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Literature summary 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

Cloned(Commentary)

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

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.5.1.105 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

EC Number Protein Variants Comment Organism
3.5.1.105 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]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.5.1.105 0.24
-
 GlcNAc-beta-(1,4)-GlcNAc pH 7.0, 37°C, recombinant enzyme Vibrio parahaemolyticus
3.5.1.105 1.93
-
 GlcNAc-beta-(1,4)-GlcNAc pH 7.0, 37°C, recombinant mutant enzyme lacking the carbohydrate-binding domains Vibrio parahaemolyticus

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.5.1.105 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)

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

Organism

EC Number Organism UniProt Comment Textmining
3.5.1.105 Vibrio parahaemolyticus A6P4T5
-
-
3.5.1.105 Vibrio parahaemolyticus KN1699 A6P4T5
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
3.5.1.105 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)

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

Subunits

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

Synonyms

EC Number Synonyms Comment Organism
3.5.1.105 chitin oligosaccharide deacetylase
-
 Vibrio parahaemolyticus
3.5.1.105 Vp-COD
-
 Vibrio parahaemolyticus

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
3.5.1.105 37
-
 assay at Vibrio parahaemolyticus

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.5.1.105 21.6
-
 GlcNAc-beta-(1,4)-GlcNAc pH 7.0, 37°C, recombinant mutant enzyme lacking the carbohydrate-binding domains Vibrio parahaemolyticus
3.5.1.105 29.5
-
 GlcNAc-beta-(1,4)-GlcNAc pH 7.0, 37°C, recombinant enzyme Vibrio parahaemolyticus

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.5.1.105 7
-
 assay at Vibrio parahaemolyticus

General Information

EC Number General Information Comment Organism
3.5.1.105 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
3.5.1.105 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
3.5.1.105 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]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
3.5.1.105 11.2
-
 GlcNAc-beta-(1,4)-GlcNAc pH 7.0, 37°C, recombinant mutant enzyme lacking the carbohydrate-binding domains Vibrio parahaemolyticus
3.5.1.105 122
-
 GlcNAc-beta-(1,4)-GlcNAc pH 7.0, 37°C, recombinant enzyme Vibrio parahaemolyticus