PDBsum entry 3emc

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Hydrolase PDB id
Protein chain
331 a.a. *
MPD ×2
Waters ×276
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of xynb, an intracellular xylanase from paenibacillus barcinonensis
Structure: Endo-1,4-beta-xylanase. Chain: a. Synonym: xylanase. Engineered: yes
Source: Bacillus sp. Bp-23. Organism_taxid: 89769. Gene: xynb. Expressed in: escherichia coli. Expression_system_taxid: 562
2.10Å     R-factor:   0.186     R-free:   0.248
Authors: J.Sanz-Aparicio,P.Isorna,B.Gonzalez
Key ref: O.Gallardo et al. (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. PubMed id: 19940147
24-Sep-08     Release date:   29-Sep-09    
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Protein chain
Pfam   ArchSchema ?
O69231  (XYNB_PAEBA) -  Endo-1,4-beta-xylanase B
332 a.a.
331 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!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     hydrolase activity     4 terms  


J Biol Chem 285:2721-2733 (2010)
PubMed id: 19940147  
Structural insights into the specificity of Xyn10B from Paenibacillus barcinonensis and its improved stability by forced protein evolution.
O.Gallardo, F.I.Pastor, J.Polaina, P.Diaz, R.Łysek, P.Vogel, P.Isorna, B.González, J.Sanz-Aparicio.
Paenibacillus barcinonensis is a soil bacterium bearing a complex set of enzymes for xylan degradation, including several secreted enzymes and Xyn10B, one of the few intracellular xylanases reported to date. The crystal structure of Xyn10B has been determined by x-ray analysis. The enzyme folds into the typical (beta/alpha)(8) barrel of family 10 glycosyl hydrolases (GH10), with additional secondary structure elements within the beta/alpha motifs. One of these loops -L7- located at the beta7 C terminus, was essential for xylanase activity as its partial deletion yielded an inactive enzyme. The loop contains residues His(249)-Glu(250), which shape a pocket opened to solvent in close proximity to the +2 subsite, which has not been described in other GH10 enzymes. This wide cavity at the +2 subsite, where methyl-2,4-pentanediol from the crystallization medium was found, is a noteworthy feature of Xyn10B, as compared with the narrow crevice described for other GH10 xylanases. Docking analysis showed that this open cavity can accommodate glucuronic acid decorations of xylo-oligosaccharides. Co-crystallization experiments with conduramine derivative inhibitors supported the importance of this open cavity at the +2 subsite for Xyn10B activity. Several mutant derivatives of Xyn10B with improved thermal stability were obtained by forced evolution. Among them, mutant xylanases S15L and M93V showed increased half-life, whereas the double mutant S15L/M93V exhibited a further increase in stability, showing a 20-fold higher heat resistance than the wild type xylanase. All the mutations obtained were located on the surface of Xyn10B. Replacement of a Ser by a Leu residue in mutant xylanase S15L can increase hydrophobic packing efficiency and fill a superficial indentation of the protein, giving rise to a more compact structure of the enzyme.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20656870 O.Gallardo, M.Fernández-Fernández, C.Valls, S.V.Valenzuela, M.B.Roncero, T.Vidal, P.Díaz, and F.I.Pastor (2010).
Characterization of a family GH5 xylanase with activity on neutral oligosaccharides and evaluation as a pulp bleaching aid.
  Appl Environ Microbiol, 76, 6290-6294.  
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