PDBsum entry: 1gwm

Carbohydrate binding domain

PDB id: 1gwm

Contents

Protein chain

153 a.a.

Ligands

GLC-BGC-BGC-BGC-BGC-BGC

EDO ×8

Metals

_CO

Waters ×207

PDB id:

1gwm

Name:

Carbohydrate binding domain

Title:

Carbohydrate binding module family29 complexed with glucohexaose

Structure:

Non-catalytic protein 1. Chain: a. Fragment: carbohydrate binding module family 29, residue 335-478. Synonym: ncp1. Engineered: yes

Source:

Piromyces equi. Organism_taxid: 99929. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

1.15Å R-factor: 0.129 R-free: 0.156

Authors:

S.J.Charnock,D.Nurizzo,G.J.Davies

Key ref:

S.J.Charnock et al. (2002). Promiscuity in ligand-binding: The three-dimensional structure of a Piromyces carbohydrate-binding module, CBM29-2, in complex with cello- and mannohexaose. Proc Natl Acad Sci U S A, 99, 14077-14082. PubMed id: 12391332 DOI: 10.1073/pnas.212516199

Date:

19-Mar-02 Release date: 20-Mar-03

Protein chain

Q9C171  (Q9C171_PIREQ) -  Non-catalytic protein 1

Seq: 478 a.a.

Struc: 153 a.a.*

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

DOI no: 10.1073/pnas.212516199

Proc Natl Acad Sci U S A 99:14077-14082 (2002)

PubMed id: 12391332

Promiscuity in ligand-binding: The three-dimensional structure of a Piromyces carbohydrate-binding module, CBM29-2, in complex with cello- and mannohexaose.

S.J.Charnock, D.N.Bolam, D.Nurizzo, L.Szabó, V.A.McKie, H.J.Gilbert, G.J.Davies.

ABSTRACT

Carbohydrate-protein recognition is central to many biological processes. Enzymes that act on polysaccharide substrates frequently contain noncatalytic domains, "carbohydrate-binding modules" (CBMs), that target the enzyme to the appropriate substrate. CBMs that recognize specific plant structural polysaccharides are often able to accommodate both the variable backbone and the side-chain decorations of heterogeneous ligands. "CBM29" modules, derived from a noncatalytic component of the Piromyces equi cellulase/hemicellulase complex, provide an example of this selective yet flexible recognition. They discriminate strongly against some polysaccharides while remaining relatively promiscuous toward both beta-1,4-linked manno- and cello-oligosaccharides. This feature may reflect preferential, but flexible, targeting toward glucomannans in the plant cell wall. The three-dimensional structure of CBM29-2 and its complexes with cello- and mannohexaose reveal a beta-jelly-roll topology, with an extended binding groove on the concave surface. The orientation of the aromatic residues complements the conformation of the target sugar polymer while accommodation of both manno- and gluco-configured oligo- and polysaccharides is conferred by virtue of the plasticity of the direct interactions from their axial and equatorial 2-hydroxyls, respectively. Such flexible ligand recognition targets the anaerobic fungal complex to a range of different components in the plant cell wall and thus plays a pivotal role in the highly efficient degradation of this composite structure by the microbial eukaryote.

Selected figure(s)

Figure 2.
Fig 2. Three-dimensional structure of the cellohexaose complex of CBM29. (a) Topological protein cartoon, color-ramped from N to C terminus, with the ligand in "ball-and-stick" representation and the cobalt ion as a sphere, prepared by using MOLSCRIPT/BOBSCRIPT (29, 30). (b) "Hydrophobic surface" figure generated with the SURFGEN algorithm (available at www.biop.ox.ac.uk). Hydrophobic interaction surfaces are color-ramped from red (most hydrophobic) through white to blue (least hydrophobic).

Figure 4.
Fig 4. Schematic representation of the direct (nonsolvent mediated) interactions between CBM29 and ligand cellohexaose (a) and mannohexaose (b). The statistical disorder of the glucosyl moiety in subsite 2 is shown in blue, and hydrogen bonds only observed in the mannohexaose complex (subsites 5 and 2) are shown in red.

Figures were selected by an automated process.