1BK1

ENDO-1,4-BETA-XYLANASE C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic and mutational analyses of an extremely acidophilic and acid-stable xylanase: biased distribution of acidic residues and importance of Asp37 for catalysis at low pH.

Fushinobu, S.Ito, K.Konno, M.Wakagi, T.Matsuzawa, H.

(1998) Protein Eng. 11: 1121-1128


  • PubMed Abstract: 
  • Xylanase C from Aspergillus kawachii has an optimum pH of 2.0 and is stable at pH 1.0. The crystal structure of xylanase C was determined at 2.0 A resolution (R-factor = 19.4%). The overall structure was similar to those of other family 11 xylanases. ...

    Xylanase C from Aspergillus kawachii has an optimum pH of 2.0 and is stable at pH 1.0. The crystal structure of xylanase C was determined at 2.0 A resolution (R-factor = 19.4%). The overall structure was similar to those of other family 11 xylanases. Asp37 and an acid-base catalyst, Glu170, are located at a hydrogen-bonding distance (2.8 A), as in other xylanases with low pH optima. Asp37 of xylanase C was replaced with asparagine and other residues by site-directed mutagenesis. Analyses of the wild-type and mutant enzymes showed that Asp37 is important for high enzyme activity at low pH. In the case of the asparagine mutant, the optimum pH shifted to 5.0 and the maximum specific activity decreased to about 15% of that of the wild-type enzyme. On structural comparison with xylanases with higher pH optima, another striking feature of the xylanase C structure was found; the enzyme has numerous acidic residues concentrated on the surface (so-called 'Ser/Thr surface' in most family 11 xylanases). The relationship of the stability against extreme pH conditions and high salt concentrations with the spatially biased distribution of charged residues on the proteins is discussed.


    Related Citations: 
    • Purification and Properties of Acid Stable Xylanases from Aspergillus Kawachii
      Ito, K.,Ogasawara, H.,Sugimoto, T.,Ishikawa, T.
      (1992) Biosci.Biotechnol.Biochem. 56: 547
    • Cloning and Sequencing of the Xync Gene Encoding Acid Xylanase of Aspergillus Kawachii
      Ito, K.,Iwashita, K.,Iwano, K.
      (1992) Biosci.Biotechnol.Biochem. 56: 1338


    Organizational Affiliation

    Department of Biotechnology, University of Tokyo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDO-1,4-B-XYLANASE C
A
184Aspergillus kawachii (strain NBRC 4308)Mutation(s): 0 
Gene Names: xynC
EC: 3.2.1.8
Find proteins for P33557 (Aspergillus kawachii (strain NBRC 4308))
Go to UniProtKB:  P33557
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.194 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 62.065α = 90.00
b = 62.065β = 90.00
c = 113.291γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORmodel building
SCALEPACKdata scaling
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance