Homology modeling of the three AtXyn1 CBMs from Arabidopsis thaliana using the CBM 22 modules from a xylanase of Clostridium thermocellum

GRISOLIA, M.J.; PERALTA, D.A.; GOMEZ-CASATI, D.F; BUSI, M.V.

Salta

Congreso; XXXIX Annual Meeting of the Argentinean Biophysical Society 2010 - 3rd Latin American Protein Society Meeting; 2010

Argentinean Biophysical Society - Latin American Protein Society

The Arabidopsis thaliana genome codifies for the xylanase (RefSeq=NP_176133)AtXyn1, which is predominantly expressed in vascular bundles, but not in vessel cells.Like many polysaccharide-degrading enzymes AtXyn1 displays a modular structurein which a catalytic domain (C-terminal) is attached to three in tandem non-catalyticmodules. Those modules where classified in the family 22 (previously family 4_9) ofcarbohydrate binding modules (CBM) (http://www.cazy.org/CBM22.html), accordingto sequence similarity. Strikingly, it shows the same modular organization than StarchSynthase III (SeqRef: NP_172637.1) from Arabidopsis, previously characterized in ourlaboratory, which is also capable to bind xylanes, among others carbohydrates. The Clostridiumthermocellum xylanase (XylY) (UniProt=XYNY_CLOTM) 3D structure is available,showing two CBMs classified in the family 22, shearing a 17% of identity (residues4-160) with the module Xyl2 from AtXyn1. Although there is a sequence classificationof this modules, we introduce an homology model of Xyl1, Xyl2 and Xyl3 that was builtby using the crystallographic structure of XylY (PDB= 1H6Y), achieving a good qualitymodel, consisting in a β-sandwich (classic β -jelly roll) with a shallow surface groove thatforms the xylotetraose-binding site.