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PDBsum entry 1e5c

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protein links
Hydrolase PDB id
1e5c
Jmol
Contents
Protein chain
87 a.a. *
* Residue conservation analysis
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.
NMR struc: 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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P54865  (XYND_CELFI) -  Bifunctional xylanase/deacetylase
Seq:
Struc:
 
Seq:
Struc:
644 a.a.
87 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.8  - 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: 10.1074/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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21214861 M.Bieri, A.H.Kwan, M.Mobli, G.F.King, J.P.Mackay, and P.R.Gooley (2011).
Macromolecular NMR spectroscopy for the non-spectroscopist: beyond macromolecular solution structure determination.
  FEBS J, 278, 704-715.  
21307602 Q.Yin, Y.Teng, Y.Li, M.Ding, and F.Zhao (2011).
Expression and characterization of full-length Ampullaria crossean endoglucanase EG65s and their two functional modules.
  Biosci Biotechnol Biochem, 75, 240-246.  
19908036 D.Guillén, S.Sánchez, and R.Rodríguez-Sanoja (2010).
Carbohydrate-binding domains: multiplicity of biological roles.
  Appl Microbiol Biotechnol, 85, 1241-1249.  
20424856 K.Sato, R.Suzuki, N.Nishikubo, S.Takenouchi, S.Ito, Y.Nakano, S.Nakaba, Y.Sano, R.Funada, S.Kajita, H.Kitano, and Y.Katayama (2010).
Isolation of a novel cell wall architecture mutant of rice with defective Arabidopsis COBL4 ortholog BC1 required for regulated deposition of secondary cell wall components.
  Planta, 232, 257-270.  
20689770 W.J.Kelly, S.C.Leahy, E.Altermann, C.J.Yeoman, J.C.Dunne, Z.Kong, D.M.Pacheco, D.Li, S.J.Noel, C.D.Moon, A.L.Cookson, and G.T.Attwood (2010).
The glycobiome of the rumen bacterium Butyrivibrio proteoclasticus B316(T) highlights adaptation to a polysaccharide-rich environment.
  PLoS One, 5, e11942.  
19527512 G.Ausiello, P.F.Gherardini, E.Gatti, O.Incani, and M.Helmer-Citterich (2009).
Structural motifs recurring in different folds recognize the same ligand fragments.
  BMC Bioinformatics, 10, 182.  
18422658 A.Viegas, N.F.Brás, N.M.Cerqueira, P.A.Fernandes, J.A.Prates, C.M.Fontes, M.Bruix, M.J.Romão, A.L.Carvalho, M.J.Ramos, A.L.Macedo, and E.J.Cabrita (2008).
Molecular determinants of ligand specificity in family 11 carbohydrate binding modules: an NMR, X-ray crystallography and computational chemistry approach.
  FEBS J, 275, 2524-2535.  
18292090 K.J.Gregg, R.Finn, D.W.Abbott, and A.B.Boraston (2008).
Divergent modes of glycan recognition by a new family of carbohydrate-binding modules.
  J Biol Chem, 283, 12604-12613.
PDB codes: 2vmg 2vmh 2vmi 2vng 2vno 2vnr
17630303 S.J.Yang, B.C.Min, Y.W.Kim, S.M.Jang, B.H.Lee, and K.H.Park (2007).
Changes in the catalytic properties of Pyrococcus furiosus thermostable amylase by mutagenesis of the substrate binding sites.
  Appl Environ Microbiol, 73, 5607-5612.  
17294188 S.K.Park, C.W.Kim, H.Kim, J.S.Jung, and G.E.Harman (2007).
Cloning and high-level production of a chitinase from Chromobacterium sp. and the role of conserved or nonconserved residues on its catalytic activity.
  Appl Microbiol Biotechnol, 74, 791-804.  
16707677 L.E.Taylor, B.Henrissat, P.M.Coutinho, N.A.Ekborg, S.W.Hutcheson, and R.M.Weiner (2006).
Complete cellulase system in the marine bacterium Saccharophagus degradans strain 2-40T.
  J Bacteriol, 188, 3849-3861.  
16041515 H.B.Huang, M.C.Chi, W.H.Hsu, W.C.Liang, and L.L.Lin (2005).
Construction and one-step purification of Bacillus kaustophilus leucine aminopeptidase fused to the starch-binding domain of Bacillus sp. strain TS-23 alpha-amylase.
  Bioprocess Biosyst Eng, 27, 389-398.  
14738848 I.Levy, T.Paldi, and O.Shoseyov (2004).
Engineering a bifunctional starch-cellulose cross-bridge protein.
  Biomaterials, 25, 1841-1849.  
11920869 A.Berthod, M.Rodriguez, and D.W.Armstrong (2002).
Evaluation of molecule-microbe interactions with capillary electrophoresis: procedures, utility and restrictions.
  Electrophoresis, 23, 847-857.  
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
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.  
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.