6Y0H

High resolution structure of GH11 xylanase from Nectria haematococca


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.142 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

High-resolution crystal structure and biochemical characterization of a GH11 endoxylanase from Nectria haematococca.

Andaleeb, H.Ullah, N.Falke, S.Perbandt, M.Brognaro, H.Betzel, C.

(2020) Sci Rep 10: 15658-15658

  • DOI: https://doi.org/10.1038/s41598-020-72644-w
  • Primary Citation of Related Structures:  
    6Y0H

  • PubMed Abstract: 

    Enzymatic degradation of vegetal biomass offers versatile procedures to improve the production of alternative fuels and other biomass-based products. Here we present the three-dimensional structure of a xylanase from Nectria haematococca (NhGH11) at 1.0 Å resolution and its functional properties. The atomic resolution structure provides details and insights about the complex hydrogen bonding network of the active site region and allowed a detailed comparison with homologous structures. Complementary biochemical studies showed that the xylanase can catalyze the hydrolysis of complex xylan into simple xylose aldopentose subunits of different lengths. NhGH11 can catalyze the efficient breakdown of beechwood xylan, xylan polysaccharide, and wheat arabinoxylan with turnover numbers of 1730.6 ± 318.1 min -1 , 1648.2 ± 249.3 min -1 and 2410.8 ± 517.5 min -1 respectively. NhGH11 showed maximum catalytic activity at pH 6.0 and 45 °C. The mesophilic character of NhGH11 can be explained by distinct structural features in comparison to thermophilic GH11 enzymes, including the number of hydrogen bonds, side chain interactions and number of buried water molecules. The enzymatic activity of NhGH11 is not very sensitive to metal ions and chemical reagents that are typically present in associated industrial production processes. The data we present highlights the potential of NhGH11 to be applied in industrial biomass degradation processes.


  • Organizational Affiliation

    Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Build. 22a. Notkestr. 85, 22603, Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endo-1,4-beta-xylanase193Fusarium vanettenii 77-13-4Mutation(s): 4 
Gene Names: NECHADRAFT_106153
EC: 3.2.1.8
UniProt
Find proteins for C7YSL3 (Fusarium vanettenii (strain ATCC MYA-4622 / CBS 123669 / FGSC 9596 / NRRL 45880 / 77-13-4))
Explore C7YSL3 
Go to UniProtKB:  C7YSL3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7YSL3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.142 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.446α = 90
b = 38.5β = 91.43
c = 53.591γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description