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Literature summary for 3.5.1.105 extracted from

  • Hirano, T.; Sugiyama, K.; Sakaki, Y.; Hakamata, W.; Park, S.Y.; Nishio, T.
    Structure-based analysis of domain function of chitin oligosaccharide deacetylase from Vibrio parahaemolyticus (2015), FEBS Lett., 589, 145-151.
    View publication on PubMed
Search for more literature for 3.5.1.105

Cloned(Commentary)

Cloned (Comment) Organism
recombinant expression of wild-type and mutant enzymes in Escherichia coli strain BL21(DE3) Vibrio parahaemolyticus

Crystallization (Commentary)

Crystallization (Comment) Organism
purified recombinant enzyme, hanging drop vapor diffusion method, mixing of 20 mg/ml protein in 20 mM sodium phosphate, pH 7.0, with an equal volume of reservoir solution containing 0.1 M Tris-HCl, pH 7.0, 10% w/v PEG 8000, and 0.2 M MgCl2, 4 weeks, 20°C, X-ray diffraction structure determination and analysis at 1.35 A resolution Vibrio parahaemolyticus

Protein Variants

Protein Variants Comment Organism
additional information removal of the carbohydrate-binding domains is unlikely to affect the configuration of the active center residues in the polysaccharide deacetylase domain, although that of amino acid residues interacting with (GlcNAc)2 changes slightly Vibrio parahaemolyticus

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.24
-
 GlcNAc-beta-(1,4)-GlcNAc pH 7.0, 37°C, recombinant enzyme Vibrio parahaemolyticus
1.93
-
 GlcNAc-beta-(1,4)-GlcNAc pH 7.0, 37°C, recombinant mutant enzyme lacking the carbohydrate-binding domains Vibrio parahaemolyticus

Metals/Ions

Metals/Ions Comment Organism Structure
Zn2+ one Zn2+ ion is bound in the active site pocket. The zinc ion is coordinated by the triad consisting of an aspartic acid residue (Asp36) and two histidine residues (His93 and His97), which are located near the zinc ion Vibrio parahaemolyticus

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
GlcNAc-beta-(1,4)-GlcNAc + H2O Vibrio parahaemolyticus
-
 GlcNAc-beta-(1,4)-GlcN + acetate
-
 ?
GlcNAc-beta-(1,4)-GlcNAc + H2O Vibrio parahaemolyticus KN1699
-
 GlcNAc-beta-(1,4)-GlcN + acetate
-
 ?

Organism

Organism UniProt Comment Textmining
Vibrio parahaemolyticus A6P4T5
-
-
Vibrio parahaemolyticus KN1699 A6P4T5
-
-

Purification (Commentary)

Purification (Comment) Organism
recombinant wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by ammonium sulfate fractionation, anion exchange chromatography and gel filtration Vibrio parahaemolyticus

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
GlcNAc-beta-(1,4)-GlcNAc + H2O
-
 Vibrio parahaemolyticus GlcNAc-beta-(1,4)-GlcN + acetate
-
 ?
GlcNAc-beta-(1,4)-GlcNAc + H2O
-
 Vibrio parahaemolyticus KN1699 GlcNAc-beta-(1,4)-GlcN + acetate
-
 ?

Subunits

Subunits Comment Organism
More the enzyme comprises one polysaccharide deacetylase domain and two carbohydrate-binding domains Vibrio parahaemolyticus

Synonyms

Synonyms Comment Organism
chitin oligosaccharide deacetylase
-
 Vibrio parahaemolyticus
Vp-COD
-
 Vibrio parahaemolyticus

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
37
-
 assay at Vibrio parahaemolyticus

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
21.6
-
 GlcNAc-beta-(1,4)-GlcNAc pH 7.0, 37°C, recombinant mutant enzyme lacking the carbohydrate-binding domains Vibrio parahaemolyticus
29.5
-
 GlcNAc-beta-(1,4)-GlcNAc pH 7.0, 37°C, recombinant enzyme Vibrio parahaemolyticus

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7
-
 assay at Vibrio parahaemolyticus

General Information

General Information Comment Organism
evolution the enzyme belongs to the carbohydrate esterase family 4. Amino acid residues that officiate as the metal ion-binding triad and general acid–base catalysts are generally conserved in other Zn-dependent deacetylases Vibrio parahaemolyticus
additional information His291 and Asp35, which are in the vicinity of the zinc ion-binding triad, act as the catalytic base and acid, respectively. The enzyme comprises one polysaccharide deacetylase domain and two carbohydrate-binding domains. The carbohydrate-binding domains are unlikely to affect the configuration of the active center residues in active site of polysaccharide deacetylase domain, overview Vibrio parahaemolyticus
physiological function the enzyme generates beta-N-acetyl-D-glucosaminyl-(1,4)-D-glucosamine from (GlcNAc)2, in strain KN1699, GlcNAc-GlcN is an end product of chitin degradation outside the cell Vibrio parahaemolyticus

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
11.2
-
 GlcNAc-beta-(1,4)-GlcNAc pH 7.0, 37°C, recombinant mutant enzyme lacking the carbohydrate-binding domains Vibrio parahaemolyticus
122
-
 GlcNAc-beta-(1,4)-GlcNAc pH 7.0, 37°C, recombinant enzyme Vibrio parahaemolyticus