3A3V

Crystal structure of reducing-end-xylose releasing exo-oligoxylanase Y198F mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.3 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.

(2010) J Biochem 147: 237-244

  • DOI: 10.1093/jb/mvp159
  • Primary Citation of Related Structures:  
    3A3V, 2DRS, 2DRR, 2DRQ, 2DRO

  • 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: 
    • Alternative strategy for converting an inverting glycoside hydrolase into a glycosynthase
      Honda, Y., Fushinobu, S., Hidaka, M., Wakagi, T., Shoun, H., Taniguchi, H., Kitaoka, M.
      (2008) Glycobiology 18: 325
    • The first glycosynthase derived from an inverting glycoside hydrolase
      Honda, Y., Kitaoka, M.
      (2006) J Biol Chem 281: 1426
    • 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
    • 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 Struct Biol Cryst Commun 61: 291
    • 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, The University of Tokyo, Tokyo, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Xylanase YA396Alkalihalobacillus haloduransMutation(s): 2 
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: 1.39 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.191α = 90
b = 86.207β = 90
c = 87.729γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2014-01-22
    Changes: Database references
  • Version 1.3: 2017-10-11
    Changes: Refinement description