1E5N

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 2.0 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: 362-373

  • DOI: 10.1002/1097-0134(20001115)41:3<362::aid-prot80>3.0.co;2-n
  • Primary Citation of Related Structures:  
    1E5N

  • 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 betaalpha-barrel of Pseudomonas fluorescens subsp ...

    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: 
    • 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 D Biol Crystallogr 52: 393
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENDO-1,4-BETA-XYLANASE AA, B348Pseudomonas fluorescensMutation(s): 1 
EC: 3.2.1.8
UniProt
Find proteins for P14768 (Cellvibrio japonicus (strain Ueda107))
Explore P14768 
Go to UniProtKB:  P14768
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranoseC, D5N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G47101GE
GlyCosmos:  G47101GE
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A], F [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.7α = 90
b = 96.7β = 90
c = 152.7γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
XENGENdata reduction
XENGENdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-12-08
    Type: Initial release
  • Version 1.1: 2013-01-30
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.3: 2019-10-09
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary