1NAE

Structure of CsCBM6-3 from Clostridium stercorarium in complex with xylotriose

Summary for 1NAE

• Entry DOI: 10.2210/pdb1nae/pdb
• Related PRD ID: PRD_900117
• Descriptor: putative xylanase, beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: carbohydrate-binding module, beta-sandwich, xylan, xylooligosaccharide, hydrolase
• Biological source: Clostridium stercorarium
• Total number of polymer chains: 1
• Total formula weight: 17860.39

Authors

Boraston, A.B.,Notenboom, V.,Warren, R.A.J.,Kilburn, D.G.,Rose, D.R.,Davies, G. (deposition date: 2002-11-27, release date: 2003-03-18, Last modification date: 2023-08-16)

Primary citation

Boraston, A.B.,Notenboom, V.,Warren, R.A.J.,Kilburn, D.G.,Rose, D.R.,Davies, G.
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, 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 (2.05 Å)