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PDBsum entry 1xnk

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1xnk
Jmol
Contents
Protein chains
191 a.a. *
Ligands
SO4 ×3
XS2 ×2
Waters ×449
* Residue conservation analysis
PDB id:
1xnk
Name: Hydrolase
Title: Beta-1,4-xylanase from chaetomium thermophilum complexed wit thioxylopentoside
Structure: Endoxylanase 11a. Chain: a, b. Fragment: catalytic domain. Engineered: yes
Source: Chaetomium thermophilum. Organism_taxid: 209285. Expressed in: hypocrea jecorina. Expression_system_taxid: 51453
Resolution:
1.55Å     R-factor:   0.197     R-free:   0.224
Authors: J.Hakanpaa,N.Hakulinen,J.Rouvinen
Key ref:
J.Jänis et al. (2005). Determination of thioxylo-oligosaccharide binding to family 11 xylanases using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and X-ray crystallography. FEBS J, 272, 2317-2333. PubMed id: 15853815 DOI: 10.1111/j.1742-4658.2005.04659.x
Date:
05-Oct-04     Release date:   10-May-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8J1V6  (Q8J1V6_9PEZI) -  Endo-1,4-beta-xylanase
Seq:
Struc:
261 a.a.
191 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     hydrolase activity, hydrolyzing O-glycosyl compounds     1 term  

 

 
DOI no: 10.1111/j.1742-4658.2005.04659.x FEBS J 272:2317-2333 (2005)
PubMed id: 15853815  
 
 
Determination of thioxylo-oligosaccharide binding to family 11 xylanases using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and X-ray crystallography.
J.Jänis, J.Hakanpää, N.Hakulinen, F.M.Ibatullin, A.Hoxha, P.J.Derrick, J.Rouvinen, P.Vainiotalo.
 
  ABSTRACT  
 
Noncovalent binding of thioxylo-oligosaccharide inhibitors, methyl 4-thio-alpha-xylobioside (S-Xyl2-Me), methyl 4,4II-dithio-alpha-xylotrioside (S-Xyl3-Me), methyl 4,4II,4III-trithio-alpha-xylotetroside (S-Xyl4-Me), and methyl 4,4II,4III,4IV-tetrathio-alpha-xylopentoside (S-Xyl5-Me), to three family 11 endo-1,4-beta-xylanases from Trichoderma reesei (TRX I and TRX II) and Chaetomium thermophilum (CTX) was characterized using electrospray ionization Fourier transform ion cyclotron resonance (FT-ICR) MS and X-ray crystallography. Ultra-high mass-resolving power and mass accuracy inherent to FT-ICR allowed mass measurements for noncovalent complexes to within |DeltaM|average of 2 p.p.m. The binding constants determined by MS titration experiments were in the range 10(4)-10(3) M-1, decreasing in the series of S-Xyl5-Me>or=S-Xyl4-Me>S-Xyl3-Me. In contrast, S-Xyl2-Me did not bind to any xylanase at the initial concentration of 5-200 microM, indicating increasing affinity with increasing number of xylopyranosyl units, with a minimum requirement of three. The crystal structures of CTX-inhibitor complexes gave interesting insights into the binding. Surprisingly, none of the inhibitors occupied any of the aglycone subsites of the active site. The binding to only the glycone subsites is nonproductive for catalysis, and yet this has also been observed for other family 11 xylanases in complex with beta-d-xylotetraose [Wakarchuk WW, Campbell RL, Sung WL, Davoodi J & Makoto Y (1994) Protein Sci3, 465-475, and Sabini E, Wilson KS, Danielsen S, Schulein M & Davies GJ (2001) Acta CrystallogrD57, 1344-1347]. Therefore, the role of the aglycone subsites remains controversial despite their obvious contribution to catalysis.
 
  Selected figure(s)  
 
Figure 8.
Fig. 8. Cartoon representation (A) and surface representation (B) of the crystal structure of CTX with S-Xyl5-Me. The observed part of the inhibitor (three xylopyranose rings) is shown at the active site. Carbon atoms of the inhibitor are coloured in purple, oxygen atoms in red, and sulfur atoms in orange. The figure was created with PYMOL[86].
Figure 10.
Fig. 10. Superposition of the crystal structures of CTX in complex with S-Xyl5-Me (in purple) and B. agaradhaerens xylanase in complex with Xyl4 (in blue). The PDB codes are 1XNK and 1H4H, respectively. Superpositioning was performed with O[73], and the figure was created with PYMOL[86].
 
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS J (2005, 272, 2317-2333) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20225927 A.Pollet, J.A.Delcour, and C.M.Courtin (2010).
Structural determinants of the substrate specificities of xylanases from different glycoside hydrolase families.
  Crit Rev Biotechnol, 30, 176-191.  
18320143 J.G.Berrin, and N.Juge (2008).
Factors affecting xylanase functionality in the degradation of arabinoxylans.
  Biotechnol Lett, 30, 1139-1150.  
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