BRENDA - Enzyme Database
show all sequences of 3.2.1.145

Crystal structure of a putative exo-beta-1,3-galactanase from Bifidobacterium bifidum S17

Godoy, A.S.; de Lima, M.Z.; Camilo, C.M.; Polikarpov, I.; Acta Crystallogr. Sect. F 72, 288-293 (2016)

Data extracted from this reference:

Cloned(Commentary)
Cloned (Commentary)
Organism
gene BBNG_01788, sequence comparisons, recombinant expression of Trx-His-tagged enzyme in Escherichia coli strain Rosetta (DE3)
Bifidobacterium bifidum
Crystallization (Commentary)
Crystallization (Commentary)
Organism
purified recombinant enzyme, vapour diffusion method, mixing of 0.001 ml of 80 mg/ml protein in 0.02 M HEPES, pH 7.5, and 0.15 M NaCl, with 0.001 ml of reservoir solution containing 0.05 M calcium chloride dihydrate,0.1 M bis-Tris pH 6.5, 30% v/v polyethylene glycol monomethyl ether 550, and equilibration against 80.00 ml of reservoir solution, 17C, X-ray diffraction structure determination and analysis at 1.4 A resolution, molecular replacement using using domain I of the Bacteroides thetaiotaomicron glycosyl hydrolase as search model, PDB ID 3nqh, modelling
Bifidobacterium bifidum
Molecular Weight [Da]
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
67300
-
recombinant detagged enzyme, gel filtration
Bifidobacterium bifidum
Organism
Organism
UniProt
Commentary
Textmining
Bifidobacterium bifidum
E4VCC5
-
-
Bifidobacterium bifidum NCIMB 41171
E4VCC5
-
-
Bifidobacterium bifidum S17
E4VCC5
-
-
Purification (Commentary)
Purification (Commentary)
Organism
recombinant Trx-His-tagged enzyme from Escherichia coli strain Rosetta (DE3) by nickel affinity chromatography, tag cleavage through TEV protease, and another step of nickel affinity chromatography, followed by gel filtration, to homogeneity
Bifidobacterium bifidum
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
Substrate Product ID
additional information
the recombinant BbGal43A shows activity towards synthetic galactosides
752397
Bifidobacterium bifidum
?
-
-
-
-
additional information
the recombinant BbGal43A shows activity towards synthetic galactosides
752397
Bifidobacterium bifidum S17
?
-
-
-
-
additional information
the recombinant BbGal43A shows activity towards synthetic galactosides
752397
Bifidobacterium bifidum NCIMB 41171
?
-
-
-
-
Subunits
Subunits
Commentary
Organism
dimer
2 * 34000, recombinant detagged enzyme, SDS-PAGE
Bifidobacterium bifidum
More
crystal contact analysis predicts the formation of a dimer in solution. The structure shows a single-domain molecule, differing from known homologues. BbGal43A has a typical fivefold beta-propeller fold, with the propellers formed by four beta-sheets
Bifidobacterium bifidum
Synonyms
Synonyms
Commentary
Organism
BbGal43A
-
Bifidobacterium bifidum
exo-beta-1,3-galactanase
-
Bifidobacterium bifidum
Cloned(Commentary) (protein specific)
Commentary
Organism
gene BBNG_01788, sequence comparisons, recombinant expression of Trx-His-tagged enzyme in Escherichia coli strain Rosetta (DE3)
Bifidobacterium bifidum
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified recombinant enzyme, vapour diffusion method, mixing of 0.001 ml of 80 mg/ml protein in 0.02 M HEPES, pH 7.5, and 0.15 M NaCl, with 0.001 ml of reservoir solution containing 0.05 M calcium chloride dihydrate,0.1 M bis-Tris pH 6.5, 30% v/v polyethylene glycol monomethyl ether 550, and equilibration against 80.00 ml of reservoir solution, 17C, X-ray diffraction structure determination and analysis at 1.4 A resolution, molecular replacement using using domain I of the Bacteroides thetaiotaomicron glycosyl hydrolase as search model, PDB ID 3nqh, modelling
Bifidobacterium bifidum
Molecular Weight [Da] (protein specific)
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
67300
-
recombinant detagged enzyme, gel filtration
Bifidobacterium bifidum
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant Trx-His-tagged enzyme from Escherichia coli strain Rosetta (DE3) by nickel affinity chromatography, tag cleavage through TEV protease, and another step of nickel affinity chromatography, followed by gel filtration, to homogeneity
Bifidobacterium bifidum
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ID
additional information
the recombinant BbGal43A shows activity towards synthetic galactosides
752397
Bifidobacterium bifidum
?
