3VZN

Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35E mutant with Glu78 covalently bonded to 2-deoxy-2-fluoro-xylobiose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Strategies for modulating the pH-dependent activity of a family 11 glycoside hydrolase

Ludwiczek, M.L.D'Angelo, I.Yalloway, G.N.Brockerman, J.A.Okon, M.Nielsen, J.E.Strynadka, N.C.Withers, S.G.McIntosh, L.P.

(2013) Biochemistry 52: 3138-3156

  • DOI: 10.1021/bi400034m
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The pH-dependent activity of wild-type Bacillus circulans xylanase (BcX) is set by the pK(a) values of its nucleophile Glu78 and general acid/base Glu172. Herein, we examined several strategies to manipulate these pK(a) values and thereby shift the p ...

    The pH-dependent activity of wild-type Bacillus circulans xylanase (BcX) is set by the pK(a) values of its nucleophile Glu78 and general acid/base Glu172. Herein, we examined several strategies to manipulate these pK(a) values and thereby shift the pH(opt) at which BcX is optimally active. Altering the global charge of BcX through random succinylation had no significant effect. Mutation of residues near or within the active site of BcX, but not directly contacting the catalytic carboxyls, either had little effect or reduced its pH(opt), primarily by lowering the apparent pK(a) value of Glu78. However, mutations causing the largest pK(a) changes also impaired activity. Although not found as a general acid/base in naturally occurring xylanases, substitution of Glu172 with a His lowered the pH(opt) of BcX from 5.6 to 4.7 while retaining 8% activity toward a xylobioside substrate. Mutation of Asn35, which contacts Glu172, to either His or Glu also led to a reduction in pH(opt) by ~1.2 units. Detailed pK(a) measurements by NMR spectroscopy revealed that, despite the opposite charges of the introduced residues, both the N35H and N35E forms of BcX utilize a reverse protonation mechanism. In this mechanism, the pK(a) value of the general acid is lower than that of the nucleophile, and only a small population of enzyme is in a catalytically competent ionization state. However, overall activity is maintained due to the increased strength of the general acid. This study illustrates several routes for altering the pH-dependent properties of xylanases, while also providing valuable insights into complex protein electrostatics.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endo-1,4-beta-xylanase
A, B
185Bacillus circulansMutation(s): 1 
Gene Names: xlnA
EC: 3.2.1.8
Find proteins for P09850 (Bacillus circulans)
Go to UniProtKB:  P09850
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
A, B
BETA-D-XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
 Ligand Interaction
DFX
Query on DFX

Download SDF File 
Download CCD File 
A, B
1,2-DEOXY-2-FLUORO-XYLOPYRANOSE
C5 H9 F O3
YIJTWYXBSRZXRS-VPENINKCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.395α = 90.00
b = 63.038β = 104.89
c = 64.360γ = 90.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2013-07-31
    Type: Database references