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Literature summary for 3.2.1.139 extracted from

  • Wang, W.; Yan, R.; Nocek, B.P.; Vuong, T.V.; Di Leo, R.; Xu, X.; Cui, H.; Gatenholm, P.; Toriz, G.; Tenkanen, M.; Savchenko, A.; Master, E.R.
    Biochemical and structural characterization of a five-domain GH115 alpha-Glucuronidase from the marine bacterium Saccharophagus degradans 2-40T (2016), J. Biol. Chem., 291, 14120-14133.
    View publication on PubMedView publication on EuropePMC
Search for more literature for 3.2.1.139

Cloned(Commentary)

Cloned (Comment) Organism
expression in Escherichia coli Saccharophagus degradans

Crystallization (Commentary)

Crystallization (Comment) Organism
structure reveals a five-domain architecture, with an additional insertion C+ domain that has significant impact on the domain arrangement of the protein monomer and its dimerization. The participation of domain C+ in substrate binding is supported by reduced substrate inhibition upon introducing W773A, W689A, and F696A substitutions within this domain. In addition to Asp335, residue Glu216 is essential for the catalytic activtiy Saccharophagus degradans

Protein Variants

Protein Variants Comment Organism
D215A 15fold decrease in catalytic efficiency Saccharophagus degradans
D335A complete loss of activtiy Saccharophagus degradans
D335A weak binding of substrate Saccharophagus degradans
E216A complete loss of activtiy Saccharophagus degradans
E381A 330fold decrease in catalytic efficiency Saccharophagus degradans
F696A 3-5fold decrease in kcat value Saccharophagus degradans
R331A 26000fold decrease in catalytic efficiency Saccharophagus degradans
W689A 3-5fold decrease in kcat value Saccharophagus degradans
W773A 3-5fold decrease in kcat value Saccharophagus degradans

Inhibitors

Inhibitors Comment Organism Structure
Ag+ 1 mM, 30% residual activity Saccharophagus degradans
Cd2+ 1 mM, 40% residual activity Saccharophagus degradans
Cu2+ 1 mM, no residual activity Saccharophagus degradans
Hg2+ 1 mM, no residual activity Saccharophagus degradans
additional information not inhibitory: EDTA at 10 mM Saccharophagus degradans
Ni2+ 1 mM, 70% residual activity Saccharophagus degradans
Zn2+ 1 mM, 10% residual activity Saccharophagus degradans

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
 birchwood xylan km vaule of wild-type 43 mg/ml, pH 6.5, 40°C Saccharophagus degradans

Molecular Weight [Da]

Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
70800
-
 sedimentation-equilibrium ultracentrifugation Saccharophagus degradans

Organism

Organism UniProt Comment Textmining
Saccharophagus degradans Q21JW4
-
-
Saccharophagus degradans DSM 17024 Q21JW4
-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
birchwood xylan + H2O
-
 Saccharophagus degradans 4-O-methyl-D-glucuronic acid + D-glucuronic acid + ?
-
 ?
birchwood xylan + H2O
-
 Saccharophagus degradans DSM 17024 4-O-methyl-D-glucuronic acid + D-glucuronic acid + ?
-
 ?
additional information the enzyme shows activity toward glucuronoxylan and oligomers thereof with preference toward 4-O-methyl glucopyranosyluronic acid linked to internal xylopyranosyl residues Saccharophagus degradans ?
-
 ?
additional information the enzyme shows activity toward glucuronoxylan and oligomers thereof with preference toward 4-O-methyl glucopyranosyluronic acid linked to internal xylopyranosyl residues Saccharophagus degradans DSM 17024 ?
-
 ?
oat spelt xylan + H2O
-
 Saccharophagus degradans 4-O-methyl-D-glucuronic acid + D-glucuronic acid + ? 1% of the activity with birchwood xylan ?
oat spelt xylan + H2O
-
 Saccharophagus degradans DSM 17024 4-O-methyl-D-glucuronic acid + D-glucuronic acid + ? 1% of the activity with birchwood xylan ?
spruce arabinoxylan + H2O
-
 Saccharophagus degradans 4-O-methyl-D-glucuronic acid + D-glucuronic acid + ? 37% of the activity with birchwood xylan ?
spruce arabinoxylan + H2O
-
 Saccharophagus degradans DSM 17024 4-O-methyl-D-glucuronic acid + D-glucuronic acid + ? 37% of the activity with birchwood xylan ?

Subunits

Subunits Comment Organism
dimer 2 * 109992, calculated Saccharophagus degradans

Synonyms

Synonyms Comment Organism
Agu115A
-
 Saccharophagus degradans
Sde_1755
-
 Saccharophagus degradans

Temperature Stability [°C]

Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
35
-
 half-life 90 min Saccharophagus degradans
40
-
 half-life 60 min Saccharophagus degradans
50
-
 half-life 2 min Saccharophagus degradans
70
-
 2 min, complete loss of activtiy Saccharophagus degradans

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.008
-
 birchwood xylan mutant R331A, pH 6.5, 40°C Saccharophagus degradans
0.3
-
 birchwood xylan mutant E381A, pH 6.5, 40°C Saccharophagus degradans
1
-
 birchwood xylan mutant D215A, pH 6.5, 40°C Saccharophagus degradans
86
-
 birchwood xylan mutant F696A, pH 6.5, 40°C Saccharophagus degradans
116
-
 birchwood xylan mutant W689A, pH 6.5, 40°C Saccharophagus degradans
129
-
 birchwood xylan mutant W773A, pH 6.5, 40°C Saccharophagus degradans
289
-
 birchwood xylan wild-type, pH 6.5, 40°C Saccharophagus degradans

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
6.5
-
-
 Saccharophagus degradans

pH Stability

pH Stability pH Stability Maximum Comment Organism
5.5 9.5 4°C, 24 h, more than 50% resiudal activity Saccharophagus degradans

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
additional information
-
 birchwood xylan kcat/Km value of wild-type 6.7 ml/s/ml, pH 6.5, 40°C Saccharophagus degradans