Investigating the binding of beta-1,4-galactan to Bacillus licheniformis beta-1,4-galactanase by crystallography and computational modeling.
Microbial beta-1,4-galactanases are glycoside hydrolases belonging to family 53, which degrade galactan and arabinogalactan side chains in the hairy regions of pectin, a major plant cell wall component. They belong to the larger clan GH-A of glycoside hydrolases, which cover many different poly- and oligosaccharidase specificities. Crystallographic complexes of Bacillus licheniformis beta-1,4-galactanase and its inactive nucleophile mutant have been obtained with methyl-beta(1-->4)-galactotetraoside, providing, for the first time, information on substrate binding to the aglycone side of the beta-1,4-galactanase substrate binding groove. Using the experimentally determined subsites as a starting point, a beta(1-->4)-galactononaose was built into the structure and subjected to molecular dynamics simulations giving further insight into the residues involved in the binding of the polysaccharide from subsite -4 to +5. In particular, this analysis newly identified a conserved beta-turn, which contributes to subsites -2 to +3. This beta-turn is unique to family 53 beta-1,4-galactanases among all clan GH-A families that have been structurally characterized and thus might be a structural signature for endo-beta-1,4-galactanase specificity.
Le Nours
Jérôme
J
Biophysical Chemistry Group, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark.
De Maria
Leonardo
L
Welner
Ditte
D
Jørgensen
Christel T
CT
Christensen
Lars L H
LL
Borchert
Torben V
TV
Larsen
Sine
S
Lo Leggio
Leila
L
D000595:Amino Acid Sequence; D001407:Bacillus / Q000201:enzymology*; D001665:Binding Sites; D002236:Carbohydrate Conformation; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D005685:Galactans / Q000737:chemistry* / Q000378:metabolism; D005690:Galactose / Q000378:metabolism; D006026:Glycoside Hydrolases / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011485:Protein Binding; D016415:Sequence Alignment
D005685:Galactans; D006026:Glycoside Hydrolases; C094192:arabinogalactan endo-1,4-beta-galactosidase; D005690:Galactose