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Literature summary extracted from

  • Nakamura, T.; Yonezawa, Y.; Tsuchiya, Y.; Niiyama, M.; Ida, K.; Oshima, M.; Morita, J.; Uegaki, K.
    Substrate recognition of N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii (2016), J. Struct. Biol., 195, 286-293 .
    View publication on PubMed

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.5.1.105 hanging drop vapor-diffusion method, the crystal structure of the enzyme in complex with 2-deoxy-2-methylphosphoramido-D-glucose demonstrates that Arg92, Asp115, and His152 side chains interact with hydroxyl groups of the glucose moiety of the non-reducing-end GlcNAc residue Pyrococcus horikoshii
3.5.1.105 purified enzyme in complex with 2-deoxy-2-methylphosphoramido-D-glucose, hanging drop vapor diffusion method, mixing of 0.001 ml of 20 mg/ml protein in 10 mM MPG, 20 mM Tris-HCl, pH 8.1, and 150 mM NaCl, with 0.001 ml of reservoir solution containing either 0.4 M ammonium phosphate (reservoir 1) or 100 mM sodium acetate, pH 4.6, 10 mM CoCl2, and 1 M 1,6-hexanediol (reservoir 2), equilibration against 0.4 ml of reservoir solution, 20°C, X-ray diffraction structure determiantion and analysis at 1.8-1.9 A resolution, modelling Pyrococcus horikoshii
3.5.1.136 hanging drop vapor-diffusion method at 20°C, crystal structure of the enzyme in complex with the inhibitor 2-deoxy-2-methylphosphoramido-D-glucose Pyrococcus horikoshii

Inhibitors

EC Number Inhibitors Comment Organism Structure
3.5.1.136 2-deoxy-2-methylphosphoramido-D-glucose
-
 Pyrococcus horikoshii

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.5.1.105 Zn2+ the Ph-Dac crystal structure contains a phosphate ion bound to the metal ion, catalytic Zn2+ Pyrococcus horikoshii

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.5.1.105 N,N'-diacetylchitobiose + H2O Pyrococcus horikoshii
-
 N-acetyl-beta-D-glucosaminyl-D-glucosamine + acetate
-
 ?
3.5.1.105 N,N'-diacetylchitobiose + H2O Pyrococcus horikoshii DSM 12428
-
 N-acetyl-beta-D-glucosaminyl-D-glucosamine + acetate
-
 ?
3.5.1.105 N,N'-diacetylchitobiose + H2O Pyrococcus horikoshii NBRC 100139
-
 N-acetyl-beta-D-glucosaminyl-D-glucosamine + acetate
-
 ?
3.5.1.105 N,N'-diacetylchitobiose + H2O Pyrococcus horikoshii JCM 9974
-
 N-acetyl-beta-D-glucosaminyl-D-glucosamine + acetate
-
 ?
3.5.1.105 N,N'-diacetylchitobiose + H2O Pyrococcus horikoshii ATCC 700860
-
 N-acetyl-beta-D-glucosaminyl-D-glucosamine + acetate
-
 ?
3.5.1.105 N,N'-diacetylchitobiose + H2O Pyrococcus horikoshii OT-3
-
 N-acetyl-beta-D-glucosaminyl-D-glucosamine + acetate
-
 ?
3.5.1.136 N,N'-diacetylchitobiose + H2O Pyrococcus horikoshii the enzyme is involved in the archaea-specific chitinolytic pathways by deacetylating the disaccharide end product of chitinase beta-D-glucosaminyl-(1->4)-N-acetyl-D-glucosamine + acetate
-
 ?
3.5.1.136 N,N'-diacetylchitobiose + H2O Pyrococcus horikoshii DSM 12428 the enzyme is involved in the archaea-specific chitinolytic pathways by deacetylating the disaccharide end product of chitinase beta-D-glucosaminyl-(1->4)-N-acetyl-D-glucosamine + acetate
-
 ?
3.5.1.136 N,N'-diacetylchitobiose + H2O Pyrococcus horikoshii NBRC 100139 the enzyme is involved in the archaea-specific chitinolytic pathways by deacetylating the disaccharide end product of chitinase beta-D-glucosaminyl-(1->4)-N-acetyl-D-glucosamine + acetate
-
 ?
3.5.1.136 N,N'-diacetylchitobiose + H2O Pyrococcus horikoshii JCM 9974 the enzyme is involved in the archaea-specific chitinolytic pathways by deacetylating the disaccharide end product of chitinase beta-D-glucosaminyl-(1->4)-N-acetyl-D-glucosamine + acetate
-
 ?
3.5.1.136 N,N'-diacetylchitobiose + H2O Pyrococcus horikoshii ATCC 700860 the enzyme is involved in the archaea-specific chitinolytic pathways by deacetylating the disaccharide end product of chitinase beta-D-glucosaminyl-(1->4)-N-acetyl-D-glucosamine + acetate
-
 ?
3.5.1.136 N,N'-diacetylchitobiose + H2O Pyrococcus horikoshii OT-3 the enzyme is involved in the archaea-specific chitinolytic pathways by deacetylating the disaccharide end product of chitinase beta-D-glucosaminyl-(1->4)-N-acetyl-D-glucosamine + acetate
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
3.5.1.105 Pyrococcus horikoshii O58235
-
-
3.5.1.105 Pyrococcus horikoshii ATCC 700860 O58235
-
-
3.5.1.105 Pyrococcus horikoshii DSM 12428 O58235
-
-
3.5.1.105 Pyrococcus horikoshii JCM 9974 O58235
-
-
3.5.1.105 Pyrococcus horikoshii NBRC 100139 O58235
-
-
3.5.1.105 Pyrococcus horikoshii OT-3 O58235
-
-
3.5.1.136 Pyrococcus horikoshii O58235
-
-
3.5.1.136 Pyrococcus horikoshii ATCC 700860 O58235
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.5.1.105 N,N'-diacetylchitobiose + H2O
-
 Pyrococcus horikoshii N-acetyl-beta-D-glucosaminyl-(1->4)-D-glucosamine + acetate
-
 ?
3.5.1.105 N,N'-diacetylchitobiose + H2O
-
 Pyrococcus horikoshii DSM 12428 N-acetyl-beta-D-glucosaminyl-(1->4)-D-glucosamine + acetate
-
 ?
3.5.1.105 N,N'-diacetylchitobiose + H2O
-
 Pyrococcus horikoshii NBRC 100139 N-acetyl-beta-D-glucosaminyl-(1->4)-D-glucosamine + acetate
-
 ?
3.5.1.105 N,N'-diacetylchitobiose + H2O
-
 Pyrococcus horikoshii JCM 9974 N-acetyl-beta-D-glucosaminyl-(1->4)-D-glucosamine + acetate
-
 ?
3.5.1.105 N,N'-diacetylchitobiose + H2O
-
 Pyrococcus horikoshii ATCC 700860 N-acetyl-beta-D-glucosaminyl-(1->4)-D-glucosamine + acetate
-
 ?
3.5.1.105 N,N'-diacetylchitobiose + H2O
-
 Pyrococcus horikoshii OT-3 N-acetyl-beta-D-glucosaminyl-(1->4)-D-glucosamine + acetate
-
 ?
3.5.1.105 N,N'-diacetylchitobiose + H2O
-
 Pyrococcus horikoshii N-acetyl-beta-D-glucosaminyl-D-glucosamine + acetate
-
 ?
3.5.1.105 N,N'-diacetylchitobiose + H2O
-
 Pyrococcus horikoshii DSM 12428 N-acetyl-beta-D-glucosaminyl-D-glucosamine + acetate
-
 ?
3.5.1.105 N,N'-diacetylchitobiose + H2O
-
 Pyrococcus horikoshii NBRC 100139 N-acetyl-beta-D-glucosaminyl-D-glucosamine + acetate
-
 ?
3.5.1.105 N,N'-diacetylchitobiose + H2O
-
 Pyrococcus horikoshii JCM 9974 N-acetyl-beta-D-glucosaminyl-D-glucosamine + acetate
-
 ?
3.5.1.105 N,N'-diacetylchitobiose + H2O
-
 Pyrococcus horikoshii ATCC 700860 N-acetyl-beta-D-glucosaminyl-D-glucosamine + acetate
-
 ?
3.5.1.105 N,N'-diacetylchitobiose + H2O
-
