PDBsum entry 2xbd

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protein links
Hydrolase PDB id
Protein chain
87 a.a. *
* Residue conservation analysis
PDB id:
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.
NMR struc: 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
27-Oct-98     Release date:   21-Jul-99    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P54865  (XYND_CELFI) -  Bifunctional xylanase/deacetylase
644 a.a.
87 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Endo-1,4-beta-xylanase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of 1,4-beta-D-xylosidic linkages in xylans.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     carbohydrate binding     3 terms  


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.
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18083818 J.Navarro-Fernández, I.Martínez-Martínez, S.Montoro-García, F.García-Carmona, H.Takami, and A.Sánchez-Ferrer (2008).
Characterization of a new rhamnogalacturonan acetyl esterase from Bacillus halodurans C-125 with a new putative carbohydrate binding domain.
  J Bacteriol, 190, 1375-1382.  
16615205 E.A.Snell, N.M.Brooke, W.R.Taylor, D.Casane, H.Philippe, and P.W.Holland (2006).
An unusual choanoflagellate protein released by Hedgehog autocatalytic processing.
  Proc Biol Sci, 273, 401-407.  
15650852 S.Leskinen, A.Mäntylä, R.Fagerström, J.Vehmaanperä, R.Lantto, M.Paloheimo, and P.Suominen (2005).
Thermostable xylanases, Xyn10A and Xyn11A, from the actinomycete Nonomuraea flexuosa: isolation of the genes and characterization of recombinant Xyn11A polypeptides produced in Trichoderma reesei.
  Appl Microbiol Biotechnol, 67, 495-505.  
  16511072 T.Nakamura, K.Ishikawa, Y.Hagihara, T.Oku, A.Nakagawa, T.Inoue, M.Ataka, and K.Uegaki (2005).
Crystallization and preliminary X-ray diffraction analysis of a chitin-binding domain of hyperthermophilic chitinase from Pyrococcus furiosus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 476-478.  
16314454 T.P.Monie, H.Hernandez, C.V.Robinson, P.Simpson, S.Matthews, and S.Curry (2005).
The polypyrimidine tract binding protein is a monomer.
  RNA, 11, 1803-1808.  
14761997 H.Tsujibo, M.Kosaka, S.Ikenishi, T.Sato, K.Miyamoto, and Y.Inamori (2004).
Molecular characterization of a high-affinity xylobiose transporter of Streptomyces thermoviolaceus OPC-520 and its transcriptional regulation.
  J Bacteriol, 186, 1029-1037.  
15004011 J.L.Henshaw, D.N.Bolam, V.M.Pires, M.Czjzek, B.Henrissat, L.M.Ferreira, C.M.Fontes, and H.J.Gilbert (2004).
The family 6 carbohydrate binding module CmCBM6-2 contains two ligand-binding sites with distinct specificities.
  J Biol Chem, 279, 21552-21559.  
12191997 B.W.McLean, A.B.Boraston, D.Brouwer, N.Sanaie, C.A.Fyfe, R.A.Warren, D.G.Kilburn, and C.A.Haynes (2002).
Carbohydrate-binding modules recognize fine substructures of cellulose.
  J Biol Chem, 277, 50245-50254.  
11980475 P.J.Simpson, S.J.Jamieson, M.Abou-Hachem, E.N.Karlsson, H.J.Gilbert, O.Holst, and M.P.Williamson (2002).
The solution structure of the CBM4-2 carbohydrate binding module from a thermostable Rhodothermus marinus xylanase.
  Biochemistry, 41, 5712-5719.
PDB codes: 1k42 1k45
11327868 D.N.Bolam, H.Xie, P.White, P.J.Simpson, S.M.Hancock, M.P.Williamson, and H.J.Gilbert (2001).
Evidence for synergy between family 2b carbohydrate binding modules in Cellulomonas fimi xylanase 11A.
  Biochemistry, 40, 2468-2477.
PDB codes: 1heh 1hej
11478884 H.Xie, H.J.Gilbert, S.J.Charnock, G.J.Davies, M.P.Williamson, P.J.Simpson, S.Raghothama, C.M.Fontes, F.M.Dias, L.M.Ferreira, and D.N.Bolam (2001).
Clostridium thermocellum Xyn10B carbohydrate-binding module 22-2: the role of conserved amino acids in ligand binding.
  Biochemistry, 40, 9167-9176.
PDB codes: 1h6x 1h6y
  11673472 M.Czjzek, D.N.Bolam, A.Mosbah, J.Allouch, C.M.Fontes, L.M.Ferreira, O.Bornet, V.Zamboni, H.Darbon, N.L.Smith, G.W.Black, B.Henrissat, and H.J.Gilbert (2001).
The location of the ligand-binding site of carbohydrate-binding modules that have evolved from a common sequence is not conserved.
  J Biol Chem, 276, 48580-48587.
PDB code: 1gmm
11524680 S.Raghothama, R.Y.Eberhardt, P.Simpson, D.Wigelsworth, P.White, G.P.Hazlewood, T.Nagy, H.J.Gilbert, and M.P.Williamson (2001).
Characterization of a cellulosome dockerin domain from the anaerobic fungus Piromyces equi.
  Nat Struct Biol, 8, 775-778.
PDB codes: 1e8p 1e8q
11488929 Y.Wang, M.B.Slade, A.A.Gooley, B.J.Atwell, and K.L.Williams (2001).
Cellulose-binding modules from extracellular matrix proteins of Dictyostelium discoideum stalk and sheath.
  Eur J Biochem, 268, 4334-4345.  
10866795 J.F.Espinosa, J.L.Asensio, J.L.García, J.Laynez, M.Bruix, C.Wright, H.C.Siebert, H.J.Gabius, F.J.Cañada, and J.Jiménez-Barbero (2000).
NMR investigations of protein-carbohydrate interactions binding studies and refined three-dimensional solution structure of the complex between the B domain of wheat germ agglutinin and N,N', N"-triacetylchitotriose.
  Eur J Biochem, 267, 3965-3978.  
11025547 L.L.Leggio, J.Jenkins, G.W.Harris, and R.W.Pickersgill (2000).
X-ray crystallographic study of xylopentaose binding to Pseudomonas fluorescens xylanase A.
  Proteins, 41, 362-373.
PDB code: 1e5n
10978766 P.Tomme, A.Boraston, J.M.Kormos, R.A.Warren, and D.G.Kilburn (2000).
Affinity electrophoresis for the identification and characterization of soluble sugar binding by carbohydrate-binding modules.
  Enzyme Microb Technol, 27, 453-458.  
10508763 J.Jiménez-Barbero, J.L.Asensio, F.J.Cañada, and A.Poveda (1999).
Free and protein-bound carbohydrate structures.
  Curr Opin Struct Biol, 9, 549-555.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.