3EMZ

Crystal structure of xylanase XynB from Paenibacillus barcinonensis complexed with a conduramine derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.230 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural insights into the specificity of Xyn10B from Paenibacillus barcinonensis and its improved stability by forced protein evolution.

Gallardo, O.Pastor, F.I.Polaina, J.Diaz, P.Lysek, R.Vogel, P.Isorna, P.Gonzalez, B.Sanz-Aparicio, J.

(2010) J Biol Chem 285: 2721-2733

  • DOI: https://doi.org/10.1074/jbc.M109.064394
  • Primary Citation of Related Structures:  
    3EMC, 3EMQ, 3EMZ

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Department of Microbiology, Faculty of Biology, University of Barcelona, Av. Diagonal 645, 08028 Barcelona, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endo-1,4-beta-xylanase331Paenibacillus barcinonensisMutation(s): 0 
Gene Names: xynB
EC: 3.2.1.8
UniProt
Find proteins for O69231 (Paenibacillus barcinonensis)
Explore O69231 
Go to UniProtKB:  O69231
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO69231
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HXH
Query on HXH

Download Ideal Coordinates CCD File 
B [auth A](1S,2S,3R,6R)-6-[(4-phenoxybenzyl)amino]cyclohex-4-ene-1,2,3-triol
C19 H21 N O4
YNNCSTZOAWTUPJ-YRXWBPOGSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.022α = 90
b = 79.721β = 90
c = 91.183γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Advisory, Refinement description
  • Version 1.3: 2023-11-01
    Changes: Advisory, Data collection, Database references, Refinement description