1WU4

Crystal structure of reducing-end-xylose releasing exo-oligoxylanase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for the Specificity of the Reducing End Xylose-releasing Exo-oligoxylanase from Bacillus halodurans C-125

Fushinobu, S.Hidaka, M.Honda, Y.Wakagi, T.Shoun, H.Kitaoka, M.

(2005) J Biol Chem 280: 17180-17186

  • DOI: 10.1074/jbc.M413693200
  • Primary Citation of Related Structures:  
    1WU6, 1WU5, 1WU4

  • PubMed Abstract: 
  • Reducing end xylose-releasing exo-oligoxylanase from Bacillus halodurans C-125 (Rex) hydrolyzes xylooligosaccharides whose degree of polymerization is greater than or equal to 3, releasing the xylose unit at the reducing end. It is a unique exo-type ...

    Reducing end xylose-releasing exo-oligoxylanase from Bacillus halodurans C-125 (Rex) hydrolyzes xylooligosaccharides whose degree of polymerization is greater than or equal to 3, releasing the xylose unit at the reducing end. It is a unique exo-type glycoside hydrolase that recognizes the xylose unit at the reducing end in a very strict manner, even discriminating the beta-anomeric hydroxyl configuration from the alpha-anomer or 1-deoxyxylose. We have determined the crystal structures of Rex in unliganded and complex forms at 1.35-2.20-A resolution and revealed the structural aspects of its three subsites ranging from -2 to +1. The structure of Rex was compared with those of endo-type enzymes in glycoside hydrolase subfamily 8a (GH-8a). The catalytic machinery of Rex is basically conserved with other GH-8a enzymes. However, subsite +2 is blocked by a barrier formed by a kink in the loop before helix alpha10. His-319 in this loop forms a direct hydrogen bond with the beta-hydroxyl of xylose at subsite +1, contributing to the specific recognition of anomers at the reducing end.


    Related Citations: 
    • Crystallization and preliminary X-ray analysis of reducing-end-xylose releasing exo-oligoxylanase (Rex) form Bacillus halodurans C-125
      Honda, Y., Fushinobu, S., Hidaka, M., Wakagi, T., Shoun, H., Kitaoka, M.
      () To be published --: --
    • A family 8 glycoside hydrolase from Bacillus halodurans C-125 (BH2105) is a reducing end xylose-releasing exo-oligoxylanase
      Honda, Y., Kitaoka, M.
      (2004) J Biol Chem 279: 55097

    Organizational Affiliation

    Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan. asfushi@mail.ecc.u-tokyo.ac.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
xylanase YA396Bacillus halodurans C-125Mutation(s): 1 
Gene Names: BH2105
EC: 3.2.1.156
Find proteins for Q9KB30 (Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125))
Explore Q9KB30 
Go to UniProtKB:  Q9KB30
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.689α = 90
b = 86.018β = 90
c = 87.92γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance