1CLX

CATALYTIC CORE OF XYLANASE A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Refined crystal structure of the catalytic domain of xylanase A from Pseudomonas fluorescens at 1.8 A resolution.

Harris, G.W.Jenkins, J.A.Connerton, I.Pickersgill, R.W.

(1996) Acta Crystallogr.,Sect.D 52: 393-401

  • DOI: 10.1107/S0907444995013540
  • Also Cited By: 1E5N

  • PubMed Abstract: 
  • The three-dimensional structure of native xylanase A from Pseudomonas flouorescens subspecies cellulosa has been refined at 1.8 A resolution. The space group is P2(1)2(1)2(1) with four molecules in the asymmetric unit. The final model has an R factor ...

    The three-dimensional structure of native xylanase A from Pseudomonas flouorescens subspecies cellulosa has been refined at 1.8 A resolution. The space group is P2(1)2(1)2(1) with four molecules in the asymmetric unit. The final model has an R factor of 0.166 for 103 749 reflections with the four molecules refined independently. The tertiary structure consists of an eightfold beta/alpha-barrel, the so-called TIM-barrel fold. The active site is in an open cleft at the carboxy-terminal end of the beta/alpha-barrel, and the active-site residues are a pair of glutamates, Glu127 on strand 4 and Glu246 on strand 7. Both these catalytic glutamate residues are found on beta-bulges. An atypically long loop after strand 7 is stabilized by calcium. Unusual features include a non-proline cis-peptide residue Ala80 which is found on a beta-bulge at the end of beta-strand 3. The three beta-bulge type distortions occurring on beta-strands 3, 4 and 7 are functionally significant as they serve to orient important active-site residues. The active-site residues are further held in place by an extensive hydrogen-bonding network of active-site residues in the catalytic site of xylanase A. A chain of well ordered water molecules occupies the substrate-binding cleft, some or all of which are expelled on binding of the substrate.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Analysis of the Catalytic Domain of Xylanase a from Pseudomonas Fluorescens Subspecies Cellulosa
      Pickersgill, R.W.,Jenkins, J.A.,Scott, M.,Connerton, I.,Hazlewood, G.P.,Gilbert, H.J.
      (1993) J.Mol.Biol. 229: 246
    • 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
    • Beta-Glucosidase, Beta-Galactosidase, Family a Cellulases, Family F Xylanases and Two Barley Glycanases Form a Superfamily of Enzymes with 8-Fold Beta/Alpha Architecture and with Two Conserved Glutamates Near the Carboxy-Terminal Ends of Beta-Strands Four and Seven
      Jenkins, J.,Lo Leggio, L.,Harris, G.,Pickersgill, R.
      (1995) FEBS Lett. 362: 281


    Organizational Affiliation

    Department of Protein Engineering, Institute of Food Research, Reading Laboratory, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
XYLANASE A
A, B, C, D
347Cellvibrio japonicus (strain Ueda107)Gene Names: xynA (xyn10A)
EC: 3.2.1.8
Find proteins for P14768 (Cellvibrio japonicus (strain Ueda107))
Go to UniProtKB:  P14768
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 96.110α = 90.00
b = 97.320β = 90.00
c = 151.030γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
RESTRAINrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-06-20
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance