PDBsum entry: 1vff

Hydrolase

PDB-id: 1vff

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

423 a.a. *

Waters ×43

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1vff

Name:

Hydrolase

Title:

Beta-glycosidase from pyrococcus horikoshii

Structure:

Beta-glucosidase. Chain: a. Synonym: beta-glycosidase. Engineered: yes

Source:

Pyrococcus horikoshii. Organism_taxid: 53953. Gene: ph0366. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

UniProt:

O58104 (O58104_PYRHO)

Seq:

Struc:

Seq:

423 a.a.

Struc:

423 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Resolution:

2.50Å

R-factor:

0.176

R-free:

0.231

Authors:

T.Akiba,M.Nishio,I.Matsui,K.Harata

Key ref:

T.Akiba et al. (2004). X-ray structure of a membrane-bound beta-glycosidase from the hyperthermophilic archaeon Pyrococcus horikoshii.. Proteins, 57, 422-431. [PubMed id: 15340929] [DOI: 10.1002/prot.20203]

Date:

12-Apr-04

Release date:

29-Mar-05

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1002/prot.20203

Proteins 57:422-431 (2004)

PubMed id: 15340929

X-ray structure of a membrane-bound beta-glycosidase from the hyperthermophilic archaeon Pyrococcus horikoshii.

T.Akiba, M.Nishio, I.Matsui, K.Harata.

ABSTRACT

The beta-glycosidase of the hyperthermophilic Archaeon Pyrococcus horikoshii is a membrane-bound enzyme with the preferred substrate of alkyl-beta-glycosides. In this study, the unusual structural features that confer the extreme thermostability and substrate preferences of this enzyme were investigated by X-ray crystallography and docking simulation. The enzyme was crystallized in the presence of a neutral surfactant, and the crystal structure was 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. 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. We propose 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.

Selected figure(s)

Figure 2.
Figure 2. Stereo view of the ribbon model of the BGPh structure. The -strands and -helices of the ( )[8] barrel core are numbered. The model is viewed along the axis of the barrel. The N- and C-terminal ends are denoted by N and C, respectively. -Helices, -strands, and loops are colored in red, dark blue, and yellow, respectively.

Figure 7.
Figure 7. Surface properties of the BGPh molecule and a proposed model of its membrane bound form. (a) Arrangement of amino acid residues on the surface are depicted as follows: hydrophobic (white), aromatic (pink), basic (blue), acidic (red), and polar neutral residues (green). (b) The electrostatic potential mapped on the molecular surface; positive is in blue and negative in red. (c) Ribbon model of the protein in the same orientation as (a) and (b) for helping the reader to locate these features in the structure. The active center is indicated by arrows; the hydrophobic mound is encircled by a solid line. The electrostatic potential map was obtained with DelPhi[42] module of Insight II package. (d) Proposed model of BGPh bound to the inner surface of the cell membrane. The protein molecule is in the molecular surface model showing the calculated electrostatic potential. The CPK model of dodecyl- -glucoside is placed in the active site channel of BGPh. The membrane is modeled by an array of CPK models of glucosyl caldarchaetidic acid and glucosyl archaeol according to De Rosa et al.[26] The thickness of the membrane is 55 Å in the model, but it should be thinner in live Archaea due to the disordering of core isoprenoid chains.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 57, 422-431) copyright 2004.

Figures were selected by the author.