 Pyrococcus horikoshii OT-3 N-acetyl-beta-D-glucosaminyl-D-glucosamine + acetate
-
 ?
3.5.1.105 N-acetyl-D-glucosamine + H2O
-
 Pyrococcus horikoshii D-glucosamine + acetate
-
 ?
3.5.1.105 N-acetyl-D-glucosamine + H2O
-
 Pyrococcus horikoshii DSM 12428 D-glucosamine + acetate
-
 ?
3.5.1.105 N-acetyl-D-glucosamine + H2O
-
 Pyrococcus horikoshii NBRC 100139 D-glucosamine + acetate
-
 ?
3.5.1.105 N-acetyl-D-glucosamine + H2O
-
 Pyrococcus horikoshii JCM 9974 D-glucosamine + acetate
-
 ?
3.5.1.105 N-acetyl-D-glucosamine + H2O
-
 Pyrococcus horikoshii ATCC 700860 D-glucosamine + acetate
-
 ?
3.5.1.105 N-acetyl-D-glucosamine + H2O
-
 Pyrococcus horikoshii OT-3 D-glucosamine + acetate
-
 ?
3.5.1.136 N,N'-diacetylchitobiose + H2O the enzyme is involved in the archaea-specific chitinolytic pathways by deacetylating the disaccharide end product of chitinase Pyrococcus horikoshii beta-D-glucosaminyl-(1->4)-N-acetyl-D-glucosamine + acetate
-
 ?
3.5.1.136 N,N'-diacetylchitobiose + H2O the crystal structure of the enzyme in complex with 2-deoxy-2-methylphosphoramido-D-glucose demonstrates that Arg92, Asp115, and His152 side chains interact with hydroxyl groups of the glucose moiety of the non-reducing-end GlcNAc residue Pyrococcus horikoshii beta-D-glucosaminyl-(1->4)-N-acetyl-D-glucosamine + acetate
-
 ?
3.5.1.136 N,N'-diacetylchitobiose + H2O the enzyme is involved in the archaea-specific chitinolytic pathways by deacetylating the disaccharide end product of chitinase Pyrococcus horikoshii DSM 12428 beta-D-glucosaminyl-(1->4)-N-acetyl-D-glucosamine + acetate
-
 ?
3.5.1.136 N,N'-diacetylchitobiose + H2O the crystal structure of the enzyme in complex with 2-deoxy-2-methylphosphoramido-D-glucose demonstrates that Arg92, Asp115, and His152 side chains interact with hydroxyl groups of the glucose moiety of the non-reducing-end GlcNAc residue Pyrococcus horikoshii DSM 12428 beta-D-glucosaminyl-(1->4)-N-acetyl-D-glucosamine + acetate
-
 ?
3.5.1.136 N,N'-diacetylchitobiose + H2O the enzyme is involved in the archaea-specific chitinolytic pathways by deacetylating the disaccharide end product of chitinase Pyrococcus horikoshii NBRC 100139 beta-D-glucosaminyl-(1->4)-N-acetyl-D-glucosamine + acetate
-
 ?
3.5.1.136 N,N'-diacetylchitobiose + H2O the crystal structure of the enzyme in complex with 2-deoxy-2-methylphosphoramido-D-glucose demonstrates that Arg92, Asp115, and His152 side chains interact with hydroxyl groups of the glucose moiety of the non-reducing-end GlcNAc residue Pyrococcus horikoshii NBRC 100139 beta-D-glucosaminyl-(1->4)-N-acetyl-D-glucosamine + acetate
-
 ?
3.5.1.136 N,N'-diacetylchitobiose + H2O the enzyme is involved in the archaea-specific chitinolytic pathways by deacetylating the disaccharide end product of chitinase Pyrococcus horikoshii JCM 9974 beta-D-glucosaminyl-(1->4)-N-acetyl-D-glucosamine + acetate
-
 ?
3.5.1.136 N,N'-diacetylchitobiose + H2O the crystal structure of the enzyme in complex with 2-deoxy-2-methylphosphoramido-D-glucose demonstrates that Arg92, Asp115, and His152 side chains interact with hydroxyl groups of the glucose moiety of the non-reducing-end GlcNAc residue Pyrococcus horikoshii JCM 9974 beta-D-glucosaminyl-(1->4)-N-acetyl-D-glucosamine + acetate
-
 ?
3.5.1.136 N,N'-diacetylchitobiose + H2O the enzyme is involved in the archaea-specific chitinolytic pathways by deacetylating the disaccharide end product of chitinase Pyrococcus horikoshii ATCC 700860 beta-D-glucosaminyl-(1->4)-N-acetyl-D-glucosamine + acetate
-
 ?
3.5.1.136 N,N'-diacetylchitobiose + H2O the crystal structure of the enzyme in complex with 2-deoxy-2-methylphosphoramido-D-glucose demonstrates that Arg92, Asp115, and His152 side chains interact with hydroxyl groups of the glucose moiety of the non-reducing-end GlcNAc residue Pyrococcus horikoshii ATCC 700860 beta-D-glucosaminyl-(1->4)-N-acetyl-D-glucosamine + acetate
-
 ?
3.5.1.136 N,N'-diacetylchitobiose + H2O the enzyme is involved in the archaea-specific chitinolytic pathways by deacetylating the disaccharide end product of chitinase Pyrococcus horikoshii OT-3 beta-D-glucosaminyl-(1->4)-N-acetyl-D-glucosamine + acetate
-
 ?
3.5.1.136 N,N'-diacetylchitobiose + H2O the crystal structure of the enzyme in complex with 2-deoxy-2-methylphosphoramido-D-glucose demonstrates that Arg92, Asp115, and His152 side chains interact with hydroxyl groups of the glucose moiety of the non-reducing-end GlcNAc residue Pyrococcus horikoshii OT-3 beta-D-glucosaminyl-(1->4)-N-acetyl-D-glucosamine + acetate
-
 ?

