STRUCTURAL BASIS FOR SUBSTRATE RECOGNITION BY GH30 GLUCURONOXYLANASE FROM ERWINIA CHRYSANTHEMI
Ľubica Urbániková1, Mária Vršanská2, Kristian Bertel
Rømer Mørkeberg Krogh3, Tine Hoff3 and
Peter Biely2
1Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
2Institute of Chemistry, Center of Glycomics, Slovak Academy of Sciences, Bratislava, Slovakia
3Novozymes A/S, Krogshoejvej 36, 2880 Bagsvaerd, Denmark
The
important industrial enzymes, endo-b-1,4-xylanases (EC
3.2.1.8), have been classified into several glycoside hydrolase (GH) families
based on hydrophobic cluster analysis, three dimensional structure and mode of
action [1]. Best known enzymes belong to GH families 10 and 11. These enzymes
do not seem to be specialized for hydrolysis of a particular xylan. Unique xylanases
were assigned to GH family 30 [2]. Some of bacterial GH30 xylanases are specialized
for hydrolysis of xylans containing D-glucuronosyl or 4-O-methyl D-glucuronosyl
side residues. With enzyme species from Bacillus
subtilis (Xyn C) and Erwinia
chrysanthemi (XynA) it was clearly demonstrated that the cleavage of xylan
main chain is dependent on the presence of uronic acid side residues [3-7].
Recently, the structure of xylanase A from
the phytopathogenic bacterium E.
chrysanthemi with free active site was reported [7]. Here we report the
crystal structure of xylanase A in the complex with aldotetraouronic acid
MeGlcA2Xyl3, an analogue of the product of enzymatic
reaction. The crystal structure of the enzyme-ligand complex was solved at 1.39
Å resolution [8]. The
ligand xylotriosyl moiety occupies three earlier recognized subsites -1, -2 and
-3, while the MeGlcA residue attached to the middle xylopyranosyl residue of
xylotriose is bound to the enzyme through hydrogen bonds to five amino acids and
by the ionic interaction of the negatively charged uronic acid carboxylate with
positively charged guanidinium group of Arg293. The interaction of the enzyme
with MeGlcA residue appears to be indispensable for proper distortion of the
xylan chain and its effective hydrolysis. Such a distortion does not occur with
linear b-1,4-xylooligosaccharides which are
hydrolyzed by the enzyme at a negligible rate. In the close proximity to the
catalytic amino-acids Glu165 and Glu253 an electron density has been found into
which a molecule of imidazole was modeled. Imidazole is a part of the
crystallization buffer. It is suggested that imidazole occupies +1 subsite
binding xylose or xylosyl residues of the enzyme-cleaved substrates. The structure
of the protein-MeGlcA2Xyl3 complex was used for
calculation of the binding energy for the ligand itself and for its analogues.
Structural
analysis, energy calculations and experimentally measured specific activity of
the enzyme on various substrates are used to answer the question why the enzyme
does not attack efficiently linear b-1,4-linked
xylooligosaccharides.
This work was supported by VEGA grants 2/0001/10 and 2/0165/08 from the
Slovak Academy of Sciences. We acknowledge the EMBL X13 beamline at the DORIS storage ring, DESY,
1
P.M. Coutinho & B.Henrissat, Carbohydrate-active enzymes server at
http://afmb.cnrs-mrs.fr/CAZY/index.html.
2
F.J. St. John, J.M. Gonzalez & E. Pozharski, FEBS Letters, 584 (2010) 4435-4441.
3
K. Nishitani & D.J. Nevins, J. Bio.l
Chem., 266 (1991) 6539-6543.
4
J.C. Hurlbert & J.F. Preston, J.
Bacteriol., 183(2001)
2093-2100.
5
F.J. St John, J.D. Rice & J.F. Preston, J.
Bacteriol., 188 (2006) 8617-8626.
6
M. Vršanská, K. Kolenová, V. Puchart & P. Biely, Eur. J. Biochem., 274 (2007) 1666-1677.
7
S.B. Larson, J. Day, A.P. Barba de la Rosa, N.T. Keen & A. McPherson, Biochemistry, 42 (2003) 8411-8422.
8 Ľ. Urbániková, M. Vršanská, K.B.R.M. Krogh, T. Hoff & P. Biely, FEBS J., 278 (2011) submitted