PDBsum entry: 2xbd

Hydrolase

PDB-id: 2xbd

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References

PROCHECK

Protein chain

87 a.a. *

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

2xbd

Name:

Hydrolase

Title:

Internal xylan binding domain from cellulomonas fimi xylanase d, nmr, minimized average structure

Structure:

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

Source:

Cellulomonas fimi. Organism_taxid: 1708. 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

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:

1 models

Authors:

P.J.Simpson,D.N.Bolam,A.Cooper,A.Ciruela,G.P.Hazlewood, H.J.Gilbert,M.P.Williamson

Key ref:

P.J.Simpson et al. (1999). A family IIb xylan-binding domain has a similar secondary structure to a homologous family IIa cellulose-binding domain but different ligand specificity.. Structure, 7, 853-864. [PubMed id: 10425686] [DOI: 10.1016/S0969-2126(99)80108-7]

Date:

27-Oct-98

Release date:

21-Jul-99

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Clefts

Surface

Key reference

DOI no: 10.1016/S0969-2126(99)80108-7

Structure 7:853-864 (1999)

PubMed id: 10425686

A family IIb xylan-binding domain has a similar secondary structure to a homologous family IIa cellulose-binding domain but different ligand specificity.

P.J.Simpson, D.N.Bolam, A.Cooper, A.Ciruela, G.P.Hazlewood, H.J.Gilbert, M.P.Williamson.

ABSTRACT

BACKGROUND: Many enzymes that digest polysaccharides contain separate polysaccharide-binding domains. Structures have been previously determined for a number of cellulose-binding domains (CBDs) from cellulases. RESULTS: The family IIb xylan-binding domain 1 (XBD1) from Cellulomonas fimi xylanase D is shown to bind xylan but not cellulose. Its structure is similar to that of the homologous family IIa CBD from C. fimi Cex, consisting of two four-stranded beta sheets that form a twisted 'beta sandwich'. The xylan-binding site is a groove made from two tryptophan residues that stack against the faces of the sugar rings, plus several hydrogen-bonding polar residues. CONCLUSIONS: The biggest difference between the family IIa and IIb domains is that in the former the solvent-exposed tryptophan sidechains are coplanar, whereas in the latter they are perpendicular, forming a twisted binding site. The binding sites are therefore complementary to the secondary structures of the ligands cellulose and xylan. XBD1 and CexCBD represent a striking example of two proteins that have high sequence similarity but a different function.

Selected figure(s)

Figure 7.
Figure 7. A ribbon representation of XBD1 with xylohexaose (yellow) docked into the binding site, showing the complementarity of the twisted binding site and xylohexaose. Residues whose sidechains are implicated in binding are highlighted: Trp259, Trp291 (in blue), Glu257, Asp261, Arg262, Asn264, Gln288, Asn292 and Thr316 (in green).

The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 853-864) copyright 1999.

Figure was selected by an automated process.