Subunits

EC Number Subunits Comment Organism
3.5.1.105 hexamer dimer of trimers Pyrococcus horikoshii
3.5.1.105 More the Pyrococcus Dac enzyme forms a homohexamer composed of two trimers. A deep cleft exists between two polypeptides in each trimeric assembly, with the central Zn being chelated at the bottom by two His residues and one Asp residue. Determination, analysis and modelling of tertiary structure of Ph-Dac Pyrococcus horikoshii
3.5.1.136 homohexamer compoed of two trimers Pyrococcus horikoshii

Synonyms

EC Number Synonyms Comment Organism
3.5.1.105 CE-14 deacetylase
-
 Pyrococcus horikoshii
3.5.1.105 Dac
-
 Pyrococcus horikoshii
3.5.1.105 N,N'-diacetylchitobiose deacetylase
-
 Pyrococcus horikoshii
3.5.1.105 Ph-Dac
-
 Pyrococcus horikoshii
3.5.1.105 PH0499
-
 Pyrococcus horikoshii
3.5.1.136 Dac
-
 Pyrococcus horikoshii
3.5.1.136 N,N'-diacetylchitobiose deacetylase
-
 Pyrococcus horikoshii

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
3.5.1.105 25
-
 assay at Pyrococcus horikoshii

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.5.1.105 7
-
 assay at Pyrococcus horikoshii

General Information

EC Number General Information Comment Organism
3.5.1.105 evolution the enzyme belongs to carbohydrate esterase (CE) family 14 Pyrococcus horikoshii
3.5.1.105 metabolism N,N'-diacetylchitobiose deacetylase (Dac) belongs to the CE-14 family and plays a role in the chitinolytic pathway in archaea by deacetylating N,N'-diacetylchitobiose (GlcNAc2), which is the end product of chitinase Pyrococcus horikoshii
3.5.1.105 additional information enzyme structure analysis and modelling, molecular dynamics simulation Pyrococcus horikoshii