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Literature summary for 4.2.2.19 extracted from

  • Michel, G.; Pojasek, K.; Li, Y.; Sulea, T.; Linhardt, R.J.; Raman, R.; Prabhakar, V.; Sasisekharan, R.; Cygler, M.
    The structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery (2004), J. Biol. Chem., 279, 32882-32896.
    View publication on PubMedView publication on EuropePMC
Search for more literature for 4.2.2.19

Crystallization (Commentary)

Crystallization (Comment) Organism
purified recombinant wild-type enzyme complexed with dermatan sulfate pentasaccharide and hexasaccharide, or chondroitin-4-sulfate tetrasacharide, X-ray diffraction structure determination and analysis at 1.7-1.8 A resolution, modeling of substrate binding in the active site groove Pedobacter heparinus

Protein Variants

Protein Variants Comment Organism
E243A site-directed mutagenesis, Ca2+-binding residue, about 3.6fold reduced activity compared to the wild-type enzyme Pedobacter heparinus
E243A/E245A site-directed mutagenesis, Ca2+-binding residue, about 4fold reduced activity compared to the wild-type enzyme Pedobacter heparinus
E245A site-directed mutagenesis, Ca2+-binding residue, about 6fold reduced activity compared to the wild-type enzyme Pedobacter heparinus
N213Q site-directed mutagenesis, Ca2+-binding residue, about 6fold reduced activity compared to the wild-type enzyme Pedobacter heparinus
R271E site-directed mutagenesis, active site mutant, catalytically inactive Pedobacter heparinus
R271K site-directed mutagenesis, active site mutant, about 10fold reduced activity compared to the wild-type enzyme Pedobacter heparinus

Inhibitors

Inhibitors Comment Organism Structure
EGTA complete inhibition Pedobacter heparinus

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.0012
-
 dermatan sulfate recombinant wild-type enzyme, pH 8.0, 30°C, in presence of 5 mM Ca2+ Pedobacter heparinus
0.0043
-
 dermatan sulfate recombinant wild-type enzyme, pH 8.0, 30°C, in presence of 0.01 mM Ca2+ Pedobacter heparinus

Metals/Ions

Metals/Ions Comment Organism Structure
Ca2+ dependent on, required for catalysis, activates, protein-Ca2+-oligosaccharide complex Pedobacter heparinus

Organism

Organism UniProt Comment Textmining
Pedobacter heparinus Q46079 i.e. Flavobacterium heparinum
-

Reaction

Reaction Comment Organism Reaction ID
[dermatan sulfate]n = [dermatan sulfate]n-1 + 4-deoxy-beta-D-gluc-4-enuronosyl-1,3-GalNAc acts on dermatan sulfate as sole substrate, enzyme cleaves the beta(1,4)-linkage of dermatan sulfate in a random manner, yielding 4,5-unsaturated dermatan sulfate disaccharides, calcium-dependent catalytic mechanism, active site structure Pedobacter heparinus
a

Specific Activity [micromol/min/mg]

Specific Activity Minimum [µmol/min/mg] Specific Activity Maximum [µmol/min/mg] Comment Organism
additional information
-
-
 Pedobacter heparinus

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
dermatan sulfate strictly specific for Pedobacter heparinus ?
-
 ?

Synonyms

Synonyms Comment Organism
ChonB
-
 Pedobacter heparinus
chondroitinase B
-
 Pedobacter heparinus

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
30
-
 assay at Pedobacter heparinus

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
210
-
 dermatan sulfate recombinant wild-type enzyme, pH 8.0, 30°C, in presence of 0.01 mM Ca2+ Pedobacter heparinus
410
-
 dermatan sulfate recombinant wild-type enzyme, pH 8.0, 30°C, in presence of 5 mM Ca2+ Pedobacter heparinus

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
8
-
 assay at Pedobacter heparinus