PDBsum entry: 1e5c

Hydrolase

PDB-id: 1e5c

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

87 a.a. *

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1e5c

Name:

Hydrolase

Title:

Internal xylan binding domain from c. Fimi xyn10a, r262g mutant

Structure:

Xylanase d. Chain: a. Fragment: xylan binding domain 1. Synonym: xbd1,endo-1,4-beta-xylanase d. Engineered: yes. Mutation: yes

Source:

Cellulomonas fimi. Organism_taxid: 1708. Strain: jm83. Expressed in: escherichia coli. Expression_system_taxid: 562.

UniProt:

P54865 (XYND_CELFI)

Seq:

Struc:

Seq:

Struc:

Seq:

644 a.a.

Struc:

87 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

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

Enzyme class:

E.C.3.2.1.8   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Endohydrolysis of 1,4-beta-D-xylosidic linkages in xylans.

Resolution:

not givenÅ

NMR structure:

5 models

Authors:

P.J.Simpson,X.Hefang,D.N.Bolam,H.J.Gilbert,M.P.Williamson

Key ref:

P.J.Simpson et al. (2000). The structural basis for the ligand specificity of family 2 carbohydrate-binding modules.. J Biol Chem, 275, 41137-41142. [PubMed id: 10973978] [DOI: 10.1074/jbc.M006948200]

Date:

24-Jul-00

Release date:

25-May-01

Related entries:

2xbd internal xylan binding domain from cellulomonas fimi xylanase d, nmr, minimized average structure
1xbd internal xylan binding domain from cellulomonas fimi xylanase d, nmr, 5 structures
1e5b internal xylan binding domain from c. Fimi xyn10a, r262g mutant

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Clefts

Surface

Key reference

DOI no: 10.1074/jbc.M006948200

J Biol Chem 275:41137-41142 (2000)

PubMed id: 10973978

The structural basis for the ligand specificity of family 2 carbohydrate-binding modules.

P.J.Simpson, H.Xie, D.N.Bolam, H.J.Gilbert, M.P.Williamson.

ABSTRACT

The interactions of proteins with polysaccharides play a key role in the microbial hydrolysis of cellulose and xylan, the most abundant organic molecules in the biosphere, and are thus pivotal to the recycling of photosynthetically fixed carbon. Enzymes that attack these recalcitrant polymers have a modular structure comprising catalytic modules and non-catalytic carbohydrate-binding modules (CBMs). The largest prokaryotic CBM family, CBM2, contains members that bind cellulose (CBM2a) and xylan (CBM2b), respectively. A possible explanation for the different ligand specificity of CBM2b is that one of the surface tryptophans involved in the protein-carbohydrate interaction is rotated by 90 degrees compared with its position in CBM2a (thus matching the structure of the binding site to the helical secondary structure of xylan), which may be promoted by a single amino acid difference between the two families. Here we show that by mutation of this single residue (Arg-262-->Gly), a CBM2b xylan-binding module completely loses its affinity for xylan and becomes a cellulose-binding module. The structural effect of the mutation has been revealed using NMR spectroscopy, which confirms that Trp-259 rotates 90 degrees to lie flat against the protein surface. Except for this one residue, the mutation only results in minor changes to the structure. The mutated protein interacts with cellulose using the same residues that the wild-type CBM2b uses to interact with xylan, suggesting that the recognition is of the secondary structure of the polysaccharide rather than any specific recognition of the absence or presence of functional groups.

Selected figure(s)

Figure 2.
Fig. 2. The major functional difference between CBM Families 2a and 2b. MOLSCRIPT (28) depictions of the key surface tryptophan, and the residue (Gly or Arg) that determines its orientation.

Figure 4.
Fig. 4. Structure of R262G in a stereo view of the backbone for an ensemble of 33 structures, superimposed for best fit on the lowest energy structure. Trp-259 and Trp-291 sidechains are indicated.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 41137-41142) copyright 2000.

Figures were selected by an automated process.