PDBsum entry: 2okx

Hydrolase

PDB id: 2okx

Contents

Protein chains

954 a.a. *

Ligands

GOL ×43

Metals

_CA ×4

Waters ×1755

* Residue conservation analysis

PDB id:

2okx

Name:

Hydrolase

Title:

Crystal structure of gh78 family rhamnosidase of bacillus sp 1.9 a

Structure:

Rhamnosidase b. Chain: a, b. Engineered: yes

Source:

Bacillus sp.. Organism_taxid: 84635. Strain: gl1. Gene: rhab. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.90Å R-factor: 0.182 R-free: 0.214

Authors:

Z.Cui,B.Mikami,W.Hashimoto,K.Murata

Key ref:

Z.Cui et al. (2007). Crystal structure of glycoside hydrolase family 78 alpha-L-Rhamnosidase from Bacillus sp. GL1. J Mol Biol, 374, 384-398. PubMed id: 17936784 DOI: 10.1016/j.jmb.2007.09.003

Date:

17-Jan-07 Release date: 13-Nov-07

Protein chains

Q93RE7  (Q93RE7_BACGL) -  Rhamnosidase B

Seq: 956 a.a.

Struc: 954 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (1 term)
• Biochemical function: catalytic activity (1 term)

DOI no: 10.1016/j.jmb.2007.09.003

J Mol Biol 374:384-398 (2007)

PubMed id: 17936784

Crystal structure of glycoside hydrolase family 78 alpha-L-Rhamnosidase from Bacillus sp. GL1.

Z.Cui, Y.Maruyama, B.Mikami, W.Hashimoto, K.Murata.

ABSTRACT

alpha-L-Rhamnosidase (EC 3.2.1.40) catalyzes the hydrolytic release of rhamnose from polysaccharides and glycosides. Bacillus sp. GL1 alpha-L-rhamnosidase (RhaB), a member of glycoside hydrolase (GH) family 78, is responsible for degrading the bacterial biofilm gellan, and also functions as a debittering agent for citrus fruit in the food and beverage industries through the release of rhamnose from plant glycoside, naringin. The X-ray crystal structure of RhaB was determined by single-wavelength anomalous diffraction using a selenomethionine derivative and refined at 1.9 A resolution with a final R-factor of 18.2%. As is seen in the homodimeric form of the active enzyme, the structure of RhaB in crystal packing is a homodimer containing 1908 amino acids (residues 3-956), 43 glycerol molecules, four calcium ions, and 1755 water molecules. The overall structure consists of five domains, four of which are beta-sandwich structures designated as domains N, D1, D2, and C, and an (alpha/alpha)(6)-barrel structure designated as domain A. Structural comparison by DALI showed that RhaB shares its highest level of structural similarity with chitobiose phosphorylase (Z score of 25.3). The structure of RhaB in complex with the reaction product rhamnose (inhibitor constant, K(i)=1.8 mM) was also determined and refined at 2.1 A with a final R-factor of 19.5%. Rhamnose is bound to the deep cleft of the (alpha/alpha)(6)-barrel domain, as is seen in the clan-L GHs. Several negatively charged residues, such as Asp567, Glu572, Asp579, and Glu841, conserved in GH family 78 enzymes, interact with rhamnose, and RhaB mutants of these residues have drastically reduced enzyme activity, indicating that the residues are crucial for enzyme catalysis and/or substrate binding. To our knowledge, this is the first report on the determination of the crystal structure of alpha-L-rhamnosidase and identification of its clan-L (alpha/alpha)(6)-barrel as a catalytic domain.

Selected figure(s)

Figure 2.
Figure 2. Overall structure of RhaB. (a) Forward view of the homodimer structure. (b) Side view of the structure. These Figures were drawn using the PyMOL program [http://www.pymol.org]. (c) Topology diagram of RhaB. Cylinder, α-helices; arrows, β-strands; gray ball, calcium ion; green stick and red ball, glycerol. Red, domain N; blue, domain D1; green, domain D2; yellow, domain A; cyan, domain C.

Figure 6.
Figure 6. Catalytic (α/α)[6]-barrel domain. (a) Superimposition of catalytic domains of RhaB, ChBP, and GD. Green, RhaB; red, ChBP; blue, GD. Note ligands (ball-and-stick models) in the deep cleft of ChBP and GD (α/α)[6]-barrel domains. (b) Catalytic (α/α)[6]-barrel domain of RhaB. The omit map indicated by thin blue lines for >3σ corresponds to the rhamnose molecule accommodated in domain A. These Figures were drawn using the PyMOL program.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 374, 384-398) copyright 2007.

Figures were selected by an automated process.