Any feedback?
Please rate this page
(literature.php)
(0/150)

BRENDA support

Literature summary 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 .
    View publication on PubMed

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.2.1.B40 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
3.2.1.B40 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

EC Number Localization Comment Organism GeneOntology No. Textmining
3.2.1.B40 membrane
-
 Pyrococcus horikoshii 16020
-
3.2.1.B40 membrane bound to Pyrococcus horikoshii 16020
-

Organism

EC Number Organism UniProt Comment Textmining
3.2.1.B40 Pyrococcus horikoshii O58104
-
-
3.2.1.B40 Pyrococcus horikoshii OT-3 O58104
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.2.1.B40 additional information preferred substrate are alkyl beta-glycosides Pyrococcus horikoshii ?
-
 ?
3.2.1.B40 additional information preferred substrate are alkyl beta-glycosides Pyrococcus horikoshii OT-3 ?
-
 ?