Annual Report 2006

B
iochemistry Department
Structural biology
X-ray crystallographic analysis
of proteins
Crystal structure studies of several
biologically important proteins have been
carried out. α-Galactosidases catalyze the
hydrolysis of α-linked galactosyl residues from
galacto-oligosaccharides and polymeric galacto-
(gluco)mannans. The crystal structure of
α-galactosidase I was
determined at 1.6 resolution (Fig. 1). The
structure consisted of a catalytic domain
comprising a (β/α)8-barrel structure and a C-
terminal domain made up of eight β-strands
containing a Greek key motif. Owing to the high
resolution X-ray data, four carbohydrate chains
were observed in one α-galactosidase I
molecule and their structures were identified to
be high mannose type. α-Galactosidase I seemed
to form a tetramer around the crystallographic
four-fold axis.
The crystal structure of elapid snake
toxins pseudechetoxin (PsTx) and pseudecin
(Pdc) have been determined at around 2
resolution. These proteins belong to the
cysteine-rich secretory protein family isolated
from the snake venom and target cyclic
nucleotide-gated ion channels. The structure
consisted of an N-terminal domain that has a
fold similar to the group 1 plant pathogenesisrelated
proteins and a cysteine-rich C-terminal
domain. The multidomain strucutre seemed to
play an important role to recognize the target
proteins.
3D-structure of barnacle cement
protein, -20k
Structure determination by X-ray
crystallography and/or NMR spectroscopy is
the powerful tool for research of proteins with
unknown functions because protein function is
strictly regulated by three-dimensional (3D)
structure. Barnacle cement proteins, which are
secreted for underwater adhesion, were
recently isolated and cloned. The molecular
functions of these proteins in adhesion are not
to be established. We have determined the 3Dstructure
of one of these proteins, cp-20k, in
solution by NMR spectroscopy in order to
obtain insight into its biological function.
cp-20k contains 32 cysteine residues.
They are assembled in regular repetitive
positions in the primary structure, leading to
Fig. 1
The ribbon model of the crystal structure of
α-galactosidase I
Two catalytic residues, disulfide bridges and
the sugar chains were shown as black balland-stick
drawings in red, yellow and gray
color, respectively.
Fig.2
Structure of -20k
Six homologous units are numbered, and the boundaries of
each repeats are marked by dotted lines. Cystines are shown
in yellow sticks.