 |
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
 |
|
 |
|
 |
|
|
Gene Ontology (GO) functional annotation
|
|
|
|
 |
 |
 |
|
 |
 |
 |
 |
|
 |
|
Biological process
|
metabolic process
|
1 term
|
 |
|
Biochemical function
|
catalytic activity
|
1 term
|
 |
|
|
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
|
|
|
| |
|
DOI no:
|
J Mol Biol
374:384-398
(2007)
|
|
PubMed id:
|
|
|
|
|
| |
|
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.
|
|
|
|
|
 |
 |
|
 |
 |
 |
 |
 |
 |
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
 |
| |
PubMed id
|
 |
Reference
|
 |
|
|
|
 |
J.Calveras,
M.Egido-Gabás,
L.Gómez,
J.Casas,
T.Parella,
J.Joglar,
J.Bujons,
and
P.Clapés
(2009).
Dihydroxyacetone phosphate aldolase catalyzed synthesis of structurally diverse polyhydroxylated pyrrolidine derivatives and evaluation of their glycosidase inhibitory properties.
|
| |
Chemistry, 15,
7310-7328.
|
 |
|
|
|
|
 |
L.S.Mazzaferro,
G.A.Orrillo,
P.Ledesma,
and
J.D.Breccia
(2008).
Dose-dependent significance of monosaccharides on intracellular alpha-L-rhamnosidase activity from Pseudoalteromonas sp.
|
| |
Biotechnol Lett, 30,
2147-2150.
|
 |
|
|
|
|
 |
T.Koseki,
Y.Mese,
N.Nishibori,
K.Masaki,
T.Fujii,
T.Handa,
Y.Yamane,
Y.Shiono,
T.Murayama,
and
H.Iefuji
(2008).
Characterization of an alpha-L-rhamnosidase from Aspergillus kawachii and its gene.
|
| |
Appl Microbiol Biotechnol, 80,
1007-1013.
|
 |
|
 |
 |
|
The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
|
|