PDBsum entry: 2c4x

Hydrolase

PDB-id: 2c4x

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

250 a.a. *

Ligands

EDO ×3

Metal ions

_CA ×2

Waters ×381

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

2c4x

Name:

Hydrolase

Title:

Structural basis for the promiscuous specificity of the carbohydrate-binding modules from the beta-sandwich super family

Structure:

Endoglucanase. Chain: a. Fragment: c-terminal pkd and cbm44 domains, residues 1353-1601. Synonym: ctcel9d-cel44a. Engineered: yes. Mutation: yes. Other_details: contains 2 calcium ions

Source:

Clostridium thermocellum. Organism_taxid: 1515. Strain: ys. Expressed in: escherichia coli. Expression_system_taxid: 562.

UniProt:

P71140 (P71140_CLOTM)

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

1601 a.a.

Struc:

250 a.a.*

Key:	PfamA domain	PfamB domain
Secondary structure

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

Resolution:

2.0Å

R-factor:

0.181

R-free:

0.215

Authors:

S.Najmudin,C.I.P.D.Guerreiro,A.L.Carvalho,D.N.Bolam, J.A.M.Prates,M.A.S.Correia,V.D.Alves,L.M.A.Ferreira, M.J.Romao,H.J.Gilbert,C.M.G.A.Fontes

Key ref:

S.Najmudin et al. (2006). Xyloglucan is recognized by carbohydrate-binding modules that interact with beta-glucan chains.. J Biol Chem, 281, 8815-8828. [PubMed id: 16314409] [DOI: 10.1074/jbc.M510559200]

Date:

25-Oct-05

Release date:

27-Oct-05

Related entries:

1wmx crystal structure of family 30 carbohydrate binding module
1wzx crystal structure of family 30 carbohydrate binding module.
2c24 family 30 carbohydrate-binding module of cellulosomal cellulase cel9d-cel44b of clostridium thermocellum
2c26 structural basis for the promiscuous specificity of the carbohydrate-binding modules from the beta-sandwich super family

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1074/jbc.M510559200

J Biol Chem 281:8815-8828 (2006)

PubMed id: 16314409

Xyloglucan is recognized by carbohydrate-binding modules that interact with beta-glucan chains.

S.Najmudin, C.I.Guerreiro, A.L.Carvalho, J.A.Prates, M.A.Correia, V.D.Alves, L.M.Ferreira, M.J.Romão, H.J.Gilbert, D.N.Bolam, C.M.Fontes.

ABSTRACT

Enzyme systems that attack the plant cell wall contain noncatalytic carbohydrate-binding modules (CBMs) that mediate attachment to this composite structure and play a pivotal role in maximizing the hydrolytic process. Although xyloglucan, which includes a backbone of beta-1,4-glucan decorated primarily with xylose residues, is a key component of the plant cell wall, CBMs that bind to this polymer have not been identified. Here we showed that the C-terminal domain of the modular Clostridium thermocellum enzyme CtCel9D-Cel44A (formerly known as CelJ) comprises a novel CBM (designated CBM44) that binds with equal affinity to cellulose and xyloglucan. We also showed that accommodation of xyloglucan side chains is a general feature of CBMs that bind to single cellulose chains. The crystal structures of CBM44 and the other CBM (CBM30) in CtCel9D-Cel44A display a beta-sandwich fold. The concave face of both CBMs contains a hydrophobic platform comprising three tryptophan residues that can accommodate up to five glucose residues. The orientation of these aromatic residues is such that the bound ligand would adopt the twisted conformation displayed by cello-oligosaccharides in solution. Mutagenesis studies confirmed that the hydrophobic platform located on the concave face of both CBMs mediates ligand recognition. In contrast to other CBMs that bind to single polysaccharide chains, the polar residues in the binding cleft of CBM44 play only a minor role in ligand recognition. The mechanism by which these proteins are able to recognize linear and decorated beta-1,4-glucans is discussed based on the structures of CBM44 and the other CBMs that bind single cellulose chains.

Selected figure(s)

Figure 5.
FIGURE 5. The three-dimensional structure and the hydrophobic platform of PKD-CBM44. The overall structure of the PKD-CBM44 highlighting the secondary structural elements, with the -strands of each -sheet colored the same as is shown in a. The Trps in the binding cleft are depicted as sticks, and the calcium atoms depicted as red spheres. The hydrogen bond between the OH of Ser^92 and carbonyl O of Thr^94 in the linker region is shown in cyan. Note -strand 2 of PKD has a kink at residues 29/30. b, comparison of the calcium-binding sites Ca1 in the PKD and Ca2 in the CBM44 domains and their corresponding coordinating amino acid residues. The electron density was contoured at 2 . c depicts a top down view of the CBM44 binding cleft showing the amino acids (as sticks) that are in the vicinity of the three tryptophan residues (as balls and sticks) that comprise the hydrophobic platform. All the ribbon figures in Figs. 5, 6, and 8 were prepared using MOLSCRIPT (58) and RASTER3D (59) and the electron density figures with TURBO-FRODO (60).

Figure 8.
FIGURE 8. Superpositioning of CBM30 and CBM29 on CBM44. CBM44 is shown in blue, CBM30 in green and CBM29 (Protein Data Bank code 1gwm) in sky blue trace, with the aromatics (Trp^189, Trp^194, and Trp^198 for CBM44; Trp^27, Trp^68, and Trp^78 for CBM30; and Trp^24, Trp^26, and Tyr^46 for CBM29) as ball and sticks.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 8815-8828) copyright 2006.

Figures were selected by an automated process.