-
-
-
-
additional information
the recombinant BbGal43A shows activity towards synthetic galactosides
752397
Bifidobacterium bifidum S17
?
-
-
-
-
additional information
the recombinant BbGal43A shows activity towards synthetic galactosides
752397
Bifidobacterium bifidum NCIMB 41171
?
-
-
-
-
Subunits (protein specific)
Subunits
Commentary
Organism
dimer
2 * 34000, recombinant detagged enzyme, SDS-PAGE
Bifidobacterium bifidum
More
crystal contact analysis predicts the formation of a dimer in solution. The structure shows a single-domain molecule, differing from known homologues. BbGal43A has a typical fivefold beta-propeller fold, with the propellers formed by four beta-sheets
Bifidobacterium bifidum
General Information
General Information
Commentary
Organism
evolution
the enzyme belongs to the glycosyl hydrolase family 43, GH43. Structure comparisons reveal that structural and sequence homology between BbGal43A, Clostridium thermocellum Ct1,3Gal43A (PDB ID 3vsf), and Bacteroides thetaiotaomicron BT2959 (PDB ID 3nqh) indicate that all three enzymes might be different types of exo-beta-1,3-galactanase
Bifidobacterium bifidum
General Information (protein specific)
General Information
Commentary
Organism
evolution
the enzyme belongs to the glycosyl hydrolase family 43, GH43. Structure comparisons reveal that structural and sequence homology between BbGal43A, Clostridium thermocellum Ct1,3Gal43A (PDB ID 3vsf), and Bacteroides thetaiotaomicron BT2959 (PDB ID 3nqh) indicate that all three enzymes might be different types of exo-beta-1,3-galactanase
Bifidobacterium bifidum
Other publictions for EC
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Synonyms
Temperature Optimum [C]
Temperature Range [C]
Temperature Stability [C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [C] (protein specific)
Temperature Range [C] (protein specific)
Temperature Stability [C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
752571
Fujita
Degradative enzymes for type ...
Bifidobacterium longum subsp. Longum
Appl. Microbiol. Biotechnol.
103
1299-1310
2019
-
-
1
-
-
-
-
-
-
-
-
-
-
3
-
-
1
-
-
-
-
-
6
1
6
1
-
-
-
1
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
6
1
1
-
-
-
1
-
-
-
-
3
3
-
-
-
752397
Godoy
Crystal structure of a putati ...
Bifidobacterium bifidum, Bifidobacterium bifidum NCIMB 41171, Bifidobacterium bifidum S17
Acta Crystallogr. Sect. F
72
288-293
2016
-
-
1
1
-
-
-
-
-
-
1
-
-
5
-
-
1
-
-
-
-
-
3
2
2
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
1
-
-
-
-
-
-
-
-
1
-
-
-
-
1
-
-
-
-
3
2
-
-
-
-
-
-
-
-
-
1
1
-
-
-
731184
Fujita
Bifidobacterium longum subsp. ...
Bifidobacterium longum, Bifidobacterium longum JCM 1217
Appl. Environ. Microbiol.
80
4577-4584
2014
-
-
1
-
1
-
-
1
-
-
1
-
-
6
-
-
-
-
-
-
9
-
14
-
2
1
-
-
-
1
-
-
-
-
-
-
-
-
1
-
-
1
-
-
-
-
1
-
-
1
-
-
-
-
-
-
-
9
-
14
-
1
-
-
-
1
-
-
-
1
2
2
1
-
-
731202
Okawa
Identification of an exo-beta- ...
Fusarium oxysporum 12S, Fusarium oxysporum
Appl. Microbiol. Biotechnol.
97
9685-9694
2013
-
-
1
-
-
-
-
-
-
-
-
-
-
5
-
-
1
-
-
-
1
-
12
1
2
1
-
-
-
1
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
1
-
12
1
1
-
-
-
1
-
-
-
-
1
1
-
-
-
731581
Ling
An exo-beta-(1->3)-D-galactana ...
Streptomyces sp. 19(2012), Streptomyces sp.
