 |
PDBsum entry 2exj
|
|
|
|
References listed in PDB file
|
 |
|
Key reference
|
|
|
Title
|
|
The structure of an inverting gh43 beta-Xylosidase from geobacillus stearothermophilus with its substrate reveals the role of the three catalytic residues.
|
|
|
Authors
|
|
C.BrüX,
A.Ben-David,
D.Shallom-Shezifi,
M.Leon,
K.Niefind,
G.Shoham,
Y.Shoham,
D.Schomburg.
|
|
|
Ref.
|
|
J Mol Biol, 2006,
359,
97-109.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Abstract
|
|
|
beta-D-Xylosidases are glycoside hydrolases that catalyze the release of xylose
units from short xylooligosaccharides and are engaged in the final breakdown of
plant cell-wall hemicellulose. Here we describe the enzyme-substrate crystal
structure of an inverting family 43 beta-xylosidase, from Geobacillus
stearothermophilus T-6 (XynB3). Each XynB3 monomeric subunit is organized in two
domains: an N-terminal five-bladed beta-propeller catalytic domain, and a
beta-sandwich domain. The active site possesses a pocket topology, which is
mainly constructed from the beta-propeller domain residues, and is closed on one
side by a loop that originates from the beta-sandwich domain. This loop
restricts the length of xylose units that can enter the active site, consistent
with the exo mode of action of the enzyme. Structures of the enzyme-substrate
(xylobiose) complex provide insights into the role of the three catalytic
residues. The xylose moiety at the -1 subsite is held by a large number of
hydrogen bonds, whereas only one hydroxyl of the xylose unit at the +1 subsite
can create hydrogen bonds with the enzyme. The general base, Asp15, is located
on the alpha-side of the -1 xylose sugar ring, 5.2 Angstroms from the anomeric
carbon. This location enables it to activate a water molecule for a
single-displacement attack on the anomeric carbon, resulting in inversion of the
anomeric configuration. Glu187, the general acid, is 2.4 Angstroms from the
glycosidic oxygen atom and can protonate the leaving aglycon. The third
catalytic carboxylic acid, Asp128, is 4 Angstroms from the general acid;
modulating its pK(a) and keeping it in the correct orientation relative to the
substrate. In addition, Asp128 plays an important role in substrate binding via
the 2-O of the glycon, which is important for the transition-state
stabilization. Taken together, these key roles explain why Asp128 is an
invariant among all five-bladed beta-propeller glycoside hydrolases.
|
|
|
|
|
|
|
|
Figure 2.
Figure 2. The dimer assembly of XynB3. A ribbon representation
of two monomers of G. stearothermophilus β-xylosidase, which
form a dimer. The monomers are aligned antiparallel to one
another, in such a manner that the five-bladed β-propeller
domain of one monomer interacts with the β-sandwich domain of
the neighboring monomer and vice versa. Figure 2. The dimer
assembly of XynB3. A ribbon representation of two monomers of G.
stearothermophilus β-xylosidase, which form a dimer. The
monomers are aligned antiparallel to one another, in such a
manner that the five-bladed β-propeller domain of one monomer
interacts with the β-sandwich domain of the neighboring monomer
and vice versa.
|
|
Figure 3.
Figure 3. The tetrameric structure of XynB3. Ribbon
illustration of the four XynB3 monomers that form a tetramer.
The four monomers are colored red, green, orange, and azure. The
tetramerization is formed by a 90° twist of the dimers.
Figure 3. The tetrameric structure of XynB3. Ribbon illustration
of the four XynB3 monomers that form a tetramer. The four
monomers are colored red, green, orange, and azure. The
tetramerization is formed by a 90° twist of the dimers.
|
|
|
|
|
|
The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2006,
359,
97-109)
copyright 2006.
|
|
|
|
|
|
|
