1E5N

E246C mutant of P fluorescens subsp. cellulosa xylanase A in complex with xylopentaose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

X-Ray Crystallographic Study of Xylopentaose Binding to Pseudomonas Fluorescens Xylanase A.

Leggio, L.L.Jenkins, J.Harris, G.W.Pickersgill, R.W.

(2000) Proteins 41: 362


  • PubMed Abstract: 
  • The structure of the complex between a catalytically compromised family 10 xylanase and a xylopentaose substrate has been determined by X-ray crystallography and refined to 3.2 A resolution. The substrate binds at the C-terminal end of the eightfold ...

    The structure of the complex between a catalytically compromised family 10 xylanase and a xylopentaose substrate has been determined by X-ray crystallography and refined to 3.2 A resolution. The substrate binds at the C-terminal end of the eightfold betaalpha-barrel of Pseudomonas fluorescens subsp. cellulosa xylanase A and occupies substrate binding subsites -1 to +4. Crystal contacts are shown to prevent the expected mode of binding from subsite -2 to +3, because of steric hindrance to subsite -2. The loss of accessible surface at individual subsites on binding of xylopentaose parallels well previously reported experimental measurements of individual subsites binding energies, decreasing going from subsite +2 to +4. Nine conserved residues contribute to subsite -1, including three tryptophan residues forming an aromatic cage around the xylosyl residue at this subsite. One of these, Trp 313, is the single residue contributing most lost accessible surface to subsite -1, and goes from a highly mobile to a well-defined conformation on binding of the substrate. A comparison of xylanase A with C. fimi CEX around the +1 subsite suggests that a flatter and less polar surface is responsible for the better catalytic properties of CEX on aryl substrates. The view of catalysis that emerges from combining this with previously published work is the following: (1) xylan is recognized and bound by the xylanase as a left-handed threefold helix; (2) the xylosyl residue at subsite -1 is distorted and pulled down toward the catalytic residues, and the glycosidic bond is strained and broken to form the enzyme-substrate covalent intermediate; (3) the intermediate is attacked by an activated water molecule, following the classic retaining glycosyl hydrolase mechanism.


    Related Citations: 
    • Structure of the Catalytic Core of the Family F Xylanase from Pseudomonas Fluorescens and Identification of the Xylopentaose-Binding Sites
      Harris, G.W.,Jenkins, J.A.,Connerton, I.,Cummings, N.,Lo Leggio, L.,Scott, M.,Hazlewood, G.P.,Laurie, J.I.,Gilbert, H.J.,Pickersgill, R.W.
      (1994) Structure 2: 1107
    • Xylanase-Oligosaccharide Interactions Studied by a Competitive Enzyme Assay
      Lo Leggio, L.,Pickersgill, R.W.
      (1999) Enzyme Microb.Technol. 25: 701
    • Refined Crystal Structure of the Catalytic Domain of Xylanase a from Pseudomonas Fluorescens at 1.8 Angstrom Resolution
      Harris, G.W.,Jenkins, J.A.,Connerton, I.,Pickersgill, R.W.
      (1996) Acta Crystallogr.,Sect.D 52: 393


    Organizational Affiliation

    Centre for Crystallographic Studies, Chemical Institute, University of Copenhagen, Copenhagen, Denmark. leila@ccs.ki.ku.dk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDO-1,4-BETA-XYLANASE A
A, B
348Cellvibrio japonicus (strain Ueda107)Mutation(s): 1 
Gene Names: xynA (xyn10A)
EC: 3.2.1.8
Find proteins for P14768 (Cellvibrio japonicus (strain Ueda107))
Go to UniProtKB:  P14768
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.190 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 96.700α = 90.00
b = 96.700β = 90.00
c = 152.700γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
XENGENdata scaling
X-PLORphasing
XENGENdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-12-08
    Type: Initial release
  • Version 1.1: 2013-01-30
    Type: Data collection, Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance