PDBsum entry: 1gny

Carbohydrate-binding module

PDB id: 1gny

Contents

Protein chain

153 a.a.

Ligands

XYP-XYP-XYP-XYP-XYP

Metals

_NA

Waters ×231

PDB id:

1gny

Name:

Carbohydrate-binding module

Title:

Xylan-binding module cbm15

Structure:

Xylanase 10c. Chain: a. Fragment: carbohydrate binding module 15, residues (91-244). Engineered: yes

Source:

Pseudomonas cellulosa. Organism_taxid: 155077. Expressed in: escherichia coli. Expression_system_taxid: 511693. Expression_system_variant: de3-plyss.

Resolution:

1.63Å R-factor: 0.152 R-free: 0.177

Authors:

S.Szabo,S.Jamal,H.Xie,S.J.Charnock,D.N.Bolam,H.J.Gilbert, G.J.Davies

Key ref:

L.Szabo et al. (2001). Structure of a family 15 carbohydrate-binding module in complex with xylopentaose. Evidence that xylan binds in an approximate 3-fold helical conformation. J Biol Chem, 276, 49061-49065. PubMed id: 11598143 DOI: 10.1074/jbc.M109558200

Date:

10-Oct-01 Release date: 29-Nov-01

Protein chain

Q59675  (Q59675_9GAMM) -  Endo-beta-1,4-xylanase (Precursor)

Seq: 606 a.a.

Struc: 153 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.2.1.8 - Endo-1,4-beta-xylanase.
• Reaction: Endohydrolysis of 1,4-beta-D-xylosidic linkages in xylans.

DOI no: 10.1074/jbc.M109558200

J Biol Chem 276:49061-49065 (2001)

PubMed id: 11598143

Structure of a family 15 carbohydrate-binding module in complex with xylopentaose. Evidence that xylan binds in an approximate 3-fold helical conformation.

L.Szabo, S.Jamal, H.Xie, S.J.Charnock, D.N.Bolam, H.J.Gilbert, G.J.Davies.

ABSTRACT

The recycling of photosynthetically fixed carbon by the action of microbial glycoside hydrolases is a key biological process. The consortium of degradative enzymes involved in this process frequently display catalytic modules appended to one or more noncatalytic carbohydrate-binding modules (CBMs). CBMs play a central role in the optimization of the catalytic activity of plant cell wall hydrolases through their binding to specific plant structural polysaccharides. Despite their pivotal role in the biodegradation of plant biomass, the mechanism by which these proteins recognize their target ligands is unclear. This report describes the structure of a xylan-binding CBM (CBM15) in complex with its ligand. This module, derived from Pseudomonas cellulosa xylanase Xyn10C, binds to both soluble xylan and xylooligosaccharides. The three-dimensional crystal structure of CBM15 bound to xylopentaose has been solved by x-ray crystallography to a resolution of 1.6 A. The protein displays a similar beta-jelly roll fold to that observed in many other families of binding-modules. A groove, 20-25 A in length, on the concave surface of one of the beta-sheets presents two tryptophan residues, the faces of which are orientated at approximately 240 degrees to one another. These form-stacking interactions with the n and n+2 sugars of xylopentaose complementing the approximate 3-fold helical structure of this ligand in the binding cleft of CBM15. In four of the five observed binding subsites, the 2' and 3' hydroxyls of the bound ligand are solvent-exposed, providing an explanation for the capacity of this xylan-binding CBM to accommodate the highly decorated xylans found in the plant cell wall.

Selected figure(s)

Figure 1.
Fig. 1. The three-dimensional structure of the P. cellulosa CBM15 in complex with xylopentaose. A displays the overall secondary structure of the protein with the location of bound xylopentaose. B shows the electron density of xylopentaose bound to CBM15. The map shown is a maximum-likelihood/ [A] weighted 2F[obs] F[calc] synthesis (28) calculated at a contour level of ~0.6 electrons/Å2. This figure was made with MOLSCRIPT/BOBSCRIPT (38, 39).

Figure 2.
Fig. 2. Schematic diagram of the interactions of CBM15 with xylopentaose.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 49061-49065) copyright 2001.