1DYO

Xylan-Binding Domain from CBM 22, formally x6b domain

Summary for 1DYO

• Entry DOI: 10.2210/pdb1dyo/pdb
• Descriptor: ENDO-1,4-BETA-XYLANASE Y, CALCIUM ION (3 entities in total)
• Functional Keywords: carbohydrate-binding module, xylan-binding, xylanase
• Biological source: CLOSTRIDIUM THERMOCELLUM
• Total number of polymer chains: 2
• Total formula weight: 35804.65

Authors

Davies, G.J.,Charnock, S.J.,Gilbert, H.J.,Fontes, C.M.G.A. (deposition date: 2000-02-03, release date: 2000-07-04, Last modification date: 2019-07-24)

Primary citation

Charnock, S.J.,Bolam, D.N.,Turkenburg, J.P.,Gilbert, H.J.,Ferreira, L.M.A.,Davies, G.J.,Fontes, C.M.G.A.
The X6 Thermostabilising Domains of Xylanases are Carbohydrate Binding Modules: Structure and Biochemistry of the Clostridium Thermocellum X6B Domain
Biochemistry, 39:5013-, 2000

PubMed Abstract: Many polysaccharide-degrading enzymes display a modular structure in which a catalytic module is attached to one or more noncatalytic modules. Several xylanases contain a module of previously unknown function (termed "X6" modules) that had been implicated in thermostability. We have investigated the properties of two such "thermostabilizing" modules, X6a and X6b from the Clostridium thermocellumxylanase Xyn10B. These modules, expressed either as discrete entities or as their natural fusions with the catalytic module, were assayed, and their capacity to bind various carbohydrates and potentiate hydrolytic activity was determined. The data showed that X6b, but not X6a, increased the activity of the enzyme against insoluble xylan and bound specifically to xylooligosaccharides and various xylans. In contrast, X6a exhibited no affinity for soluble or insoluble forms of xylan. Isothermal titration calorimetry revealed that the ligand-binding site of X6b accommodates approximately four xylose residues. The protein exhibited K(d) values in the low micromolar range for xylotetraose, xylopentaose, and xylohexaose; 24 microM for xylotriose; and 50 microM for xylobiose. Negative DeltaH and DeltaS values indicate that the interaction of X6b with xylooligosaccharides and xylan is driven by enthalpic forces. The three-dimensional structure of X6b has been solved by X-ray crystallography to a resolution of 2.1 A. The protein is a beta-sandwich that presents a tryptophan and two tyrosine residues on the walls of a shallow cleft that is likely to be the xylan-binding site. In view of the structural and carbohydrate-binding properties of X6b, it is proposed that this and related modules be re-assigned as family 22 carbohydrate-binding modules.

PubMed: 10819965
DOI: 10.1021/BI992821Q

Experimental method

X-RAY DIFFRACTION (2.1 Å)