1UR1

Xylanase Xyn10B mutant (E262S) from Cellvibrio mixtus in complex with arabinofuranose alpha-1,3 linked to xylobiose

Summary for 1UR1

• Entry DOI: 10.2210/pdb1ur1/pdb
• Related: 1UQY 1UQZ 1UR2
• Descriptor: ENDOXYLANASE, alpha-L-arabinofuranose-(1-3)-beta-D-xylopyranose-(1-4)-alpha-D-xylopyranose, CHLORIDE ION, ... (5 entities in total)
• Functional Keywords: hydrolase, family 10, xylanase, glycoside hydrolase, hemicellulose, xylan degradation
• Biological source: CELLVIBRIO MIXTUS
• Total number of polymer chains: 1
• Total formula weight: 43424.03

Authors

Pell, G.,Taylor, E.J.,Gloster, T.M.,Turkenburg, J.P.,Fontes, C.M.G.A.,Ferreira, L.M.A.,Davies, G.J.,Gilbert, H.J. (deposition date: 2003-10-24, release date: 2003-12-18, Last modification date: 2023-12-13)

Primary citation

Pell, G.,Taylor, E.J.,Gloster, T.M.,Turkenburg, J.P.,Fontes, C.M.G.A.,Ferreira, L.M.A.,Nagy, T.,Clark, S.,Davies, G.J.,Gilbert, H.J.
The Mechanisms by which Family 10 Glycoside Hydrolases Bind Decorated Substrates
J.Biol.Chem., 279:9597-, 2004

PubMed Abstract: Endo-beta-1,4-xylanases (xylanases), which cleave beta-1,4 glycosidic bonds in the xylan backbone, are important components of the repertoire of enzymes that catalyze plant cell wall degradation. The mechanism by which these enzymes are able to hydrolyze a range of decorated xylans remains unclear. Here we reveal the three-dimensional structure, determined by x-ray crystallography, and the catalytic properties of the Cellvibrio mixtus enzyme Xyn10B (CmXyn10B), the most active GH10 xylanase described to date. The crystal structure of the enzyme in complex with xylopentaose reveals that at the +1 subsite the xylose moiety is sandwiched between hydrophobic residues, which is likely to mediate tighter binding than in other GH10 xylanases. The crystal structure of the xylanase in complex with a range of decorated xylooligosaccharides reveals how this enzyme is able to hydrolyze substituted xylan. Solvent exposure of the O-2 groups of xylose at the +4, +3, +1, and -3 subsites may allow accommodation of the alpha-1,2-linked 4-O-methyl-d-glucuronic acid side chain in glucuronoxylan at these locations. Furthermore, the uronic acid makes hydrogen bonds and hydrophobic interactions with the enzyme at the +1 subsite, indicating that the sugar decorations in glucuronoxylan are targeted to this proximal aglycone binding site. Accommodation of 3'-linked l-arabinofuranoside decorations is observed in the -2 subsite and could, most likely, be tolerated when bound to xylosides in -3 and +4. A notable feature of the binding mode of decorated substrates is the way in which the subsite specificities are tailored both to prevent the formation of "dead-end" reaction products and to facilitate synergy with the xylan degradation-accessory enzymes such as alpha-glucuronidase. The data described in this report and in the accompanying paper indicate that the complementarity in the binding of decorated substrates between the glycone and aglycone regions appears to be a conserved feature of GH10 xylanases.

PubMed: 14668328
DOI: 10.1074/JBC.M312278200

Experimental method

X-RAY DIFFRACTION (1.43 Å)