1OD3

Structure of CSCBM6-3 From Clostridium stercorarium in complex with laminaribiose

Summary for 1OD3

• Entry DOI: 10.2210/pdb1od3/pdb
• Related: 1O8P 1O8S
• Related PRD ID: PRD_900024
• Descriptor: PUTATIVE XYLANASE, beta-D-glucopyranose-(1-3)-beta-D-glucopyranose, ACETIC ACID, ... (5 entities in total)
• Functional Keywords: hydrolase, carbohydrate binding module, beta-sandwich, laminaribiose
• Biological source: CLOSTRIDIUM STERCORARIUM
• Total number of polymer chains: 1
• Total formula weight: 18190.67

Authors

Boraston, A.B.,Notenboom, V.,Warren, R.A.J.,Kilburn, D.G.,Rose, D.R.,Davies, G.J. (deposition date: 2003-02-12, release date: 2003-03-13, Last modification date: 2023-12-13)

Primary citation

Boraston, A.B.,Notenboom, V.,Warren, R.A.J.,Kilburn, D.G.,Rose, D.R.,Davies, G.J.
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-, 2003

PubMed 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.

PubMed: 12634060
DOI: 10.1016/S0022-2836(03)00152-9

Experimental method

X-RAY DIFFRACTION (1 Å)