1YNA

ENDO-1,4-BETA-XYLANASE, ROOM TEMPERATURE, PH 4.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Thermophilic xylanase from Thermomyces lanuginosus: high-resolution X-ray structure and modeling studies.

Gruber, K.Klintschar, G.Hayn, M.Schlacher, A.Steiner, W.Kratky, C.

(1998) Biochemistry 37: 13475-13485

  • DOI: 10.1021/bi980864l
  • Primary Citation of Related Structures:  
    1YNA

  • PubMed Abstract: 
  • The crystal structure of the thermostable xylanase from Thermomyces lanuginosus was determined by single-crystal X-ray diffraction. The protein crystallizes in space group P21, a = 40.96(4) A, b = 52. 57(5) A, c = 50.47 (5) A, beta = 100.43(5) degrees, Z = 2 ...

    The crystal structure of the thermostable xylanase from Thermomyces lanuginosus was determined by single-crystal X-ray diffraction. The protein crystallizes in space group P21, a = 40.96(4) A, b = 52. 57(5) A, c = 50.47 (5) A, beta = 100.43(5) degrees, Z = 2. Diffraction data were collected at room temperature for a resolution range of 25-1.55 A, and the structure was solved by molecular replacement with the coordinates of xylanase II from Trichoderma reesei as a search model and refined to a crystallographic R-factor of 0.155 for all observed reflections. The enzyme belongs to the family 11 of glycosyl hydrolases [Henrissat, B., and Bairoch, A. (1993) Biochem. J. 293, 781-788]. pKa calculations were performed to assess the protonation state of residues relevant for catalysis and enzyme stability, and a heptaxylan was fitted into the active-site groove by homology modeling, using the published crystal structure of a complex between the Bacillus circulans xylanase and a xylotetraose. Molecular dynamics indicated the central three sugar rings to be tightly bound, whereas the peripheral ones can assume different orientations and conformations, suggesting that the enzyme might also accept xylan chains which are branched at these positions. The reasons for the thermostability of the T. lanuginosus xylanase were analyzed by comparing its crystal structure with known structures of mesophilic family 11 xylanases. It appears that the thermostability is due to the presence of an extra disulfide bridge, as well as to an increase in the density of charged residues throughout the protein.


    Related Citations: 
    • Three-Dimensional Structure of Endo-1,4-Beta-Xylanase II from Trichoderma Reesei: Two Conformational States in the Active Site
      Schlacher, A., Holzmann, K., Hayn, M., Steiner, W., Schwab, H.
      (1996) J Biotechnol 49: 211
    • Three-Dimensional Structure of Endo-1,4-Beta-Xylanase II from Trichoderma Reesei: Two Conformational States in the Active Site
      Torronen, A., Harkki, A., Rouvinen, J.
      (1994) EMBO J 13: 2493

    Organizational Affiliation

    Institut für Physikalische Chemie, Universität Graz, Austria.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENDO-1,4-BETA-XYLANASEA194Thermomyces lanuginosusMutation(s): 0 
Gene Names: XYNA
EC: 3.2.1.8
UniProt
Find proteins for O43097 (Thermomyces lanuginosus)
Explore O43097 
Go to UniProtKB:  O43097
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43097
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.96α = 90
b = 52.57β = 100.43
c = 50.47γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
CCP4data reduction
SHELXL-93model building
X-PLORmodel building
SHELXL-93refinement
X-PLORrefinement
XDSdata reduction
CCP4data scaling
SHELXL-93phasing
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-02-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-07
    Changes: Data collection
  • Version 2.0: 2019-12-25
    Changes: Derived calculations, Polymer sequence