PDBsum entry 1od3

Hydrolase

PDB id: 1od3

Contents

Protein chain

132 a.a. *

Ligands

BGC-BGC ×2

ACY

Metals

_CA

Waters ×273

* Residue conservation analysis

PDB id:

1od3

Name:

Hydrolase

Title:

Structure of cscbm6-3 from clostridium stercorarium in complex with laminaribiose

Structure:

Putative xylanase. Chain: a. Fragment: carbohydrate-binding domain, residues 285-417. Synonym: endo-xylanase, cscbm6-3, xyna. Engineered: yes

Source:

Clostridium stercorarium. Organism_taxid: 1510. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

1.00Å R-factor: 0.132 R-free: 0.149

Authors:

A.B.Boraston,V.Notenboom,R.A.J.Warren,D.G.Kilburn,D.R.Rose,G.J.Davies

Key ref:

A.B.Boraston et al. (2003). Structure and ligand binding of carbohydrate-binding module CsCBM6-3 reveals similarities with fucose-specific lectins and "galactose-binding" domains. J Mol Biol, 327, 659-669. PubMed id: 12634060 DOI: 10.1016/S0022-2836(03)00152-9

Date:

12-Feb-03 Release date: 13-Mar-03

Protein chain

Q8GJ44  (XYNA1_THEST) -  Endo-1,4-beta-xylanase A from Thermoclostridium stercorarium

Seq: 651 a.a.

Struc: 132 a.a.

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: 10.1016/S0022-2836(03)00152-9

J Mol Biol 327:659-669 (2003)

PubMed id: 12634060

Structure and ligand binding of carbohydrate-binding module CsCBM6-3 reveals similarities with fucose-specific lectins and "galactose-binding" domains.

A.B.Boraston, V.Notenboom, R.A.Warren, D.G.Kilburn, D.R.Rose, G.Davies.

ABSTRACT

Carbohydrate-binding polypeptides, including carbohydrate-binding modules (CBMs) from polysaccharidases, and lectins, are widespread in nature. Whilst CBMs are classically considered distinct from lectins, in that they are found appended to polysaccharide-degrading enzymes, this distinction is blurring. The crystal structure of CsCBM6-3, a "sequence-family 6" CBM in a xylanase from Clostridium stercorarium, at 2.3 A reveals a similar, all beta-sheet fold to that from MvX56, a module found in a family 33 glycoside hydrolase sialidase from Micromonospora viridifaciens, and the lectin AAA from Anguilla anguilla. Sequence analysis leads to the classification of MvX56 and AAA into a family distinct from that containing CsCBM6-3. Whilst these polypeptides are similar in structure they have quite different carbohydrate-binding specificities. AAA is known to bind fucose; CsCBM6-3 binds cellulose, xylan and other beta-glucans. Here we demonstrate that MvX56 binds galactose, lactose and sialic acid. Crystal structures of CsCBM6-3 in complex with xylotriose, cellobiose, and laminaribiose, 2.0 A, 1.35 A, and 1.0 A resolution, respectively, reveal that the binding site of CsCBM6-3 resides on the same polypeptide face as for MvX56 and AAA. Subtle differences in the ligand-binding surface give rise to the different specificities and biological activities, further blurring the distinction between classical lectins and CBMs.

Selected figure(s)

Figure 6.
Figure 6. Overlap of xylotriose (blue), cellobiose (green), and laminaribiose (yellow) bound to CsCBM6-3. Proline 138 is shown in ball-and-stick format. Bound calcium is shown as a large blue sphere.

Figure 7.
Figure 7. Overlap of the structure of CsCBM6-3 in complex with xylotriose (blue), MvX56 from the M. viridifaciens sialidase in complex with galactose (green), and A. anguilla agglutinin in complex with fucose (khaki). Metal ions are shown as spheres. The superimposition was prepared with SWISS-Pdb viewer.[23.]

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 327, 659-669) copyright 2003.

Figures were selected by an automated process.