Carbohydr. Res.
352
70-81
2012
-
1
1
-
-
-
-
-
-
-
3
4
-
6
-
-
1
-
-
-
1
-
12
1
4
1
-
-
-
2
-
-
-
-
1
-
-
2
2
-
-
-
-
-
-
-
-
-
-
3
4
-
-
-
2
-
-
2
-
12
2
2
-
-
-
2
-
-
2
-
1
2
-
-
-
732396
Jiang
Crystal structure of 1,3Gal43A ...
Hungateiclostridium thermocellum
J. Struct. Biol.
180
447-457
2012
-
-
1
1
2
-
-
-
-
-
2
-
-
4
-
-
1
-
-
-
-
-
1
2
3
1
-
-
-
1
-
-
-
-
-
-
-
-
1
-
1
2
-
-
-
-
-
-
-
2
-
-
-
-
1
-
-
-
-
1
2
1
-
-
-
1
-
-
-
-
2
2
-
-
-
713904
Sakamoto
Characterization of an exo-bet ...
Sphingomonas sp., Sphingomonas sp. 24T
Appl. Microbiol. Biotechnol.
90
1701-1710
2011
1
-
-
-
-
-
-
-
-
-
1
-
-
3
-
-
1
-
-
1
2
-
12
1
2
1
-
1
-
1
-
1
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
1
-
1
2
-
12
1
1
-
1
-
1
-
1
-
-
-
-
-
-
-
703061
Ling
Preparation of a new chromogen ...
Irpex lacteus
Carbohydr. Res.
344
1941-1946
2009
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
1
1
-
1
-
2
1
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
1
-
1
-
1
-
-
-
1
-
-
-
-
-
-
-
-
-
706965
Ishida
Crystallization of selenomethi ...
Phanerochaete chrysosporium
Acta Crystallogr. Sect. F
65
1274-1276
2009
-
-
1
1
-
-
-
-
-
-
-
-
-
2
-
-
1
-
-
-
-
-
-
1
3
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
707784
Kotake
Molecular cloning and expressi ...
Irpex lacteus, Irpex lacteus NBRC 5367
Biosci. Biotechnol. Biochem.
73
2303-2309
2009
-
-
1
-
-
-
-
-
-
-
1
-
-
2
-
-
1
-
-
-
1
-
4
1
2
1
1
-
-
1
1
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
1
-
-
1
-
4
1
1
1
-
-
1
1
-
-
-
-
-
-
-
-
677662
Ichinose
Characterization of an exo-bet ...
Hungateiclostridium thermocellum
Appl. Environ. Microbiol.
72
3515-3523
2006
-
-
1
-
-
-
-
-
-
-
1
-
-
4
-
-
1
-
-
-
1
-
5
-
2
2
-
-
-
1
1
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
1
-
-
1
-
5
-
2
-
-
-
1
1
-
-
-
-
-
-
-
-
678786
Ichinose
Characterization of an exo-bet ...
Streptomyces avermitilis, Streptomyces avermitilis NBRC 14893
Biosci. Biotechnol. Biochem.
70
2745-2750
2006
-
-
1
-
-
-
-
-
-
-
1
-
-
4
-
1
1
-
-
-
1
-
10
-
2
1
-
-
-
1
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
1
-
-
-
1
1
-
-
1
-
10
-
1
-
-
-
1
-
-
-
-
-
-
-
-
-
666634
Kotake
Molecular cloning of a b-galac ...
Raphanus sativus
Plant Physiol.
138
1563-1576
2005
-
-
1
-
-
-
4
3
-
-
2
-
-
4
-
-
1
-
-
-
1
-
10
1
1
1
-
1
3
1
1
-
-
-
-
-
-
-
1
-
-
-
-
-
4
-
3
-
-
2
-
-
-
-
1
-
-
1
-
10
1
1
-
1
3
1
1
-
-
-
-
-
-
-
-
171335
Tsumuraya
Purification of an exo-beta-(1 ...
Irpex lacteus
J. Biol. Chem.
265
7207-7215
1990
-
-
-
-
-
-
-
2
-
-
2
1
-
1
-
-
1
-
-
-
1
-
4
1
-
-
1
1
-
1
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
2
-
-
2
1
-
-
-
1
-
-
1
-
4
1
-
1
1
-
1
-
1
-
-
-
-
-
-
-