2DRO

Crystal structure of reducing-end-xylose releasing exo-oligoxylanase D263C mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural explanation for the acquisition of glycosynthase activity

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

(2009) J.Biochem. --: --

  • DOI: 10.1093/jb/mvp159
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glycosynthases are engineered glycoside hydrolases (GHs) that catalyse the synthesis of glycoside from glycosyl-fluoride donors and suitable acceptors. We have determined five crystal structures of the glycosynthase mutants reducing-end xylose-releas ...

    Glycosynthases are engineered glycoside hydrolases (GHs) that catalyse the synthesis of glycoside from glycosyl-fluoride donors and suitable acceptors. We have determined five crystal structures of the glycosynthase mutants reducing-end xylose-releasing exo-oligoxylanase, an inverting GH, that exhibit various levels of glycosynthetic activities. At the active site of the Y198F mutant, the most efficient glycosynthase, a water molecule is observed at the same position as nucleophilic water (NW) in the parent enzyme, and the loss of the fixation of the direction of the lone pair of water molecules in the mutant drastically decreases hydrolytic activity. Water molecules were also observed at each active site of the general base mutant, but they were shifted 1.0-3.0 A from the NW in the wild type. Their positions exhibited a strong correlation with the strength of glycosynthase activity. Here, we propose that a structural prerequisite for the sufficient glycosynthase reaction is the presence of a water molecule at the NW position, and mutation at the NW holder provides a general strategy for inverting GHs. The idea on the position of a water molecule may also be applicable to the design of efficient glycosynthases from retaining GHs.


    Related Citations: 
    • 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
    • The first glycosynthase derived from an inverting glycoside hydrolase
      Honda, Y.,Kitaoka, M.
      (2006) J.Biol.Chem. 281: 1426
    • 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
    • Crystallization and preliminary X-ray analysis of reducing-end xylose-releasing exo-oligoxylanase from Bacillus halodurans C-125
      Honda, Y.,Fushinobu, S.,Hidaka, M.,Wakagi, T.,Shoun, H.,Kitaoka, M.
      (2005) Acta Crystallogr.,Sect.F 61: 291


    Organizational Affiliation

    Department of Biotechnology, The University of Tokyo, Tokyo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Xylanase Y
A
396Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)Mutation(s): 2 
EC: 3.2.1.156
Find proteins for Q9KB30 (Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125))
Go to UniProtKB:  Q9KB30
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.242α = 90.00
b = 86.369β = 90.00
c = 87.653γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-27
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance