H2O release of L-arabinofuranose, low activity Bifidobacterium longum subsp. Longum L-arabinofuranose + ?
-
?
3.2.1.55 larch type II arabinogalactan + H2O release of L-arabinofuranose, degradation profiles of type II AG Bifidobacterium longum subsp. Longum L-arabinofuranose + ?
-
?
3.2.1.55 methyl alpha-L-Araf-(1->2)-alpha-L-Araf + H2O low activity compared to methyl alpha-L-Araf-(1->3)-alpha-L-Araf Bifidobacterium longum subsp. Longum L-arabinofuranose + L-Araf-alpha-O-methyl ether
-
?
3.2.1.55 methyl alpha-L-Araf-(1->3)-alpha-L-Araf + H2O
-
Bifidobacterium longum subsp. Longum L-arabinofuranose + L-Araf-alpha-O-methyl ether
-
?
3.2.1.55 methyl alpha-L-Araf-(1->5)-alpha-L-Araf + H2O low activity compared to methyl alpha-L-Araf-(1->3)-alpha-L-Araf Bifidobacterium longum subsp. Longum L-arabinofuranose + L-Araf-alpha-O-methyl ether
-
?
3.2.1.55 additional information the recombinant alpha-L-arabinofuranosidase releases arabinofuranose (Araf) from alpha-1,3-Araf-substituted beta-1,6-galactooligosaccharides. beta-1,6-Gal2 is additively released from larch type II arabinogalactan (AG) by the combined use of type II AG degradative enzymes, including Bl1,3Gal, Bl1,6Gal, and BlArafA. GH30_5 exo-beta-1,6-galactobiohydrolase (Bl1,6Gal, EC 3.2.1.145) and GH43_22 alpha-L-arabinofuranosidase (BlArafA, EC 3.2.1.55) are degradative enzymes for type II arabinogalactan (AG) side chains in cooperation with GH43_24 exo-beta-1,3-galactanase (Bl1,3Gal, EC 3.2.1.145). Degradative mechanism, overview. The enzyme shows 100, 86.1, and 69.1% specificities for radish root AGP, larch AG, and arabinan, respectively. Arabinoxylan is a poor substrate. BlArafA is an alpha-L-arabinofuranosidase, which recognizes oligosaccharides containing alpha-1,3-linked L-Araf structures in type II AG and arabinan Bifidobacterium longum subsp. Longum ?
-
?
3.2.1.55 radish root arabinogalactan-protein + H2O release of L-arabinofuranose Bifidobacterium longum subsp. Longum L-arabinofuranose + ?
-
?
3.2.1.145 beta-1,6-Gal2-galactitol + H2O the enzyme specifically releases beta-1,6-Gal2 but not galactose from beta-1,6-Gal2-Gat Bifidobacterium longum subsp. Longum beta-1,6-Gal2 + galactitol
-
?
3.2.1.145 beta-1,6-Gal3 + H2O
-
Bifidobacterium longum subsp. Longum beta-1,6-Gal2 + D-galactose
-
?
3.2.1.145 beta-1,6-galactooligosaccharides + H2O the enzyme releases beta-1,6-Gal2 from beta-1,6-galactooligosaccharides (beta-1,6-Gal>9) in a time-dependent manner with low rates of beta-1,6-Gal3 and beta-1,6-Gal4 Bifidobacterium longum subsp. Longum beta-1,6-Gal2 + ?
-
?
3.2.1.145 larch type II arabinogalactan + H2O degradation profiles of type II AG Bifidobacterium longum subsp. Longum ?
-
?
3.2.1.145 larch type II arabinogalactan + H2O release of galactobiose, beta-1,6-Gal2, degradation profiles of type II AG Bifidobacterium longum subsp. Longum beta-1,6-Gal2 + ?
-
?
3.2.1.145 additional information the recombinant exo-beta-1,6-galactobiohydrolase specifically releases beta-1,6-galactobiose (beta-1,6-Gal2) from the nonreducing terminal of beta-1,6-galactooligosaccharides. beta-1,6-Gal2 is additively released from larch type II arabinogalactan (AG) by the combined use of type II AG degradative enzymes, including Bl1,3Gal, Bl1,6Gal, and BlArafA. GH30_5 exo-beta-1,6-galactobiohydrolase (Bl1,6Gal, EC 3.2.1.145) and GH43_22 alpha-L-arabinofuranosidase (BlArafA, EC 3.2.1.55) are degradative enzymes for type II arabinogalactan (AG) side chains in cooperation with GH43_24 exo-beta-1,3-galactanase (Bl1,3Gal, EC 3.2.1.145). Degradative mechanism, overview Bifidobacterium longum subsp. Longum ?
-
?
3.2.1.213 (1->6)-beta-D-galactooligosaccharide + H2O degradative enzyme for type II arabinogalactan side chains in cooperation with exo-beta-1,3-galactanase. The enzyme, characterized from the bacterium Bifidobacterium longum, specifically hydrolyses (1->6)-beta-galactobiose from the non-reducing terminal of (1->6)-beta-D-galactooligosaccharides with a degree of polymerization of 3 or higher, using an exo mode of action. The enzyme cannot hydrolyse alpha-L-arabinofuranosylated (1->6)-beta-galactans (as found in arabinogalactans) and does not act on (1->3)-beta-D- or (1->4)-beta-D-galactans Bifidobacterium longum subsp. Longum (1->6)-beta-D-galactobiose + ?
-
?
3.2.1.213 (1->6)-beta-D-galactooligosaccharide + H2O the enzyme, characterized from the bacterium Bifidobacterium longum, specifically hydrolyses (1->6)-beta-galactobiose from the non-reducing terminal of (1->6)-beta-D-galactooligosaccharides with a degree of polymerization of 3 or higher, using an exo mode of action. The enzyme cannot hydrolyse alpha-L-arabinofuranosylated (1->6)-beta-galactans (as found in arabinogalactans) and does not act on (1->3)-beta-D- or (1->4)-beta-D-galactans Bifidobacterium longum subsp. Longum (1->6)-beta-D-galactobiose + ?
-
?
3.2.1.213 beta-D-Gal(1->6)-beta-D-Gal-(1->6)-D-Gal + H2O
-
Bifidobacterium longum subsp. Longum (1->6)-beta-D-galactobiose + beta-D-galactose
-
?
3.2.1.213 dearabinosylated larch arabinogalactan + H2O
-
Bifidobacterium longum subsp. Longum (1->6)-beta-D-galactobiose + ?
-
?

Subunits

EC Number Subunits Comment Organism
3.2.1.55 ? x * 133000, recombinant His-tagged enzyme without signal peptide, SDS-PAGE, x * 132981, His-tagged enzyme without signal peptide, sequence calculation Bifidobacterium longum subsp. Longum
3.2.1.145 ? x * 116000, recombinant His-tagged enzyme, SDS-PAGE, x * 113302, His-tagged enzyme, sequence calculation Bifidobacterium longum subsp. Longum

Synonyms

EC Number Synonyms Comment Organism
3.2.1.55 BlAraf
-
Bifidobacterium longum subsp. Longum
3.2.1.55 blArafA
-
Bifidobacterium longum subsp. Longum
3.2.1.55 GH43_22 alpha-L-arabinofuranosidase
-
Bifidobacterium longum subsp. Longum
3.2.1.145 Bl1,3Gal
-
Bifidobacterium longum subsp. Longum
3.2.1.145 Bl1,6Gal
-
Bifidobacterium longum subsp. Longum
3.2.1.145 exo-beta-1,3-galactanase
-
Bifidobacterium longum subsp. Longum
3.2.1.145 exo-beta-1,6-galactobiohydrolase
-
Bifidobacterium longum subsp. Longum
3.2.1.145 GH30_5 exo-beta-1,6-galactobiohydrolase
-
Bifidobacterium longum subsp. Longum
3.2.1.145 GH43_24 exo-beta-1,3-galactanase
-
Bifidobacterium longum subsp. Longum
3.2.1.213 1,6Gal
-
Bifidobacterium longum subsp. Longum
3.2.1.213 Bl1,6Gal
-
Bifidobacterium longum subsp. Longum
3.2.1.213 exo-beta-1,6-galactobiohydrolase
-
Bifidobacterium longum subsp. Longum

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
3.2.1.55 50
-
recombinant enzyme Bifidobacterium longum subsp. Longum
3.2.1.145 40
-
assay at Bifidobacterium longum subsp. Longum
3.2.1.213 40
-
substrate: beta-D-Gal(1->6)-beta-D-Gal-(1->6)-D-Gal Bifidobacterium longum subsp. Longum

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.2.1.55 220
-
larch type II arabinogalactan pH 5.5, 40°C, recombinant enzyme Bifidobacterium longum subsp. Longum
3.2.1.213 261
-
beta-D-Gal(1->6)-beta-D-Gal-(1->6)-D-Gal pH 4.5, 40°C Bifidobacterium longum subsp. Longum

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.2.1.55 5.5
-
recombinant enzyme Bifidobacterium longum subsp. Longum
3.2.1.145 4.5
-
assay at Bifidobacterium longum subsp. Longum
3.2.1.213 4.5
-
substrate: beta-D-Gal(1->6)-beta-D-Gal-(1->6)-D-Gal Bifidobacterium longum subsp. Longum

General Information

EC Number General Information Comment Organism
3.2.1.55 evolution the enzyme belongs to the glycosyl hydrolase family 43, GH43, subfamily 5. GH43_24 exo-beta-1,3-galactanase (Bl1,3Gal, EC 3.2.1.145) forms a gene cluster with GH30_5 and GH43_22 enzyme candidates, which are conserved in all Bifidobacterium longum strains Bifidobacterium longum subsp. Longum
3.2.1.55 metabolism GH30_5 exo-beta-1,6-galactobiohydrolase (Bl1,6Gal, EC 3.2.1.145) and GH43_22 alpha-L-arabinofuranosidase (BlArafA, EC 3.2.1.55) are degradative enzymes for type II arabinogalactan (AG) side chains in cooperation with GH43_24 exo-beta-1,3-galactanase (Bl1,3Gal, EC 3.2.1.145) Bifidobacterium longum subsp. Longum
3.2.1.55 physiological function type II arabinogalactan (AG) degradative enzymes, including Bl1,3Gal, Bl1,6Gal, and BlArafA. GH30_5 exo-beta-1,6-galactobiohydrolase (Bl1,6Gal, EC 3.2.1.145) and GH43_22 alpha-L-arabinofuranosidase (BlArafA, EC 3.2.1.55) are important for the acquisition of type II AG in Bifidobacterium longum Bifidobacterium longum subsp. Longum
3.2.1.145 evolution the enzyme belongs to the glycosyl hydrolase family 30, GH30, subfamily 22. GH43_24 exo-beta-1,3-galactanase (Bl1,3Gal, EC 3.2.1.145) forms a gene cluster with GH30_5 and GH43_22 enzyme candidates, which are conserved in all Bifidobacterium longum strains Bifidobacterium longum subsp. Longum
3.2.1.145 evolution the enzyme belongs to the glycosyl hydrolase family 43, GH43, subfamily 24. GH43_24 exo-beta-1,3-galactanase (Bl1,3Gal) forms a gene cluster with GH30_5 exo-beta-1,6-galactobiohydrolase (Bl1,6Gal) and GH43_22 alpha-L-arabinofuranosidase (BlArafA) enzyme candidates, which are conserved in all Bifidobacterium longum strains Bifidobacterium longum subsp. Longum
3.2.1.145 metabolism GH30_5 exo-beta-1,6-galactobiohydrolase (Bl1,6Gal, EC 3.2.1.145) and GH43_22 alpha-L-arabinofuranosidase (BlArafA, EC 3.2.1.55) are degradative enzymes for type II arabinogalactan (AG) side chains in cooperation with GH43_24 exo-beta-1,3-galactanase (Bl1,3Gal, EC 3.2.1.145) Bifidobacterium longum subsp. Longum
3.2.1.145 metabolism GH30_5 exo-beta-1,6-galactobiohydrolase (Bl1,6Gal, EC 3.2.1.145) and GH43_22 alpha-L-arabinofuranosidase (BlArafA, EC 3.2.1.55), which are degradative enzymes for type II arabinogalactan (AG) side chains in cooperation with GH43_24 exo-beta-1,3-galactanase (Bl1,3Gal, EC 3.2.1.145) Bifidobacterium longum subsp. Longum
3.2.1.145 physiological function type II arabinogalactan (AG) degradative enzymes, including Bl1,3Gal, Bl1,6Gal, and BlArafA. GH30_5 exo-beta-1,6-galactobiohydrolase (Bl1,6Gal, EC 3.2.1.145) and GH43_22 alpha-L-arabinofuranosidase (BlArafA, EC 3.2.1.55) are important for the acquisition of type II AG in Bifidobacterium longum Bifidobacterium longum subsp. Longum
3.2.1.213 physiological function degradative enzyme for type II arabinogalactan side chains in cooperation with exo-beta-1,3-galactanase Bifidobacterium longum subsp. Longum