2D24

Crystal structure of ES complex of catalytic-site mutant xylanase from Streptomyces olivaceoviridis E-86


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86

Suzuki, R.Fujimoto, Z.Ito, S.Kawahara, S.Kaneko, S.Taira, K.Hasegawa, T.Kuno, A.

(2009) J.Biochem. 146: 61-70

  • DOI: 10.1093/jb/mvp047
  • Primary Citation of Related Structures:  
  • Also Cited By: 5GQE, 5GQD

  • PubMed Abstract: 
  • Retaining glycosyl hydrolases, which catalyse both glycosylation and deglycosylation in a concerted manner, are the most abundant hydrolases. To date, their visualization has tended to be focused on glycosylation because glycosylation reactions can b ...

    Retaining glycosyl hydrolases, which catalyse both glycosylation and deglycosylation in a concerted manner, are the most abundant hydrolases. To date, their visualization has tended to be focused on glycosylation because glycosylation reactions can be visualized by inactivating deglycosylation step and/or using substrate analogues to isolate covalent intermediates. Furthermore, during structural analyses of glycosyl hydrolases with hydrolytic reaction products by the conventional soaking method, mutarotation of an anomeric carbon in the reaction products promptly and certainly occurs. This undesirable structural alteration hinders visualization of the second step in the reaction. Here, we investigated X-ray crystallographic visualization as a possible method for visualizing the conformational itinerary of a retaining xylanase from Streptomyces olivaceoviridis E-86. To clearly define the stereochemistry at the anomeric carbon during the deglycosylation step, extraneous nucleophiles, such as azide, were adopted to substitute for the missing base catalyst in an appropriate mutant. The X-ray crystallographic visualization provided snapshots of the components of the entire reaction, including the E*S complex, the covalent intermediate, breakdown of the intermediate and the enzyme-product (E*P)complex.


    Related Citations: 
    • Crystal structures of the sugar complexes of Streptomyces olivaceoviridis E-86 xylanase: sugar binding structure of the family 13 carbohydrate binding module
      Fujimoto, Z.,Kuno, A.,Kaneko, S.,Kobayashi, H.,Kusakabe, I.,Mizuno, H.
      (2002) J.Mol.Biol. 316: 65
    • PCR Cloning and Expression of the F/10 Family Xylanse Gene from Streptomyces olivaceoviridis E-86
      Kuno, A.,Shimizu, D.,Kaneko, S.,Koyama, Y.,Yoshida, S.,Kobayashi, H.,Hayashi, K.,Taira, K.,Kusakabe, I.
      (1998) J.FERMENT.BIOENG. 86: 434
    • Significant enhancement in the binding of p-nitrophenyl-beta-D-xylobioside by the E128H mutant F/10 xylanase from Streptomyces olivaceoviridis E-86
      Kuno, A.,Shimizu, D.,Kaneko, S.,Hasegawa, T.,Gama, Y.,Hayashi, K.,Kusakabe, I.,Taira, K.
      (1999) Febs Lett. 450: 299
    • Crystal structure of Streptomyces olivaceoviridis E-86 beta-xylanase containing xylan-binding domain
      Fujimoto, Z.,Kuno, A.,Kaneko, S.,Yoshida, S.,Kobayashi, H.,Kusakabe, I.,Mizuno, H.
      (2000) J.Mol.Biol. 300: 575
    • Crystal structures of decorated xylooligosaccharides bound to a family 10 xylanase from Streptomyces olivaceoviridis E-86
      Fujimoto, Z.,Kaneko, S.,Kuno, A.,Kobayashi, H.,Kusakabe, I.,Mizuno, H.
      (2004) J.Biol.Chem. 279: 9606


    Organizational Affiliation

    Department of Material and Biological Chemistry, Yamagata University, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDO-1,4-BETA-D-XYLANASE
A, B
436Streptomyces olivaceoviridisMutation(s): 2 
EC: 3.2.1.8
Find proteins for Q7SI98 (Streptomyces olivaceoviridis)
Go to UniProtKB:  Q7SI98
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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

Download SDF File 
Download CCD File 
A, B
XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-LECHCGJUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 75.704α = 90.00
b = 94.090β = 90.00
c = 138.366γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
MOLREPphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2012-02-15
    Type: Database references