 |
PDBsum entry 2z8s
|
|
|
|
References listed in PDB file
|
 |
|
Key reference
|
|
|
Title
|
|
A novel structural fold in polysaccharide lyases: bacillus subtilis family 11 rhamnogalacturonan lyase yesw with an eight-Bladed -Propeller.
|
|
|
Authors
|
|
A.Ochiai,
T.Itoh,
Y.Maruyama,
A.Kawamata,
B.Mikami,
W.Hashimoto,
K.Murata.
|
|
|
Ref.
|
|
J Biol Chem, 2007,
282,
37134-37145.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
Rhamnogalacturonan (RG) lyase produced by plant pathogenic and saprophytic
microbes plays an important role in degrading plant cell walls. An extracellular
RG lyase YesW from saprophytic Bacillus subtilis is a member of polysaccharide
lyase family 11 and cleaves glycoside bonds in polygalacturonan as well as RG
type-I through a beta-elimination reaction. Crystal structures of YesW and its
complex with galacturonan disaccharide, a reaction product analogue, were
determined at 1.4 and 2.5A resolutions with final R-factors of 16.4% and 16.6%,
respectively. The enzyme is composed of an eight-bladed beta-propeller with a
deep cleft in the center as a basic scaffold, and its structural fold has not
been seen in polysaccharide lyases analyzed thus far. Structural analysis of the
disaccharide-bound YesW and a site-directed mutagenesis study suggested that
Arg-452 and Lys-535 stabilize the carboxyl group of the acidic polysaccharide
molecule and Tyr-595 makes a stack interaction with the sugar pyranose ring. In
addition to amino acid residues binding to the disaccharide, one calcium ion,
which is coordinated by Asp-401, Glu-422, His-363, and His-399, may mediate the
enzyme activity. This is, to our knowledge, the first report of a new structural
category with a beta-propeller fold in polysaccharide lyases and provides
structural insights into substrate binding by RG lyase.
|
|
|
|
|
|
|
|
Figure 2.
FIGURE 2. Structure of YesW. A, overall structure
(stereodiagram). B, image A is turned by 90 degrees around the
x-axis. C, topology diagram. β-Sheets are shown as blue or
green arrows and helices as pink cylinders. Calcium ions are
shown as red balls.
|
|
Figure 3.
FIGURE 3. Calcium-binding sites of YesW. A, calcium ions
are included in each blade of the β-propeller. Detailed
coordination of calcium ions in blades B and E is shown in the
upper and lower insets, respectively. B, two calcium ions are
included in the central space of the β-propeller. Their
detailed coordination is shown in the upper and lower insets.
Calcium ions are shown as red balls.
|
|
|
|
|
|
The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2007,
282,
37134-37145)
copyright 2007.
|
|
|
|
|
|
|
