PDBsum entry: 2bgo

Carbohydrate binding protein

PDB-id: 2bgo

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

116 a.a. *

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

2bgo

Name:

Carbohydrate binding protein

Title:

Mannan binding module from man5c

Structure:

Endo-b1,4-mannanase 5c. Chain: a. Fragment: residues 197-328. Synonym: cbm35 from beta-1,4-mannanase man5c. Engineered: yes. Other_details: mannan specific carbohydrate binding module

Source:

Cellvibrio japonicus. Organism_taxid: 155077. Expressed in: escherichia coli. Expression_system_taxid: 562.

UniProt:

Q840C0 (Q840C0_9GAMM)

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

830 a.a.

Struc:

116 a.a.

Key:

PfamA domain

Secondary structure

Resolution:

not givenÅ

NMR structure:

5 models

Authors:

R.B.Tunnicliffe,D.N.Bolam,G.Pell,H.J.Gilbert,M.P.Williamson

Key ref:

R.B.Tunnicliffe et al. (2005). Structure of a mannan-specific family 35 carbohydrate-binding module: evidence for significant conformational changes upon ligand binding.. J Mol Biol, 347, 287-296. [PubMed id: 15740741] [DOI: 10.1016/j.jmb.2005.01.038]

Date:

04-Jan-05

Release date:

09-Mar-05

Related entries:

2bgp mannan binding module from man5c in bound conformation

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1016/j.jmb.2005.01.038

J Mol Biol 347:287-296 (2005)

PubMed id: 15740741

Structure of a mannan-specific family 35 carbohydrate-binding module: evidence for significant conformational changes upon ligand binding.

R.B.Tunnicliffe, D.N.Bolam, G.Pell, H.J.Gilbert, M.P.Williamson.

ABSTRACT

Enzymes that digest plant cell wall polysaccharides generally contain non-catalytic, carbohydrate-binding modules (CBMs) that function by attaching the enzyme to the substrate, potentiating catalytic activity. Here, we present the first structure of a family 35 CBM, derived from the Cellvibrio japonicus beta-1,4-mannanase Man5C. The NMR structure has been determined for both the free protein and the protein bound to mannopentaose. The data show that the protein displays a typical beta-jelly-roll fold. Ligand binding is not located on the concave surface of the protein, as occurs in many CBMs that display the jelly-roll fold, but is formed by the loops that link the two beta-sheets of the protein, similar to family 6 CBMs. In contrast to the majority of CBMs, which are generally rigid proteins, CBM35 undergoes significant conformational change upon ligand binding. The curvature of the binding site and the narrow binding cleft are likely to be the main determinants of binding specificity. The predicted solvent exposure of O6 at several subsites provides an explanation for the observed accommodation of decorated mannans. Two of the key aromatic residues in Man5C-CBM35 that interact with mannopentaose are conserved in mannanase-derived CBM35s, which will guide specificity predictions based on the primary sequence of proteins in this CBM family.

Selected figure(s)

Figure 2.
Figure 2. Stereo rainbow representations of the backbone atoms (N, C^a, C') of 20 structure ensembles of (a) free Man5C-CBM35 and (c) mannopentaose bound. Cartoon representation of the fold of (b) free and (d) bound protein are shown on the right, showing the b-sandwich fold maintained in both states. (b) and (d) Strands are numbered and the helical turn is highlighted in red. All protein images were produced in Pymol (DeLano Scientific; http://www.pymol.org).

Figure 7.
Figure 7. Overlay of the bound structure of Man5C-CBM35 (green) with the xylan-binding CtCBM625 (PDB 1gmm) (blue). The aromatics involved in carbohydrate binding are shown in both proteins with CBM6 binding clefts A and B highlighted. The aromatics of CtCBM6 are coloured cyan and are (from left to right) Tyr40, Tyr34 and Trp 92. The yellow aromatics of Man5C-CBM35 are (left to right) Trp109, Tyr111 and Tyr60.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 347, 287-296) copyright 2005.

Figures were selected by an automated process.