 |
PDBsum entry 2eab
|
|
|
|
References listed in PDB file
|
 |
|
Key reference
|
|
|
Title
|
|
Structural basis on the catalytic reaction mechanism of novel 1,2-Alpha-L-Fucosidase (afca) from bifidobacterium bifidum.
|
|
|
Authors
|
|
M.Nagae,
A.Tsuchiya,
T.Katayamka,
K.Yamamoto,
S.Wakatsuki,
R.Kato.
|
|
|
Ref.
|
|
J Biol Chem, 2007,
282,
18497-18509.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
1,2-alpha-L-Fucosidase (AfcA), which hydrolyzes the glycosidic linkage of
Fucalpha1-2Gal via an inverting mechanism, was recently isolated from
Bifidobacterium bifidum and classified as the first member of the novel
glycoside hydrolase family 95 (GH95). To better understand the molecular
mechanism of this enzyme, we determined the X-ray crystal structures of the AfcA
catalytic (Fuc) domain in unliganded and complexed forms with
deoxyfuconojirimycin (inhibitor), 2'-fucosyllactose (substrate), and
L-fucose and lactose (products) at 1.12-2.10 A resolution. The AfcA Fuc domain
is composed of four regions, an N-terminal beta region, a helical linker, an
(alpha/alpha)6 helical barrel domain, and a C-terminal beta region, and this
arrangement is similar to bacterial phosphorylases. In the complex structures,
the ligands were buried in the central cavity of the helical barrel domain.
Structural analyses in combination with mutational experiments revealed that the
highly conserved Glu566 likely acts as a general acid catalyst. However, no
carboxylic acid residue is found at the appropriate position for a general base
catalyst. Instead, a water molecule stabilized by Asn423 in the substrate-bound
complex is suitably located to perform a nucleophilic attack on the C1 atom of
L-fucose moiety in 2'-fucosyllactose, and its location is nearly identical
near the O1 atom of beta-L-fucose in the products-bound complex. Based on these
data, we propose and discuss a novel catalytic reaction mechanism of AfcA.
|
|
|
|
|
|
|
|
Figure 1.
FIGURE 1. Crystal structure of B. bifidum AfcA fucosidase
catalytic domain (Fuc domain). a, ribbon model of the Fuc domain
is shown. The N-terminal  region, helical linker
region, central helical barrel domain, and C-terminal region
are colored in blue, cyan, yellow, and red, respectively. b,
electrostatic surface potential map of the Fuc domain. Positive
(blue) and negative (red) potentials are mapped on the van der
Waals surfaces in the range -10 K[b]T (red) to +10 K[b]T (blue),
where K[b] is Boltzmann's constant and T is the absolute
temperature.
|
|
Figure 6.
FIGURE 6. Proposed catalytic reaction mechanism of the AfcA
fucosidase. Hydrogen bonds are depicted by dotted lines. The
directions of nucleophilic attack and proton donation are
indicated by blank arrows.
|
|
|
|
|
|
The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2007,
282,
18497-18509)
copyright 2007.
|
|
|
|
|
|
|
