1YNA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 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

  • 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) degree ...

    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
      Torronen, A.,Harkki, A.,Rouvinen, J.
      (1994) Embo J. 13: 2493
    • 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


    Organizational Affiliation

    Institut für Physikalische Chemie, Universität Graz, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDO-1,4-BETA-XYLANASE
A
194Thermomyces lanuginosusMutation(s): 0 
Gene Names: XYNA
EC: 3.2.1.8
Find proteins for O43097 (Thermomyces lanuginosus)
Go to UniProtKB:  O43097
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 40.960α = 90.00
b = 52.570β = 100.43
c = 50.470γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
CCP4data scaling
XDSdata reduction
SHELXL-93model building
XDSdata scaling
X-PLORrefinement
CCP4data reduction
SHELXL-93phasing
SHELXL-93refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1996-08-22 
  • Released Date: 1997-02-12 
  • Deposition Author(s): Gruber, K., Kratky, C.

Revision History 

  • Version 1.0: 1997-02-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-03-07
    Type: Data collection