Literature summary for 3.2.1.B40 extracted from

Akiba, T.; Nishio, M.; Matsui, I.; Harata, K.
X-ray structure of a membrane-bound beta-glycosidase from the hyperthermophilic archaeon Pyrococcus horikoshii (2004), Proteins, 57, 422-431 .

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Crystallization (Commentary)

Crystallization (Comment)	Organism
the enzyme is crystallized in the presence of a neutral surfactant, and the crystal structure is solved by the molecular replacement method and refined at 2.5 A. X-ray crystallography and docking simulation. The main-chain fold of the enzyme belongs to the (beta,alpha)8 barrel structure common to the family 1 glycosyl hydrolases. The active site is located at the center of the C-termini of the barrel beta-strands. The deep pocket of the active site accepts one sugar unit, and a hydrophobic channel extending radially from there binds the nonsugar moiety of the substrate. The docking simulation for oligosaccharides and alkylglucosides indicates that alkylglucosides with a long aliphatic chain are easily accommodated in the hydrophobic channel. This sparingly soluble enzyme has a cluster of hydrophobic residues on its surface, situated at the distal end of the active site channel and surrounded by a large patch of positively charged residues. It is proposed that this hydrophobic region can be inserted into the membrane while the surrounding positively charged residues make favorable contacts with phosphate groups on the inner surface of the membrane. The enzyme could thus adhere to the membrane in the proximity of its glycolipid substrate	Pyrococcus horikoshii
the unusual structural features that confer the extreme thermostability and substrate preferences of this enzyme for long chain alkyl-beta-glycosides are investigated by X-ray crystallography and docking simulation. The enzyme is crystallized in the presence of a neutral surfactant, and the crystal structure is solved by the molecular replacement method and refined at 2.5 A. The main-chain fold of the enzyme belongs to the (betaalpha)8 barrel structure common to the Family 1 glycosyl hydrolases. The active site is located at the center of the C-termini of the barrel beta-strands. The deep pocket of the active site accepts one sugar unit, and a hydrophobic channel extending radially from there binds the nonsugar moiety of the substrate. The docking simulation for oligosaccharides and alkylglucosides indicated that alkylglucosides with a long aliphatic chain are easily accommodated in the hydrophobic channel	Pyrococcus horikoshii

Crystallization (Comment)

Organism

the enzyme is crystallized in the presence of a neutral surfactant, and the crystal structure is solved by the molecular replacement method and refined at 2.5 A. X-ray crystallography and docking simulation. The main-chain fold of the enzyme belongs to the (beta,alpha)8 barrel structure common to the family 1 glycosyl hydrolases. The active site is located at the center of the C-termini of the barrel beta-strands. The deep pocket of the active site accepts one sugar unit, and a hydrophobic channel extending radially from there binds the nonsugar moiety of the substrate. The docking simulation for oligosaccharides and alkylglucosides indicates that alkylglucosides with a long aliphatic chain are easily accommodated in the hydrophobic channel. This sparingly soluble enzyme has a cluster of hydrophobic residues on its surface, situated at the distal end of the active site channel and surrounded by a large patch of positively charged residues. It is proposed that this hydrophobic region can be inserted into the membrane while the surrounding positively charged residues make favorable contacts with phosphate groups on the inner surface of the membrane. The enzyme could thus adhere to the membrane in the proximity of its glycolipid substrate

Pyrococcus horikoshii

the unusual structural features that confer the extreme thermostability and substrate preferences of this enzyme for long chain alkyl-beta-glycosides are investigated by X-ray crystallography and docking simulation. The enzyme is crystallized in the presence of a neutral surfactant, and the crystal structure is solved by the molecular replacement method and refined at 2.5 A. The main-chain fold of the enzyme belongs to the (betaalpha)8 barrel structure common to the Family 1 glycosyl hydrolases. The active site is located at the center of the C-termini of the barrel beta-strands. The deep pocket of the active site accepts one sugar unit, and a hydrophobic channel extending radially from there binds the nonsugar moiety of the substrate. The docking simulation for oligosaccharides and alkylglucosides indicated that alkylglucosides with a long aliphatic chain are easily accommodated in the hydrophobic channel

Pyrococcus horikoshii

Localization

Localization	Comment	Organism	GeneOntology No.	Textmining
membrane	-	Pyrococcus horikoshii	16020	-
membrane	bound to	Pyrococcus horikoshii	16020	-

Organism

Organism	UniProt	Comment	Textmining
Pyrococcus horikoshii	O58104	-	-
Pyrococcus horikoshii OT-3	O58104	-	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
additional information	preferred substrate are alkyl beta-glycosides	Pyrococcus horikoshii	?	-	?
additional information	preferred substrate are alkyl beta-glycosides	Pyrococcus horikoshii OT-3	?	-	?