PDBsum entry 2vgd

Go to PDB code: 
protein ligands metals links
Hydrolase PDB id
Protein chain
195 a.a. *
GOL ×4
Waters ×275
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of environmental isolated gh11 in complex with xylobiose and feruloyl-arabino-xylotriose
Structure: Enxyn11a. Chain: a. Engineered: yes. Other_details: gh11 catalytic domain
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 511693.
1.80Å     R-factor:   0.177     R-free:   0.203
Authors: M.Vardakou,C.Dumon,J.E.Flint,J.W.Murray,P.Christakopoulos, D.P.Weiner,N.Juge,R.J.Lewis,H.J.Gilbert
Key ref:
M.Vardakou et al. (2008). Understanding the structural basis for substrate and inhibitor recognition in eukaryotic GH11 xylanases. J Mol Biol, 375, 1293-1305. PubMed id: 18078955 DOI: 10.1016/j.jmb.2007.11.007
12-Nov-07     Release date:   25-Dec-07    
Go to PROCHECK summary

Protein chain
No UniProt id for this chain
Struc: 195 a.a.
Key:    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     hydrolase activity, hydrolyzing O-glycosyl compounds     1 term  


DOI no: 10.1016/j.jmb.2007.11.007 J Mol Biol 375:1293-1305 (2008)
PubMed id: 18078955  
Understanding the structural basis for substrate and inhibitor recognition in eukaryotic GH11 xylanases.
M.Vardakou, C.Dumon, J.W.Murray, P.Christakopoulos, D.P.Weiner, N.Juge, R.J.Lewis, H.J.Gilbert, J.E.Flint.
Endo-beta1,4-xylanases (xylanases) hydrolyse the beta1,4 glycosidic bonds in the backbone of xylan. Although xylanases from glycoside hydrolase family 11 (GH11) have been extensively studied, several issues remain unresolved. Thus, the mechanism by which these enzymes hydrolyse decorated xylans is unclear and the structural basis for the variation in catalytic activity within this family is unknown. Furthermore, the mechanism for the differences in the inhibition of fungal GH11 enzymes by the wheat protein XIP-I remains opaque. To address these issues we report the crystal structure and biochemical properties of the Neocallimastix patriciarum xylanase NpXyn11A, which displays unusually high catalytic activity and is one of the few fungal GH11 proteins not inhibited by XIP-I. Although the structure of NpXyn11A could not be determined in complex with substrates, we have been able to investigate how GH11 enzymes hydrolyse decorated substrates by solving the crystal structure of a second GH11 xylanase, EnXyn11A (encoded by an environmental DNA sample), bound to ferulic acid-1,5-arabinofuranose-alpha1,3-xylotriose (FAX(3)). The crystal structure of the EnXyn11A-FAX(3) complex shows that solvent exposure of the backbone xylose O2 and O3 groups at subsites -3 and +2 allow accommodation of alpha1,2-linked 4-methyl-D-glucuronic acid and L-arabinofuranose side chains. Furthermore, the ferulated arabinofuranose side chain makes hydrogen bonds and hydrophobic interactions at the +2 subsite, indicating that the decoration may represent a specificity determinant at this aglycone subsite. The structure of NpXyn11A reveals potential -3 and +3 subsites that are kinetically significant. The extended substrate-binding cleft of NpXyn11A, compared to other GH11 xylanases, may explain why the Neocallimastix enzyme displays unusually high catalytic activity. Finally, the crystal structure of NpXyn11A shows that the resistance of the enzyme to XIP-I is not due solely to insertions in the loop connecting beta strands 11 and 12, as suggested previously, but is highly complex.
  Selected figure(s)  
Figure 4.
Figure 4. The interactions between EnXyn11A and FAX[3.] The subsites are labelled, the broken lines represent hydrogen bonding interactions, and the interatomic distances are noted. (a) The glycone and (b) the aglycone region of the active site.
Figure 6.
Figure 6. Overlay of the XIP-I/P. funiculosum GH11 xylanase complex with wild-type and mutant NpXyn11A. (a) The structure of the XIP-I (green)/P. funiculosum GH11 xylanase (red) complex was overlaid with wild-type NpXyn11A (cyan). The loops connecting β strand 3 with 4 and β strand 11 with 12 appear to clash with the xylanase inhibitor. (b) Wild-type NpXyn11 (cyan) and the Δ3-4NpXyn11A mutant (magenta) were overlaid with the structure of XIP-I when in complex with the P. funiculosum GH11 xylanase. The mutation has reduced the size of the loop connecting β strands 3 and 4, which now no longer make steric clashes with XIP-I.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 375, 1293-1305) copyright 2008.  
  Figures were selected by an automated process.  

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.  
20852069 J.C.Mortimer, G.P.Miles, D.M.Brown, Z.Zhang, M.P.Segura, T.Weimar, X.Yu, K.A.Seffen, E.Stephens, S.R.Turner, and P.Dupree (2010).
Absence of branches from xylan in Arabidopsis gux mutants reveals potential for simplification of lignocellulosic biomass.
  Proc Natl Acad Sci U S A, 107, 17409-17414.  
19144002 C.Hervé, A.Rogowski, H.J.Gilbert, and J.Paul Knox (2009).
Enzymatic treatments reveal differential capacities for xylan recognition and degradation in primary and secondary plant cell walls.
  Plant J, 58, 413-422.  
  20431716 D.Dodd, and I.K.Cann (2009).
Enzymatic deconstruction of xylan for biofuel production.
  Glob Change Biol Bioenergy, 1, 2.  
19497379 S.Lagaert, T.Beliën, and G.Volckaert (2009).
Plant cell walls: Protecting the barrier from degradation by microbial enzymes.
  Semin Cell Dev Biol, 20, 1064-1073.  
18320143 J.G.Berrin, and N.Juge (2008).
Factors affecting xylanase functionality in the degradation of arabinoxylans.
  Biotechnol Lett, 30, 1139-1150.  
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.