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PDBsum entry 2bnj

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protein ligands links
Hydrolase PDB id
2bnj
Jmol
Contents
Protein chain
302 a.a. *
Ligands
XYP-XYP-AHR-FER
Waters ×596
* Residue conservation analysis
PDB id:
2bnj
Name: Hydrolase
Title: The xylanase ta from thermoascus aurantiacus utilizes arabinose decorations of xylan as significant substrate specificity determinants.
Structure: Endo-1,4-beta-xylanase. Chain: a. Synonym: family 10 xylanase, 1,4-beta-d-xylan xylanohydrolase, taxi. Ec: 3.2.1.8
Source: Thermoascus aurantiacus. Organism_taxid: 5087. Variant: mieche, imi 216529
Resolution:
1.6Å     R-factor:   0.117     R-free:   0.147
Authors: M.Vardakou,J.W.Murray,J.Flint,P.Christakopoulos,R.J.Lewis, H.J.Gilbert
Key ref:
M.Vardakou et al. (2005). A family 10 Thermoascus aurantiacus xylanase utilizes arabinose decorations of xylan as significant substrate specificity determinants. J Mol Biol, 352, 1060-1067. PubMed id: 16140328 DOI: 10.1016/j.jmb.2005.07.051
Date:
25-Mar-05     Release date:   07-Sep-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P23360  (XYNA_THEAU) -  Endo-1,4-beta-xylanase
Seq:
Struc:
329 a.a.
302 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 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     metabolic process   4 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
DOI no: 10.1016/j.jmb.2005.07.051 J Mol Biol 352:1060-1067 (2005)
PubMed id: 16140328  
 
 
A family 10 Thermoascus aurantiacus xylanase utilizes arabinose decorations of xylan as significant substrate specificity determinants.
M.Vardakou, J.Flint, P.Christakopoulos, R.J.Lewis, H.J.Gilbert, J.W.Murray.
 
  ABSTRACT  
 
Xylan, which is a key component of the plant cell wall, consists of a backbone of beta-1,4-linked xylose residues that are decorated with arabinofuranose, acetyl, 4-O-methyl d-glucuronic acid and ferulate. The backbone of xylan is hydrolysed by endo-beta1,4-xylanases (xylanases); however, it is unclear whether the various side-chains of the polysaccharide are utilized by these enzymes as significant substrate specificity determinants. To address this question we have determined the crystal structure of a family 10 xylanase from Thermoascus aurantiacus, in complex with xylobiose containing an arabinofuranosyl-ferulate side-chain. We show that the distal glycone subsite of the enzyme makes extensive direct and indirect interactions with the arabinose side-chain, while the ferulate moiety is solvent-exposed. Consistent with the 3D structural data, the xylanase displays fourfold more activity against xylotriose in which the non-reducing moiety is linked to an arabinose side-chain, compared to the undecorated form of the oligosacchairde. These data indicate that the sugar decorations of xylans in the T.aurantiacus family 10 xylanase, rather than simply being accommodated, can be significant substrate specificity determinants.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Schematic of the interactions of FAX2 with TaXyn10. The interactions were determined using PyMol.
Figure 3.
Figure 3. Comparison of TaXyn10 with CmXyn10B. Backbone "worm" representation of TaXyn10-FAX[2] (blue) in comparison with CmXyn10B-AX[2] (yellow). The arabinose in CmXyn10B-AX[2] is partially disordered, and was modelled in two discrete conformations. The residues that make productive enzyme:ligand interactions with the arabinose in the -2 glycone binding site in TaXyn10, Asn25 and Arg26 (pink) are not conserved in CmXyn10B, Thr44 and Ile45 (green). The protein structure in the immediate vicinity of these residues differs between the two enzymes.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 352, 1060-1067) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20971636 C.Xiros, P.Katapodis, and P.Christakopoulos (2011).
Factors affecting cellulose and hemicellulose hydrolysis of alkali treated brewers spent grain by Fusarium oxysporum enzyme extract.
  Bioresour Technol, 102, 1688-1696.  
21120468 F.Zhang, P.Shi, Y.Bai, H.Luo, T.Yuan, H.Huang, P.Yang, L.Miao, and B.Yao (2011).
An acid and highly thermostable xylanase from Phialophora sp. G5.
  Appl Microbiol Biotechnol, 89, 1851-1858.  
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.  
19940147 O.Gallardo, F.I.Pastor, J.Polaina, P.Diaz, R.Łysek, P.Vogel, P.Isorna, B.González, and J.Sanz-Aparicio (2010).
Structural insights into the specificity of Xyn10B from Paenibacillus barcinonensis and its improved stability by forced protein evolution.
  J Biol Chem, 285, 2721-2733.
PDB codes: 3emc 3emq 3emz
  20431716 D.Dodd, and I.K.Cann (2009).
Enzymatic deconstruction of xylan for biofuel production.
  Glob Change Biol Bioenergy, 1, 2.  
18320143 J.G.Berrin, and N.Juge (2008).
Factors affecting xylanase functionality in the degradation of arabinoxylans.
  Biotechnol Lett, 30, 1139-1150.  
17989872 A.E.Fazary, and Y.H.Ju (2007).
Feruloyl esterases as biotechnological tools: current and future perspectives.
  Acta Biochim Biophys Sin (Shanghai), 39, 811-828.  
16522374 K.A.Gray, L.Zhao, and M.Emptage (2006).
Bioethanol.
  Curr Opin Chem Biol, 10, 141-146.  
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.