3U7B

A new crystal structure of a Fusarium oxysporum GH10 xylanase reveals the presence of an extended loop on top of the catalytic cleft


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


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Literature

The structure of a GH10 xylanase from Fusarium oxysporum reveals the presence of an extended loop on top of the catalytic cleft.

Dimarogona, M.Topakas, E.Christakopoulos, P.Chrysina, E.D.

(2012) Acta Crystallogr.,Sect.D 68: 735-742

  • DOI: 10.1107/S0907444912007044

  • PubMed Abstract: 
  • Xylanase enzymes have been the focus of considerable research in recent decades owing to their extensive use in a variety of biotechnological applications. Previous structural studies of a number of GH10 xylanases revealed that all GH10 family member ...

    Xylanase enzymes have been the focus of considerable research in recent decades owing to their extensive use in a variety of biotechnological applications. Previous structural studies of a number of GH10 xylanases revealed that all GH10 family members have the (β/α)(8)-barrel fold and their catalytic site is conserved. The structure of a new GH10 xylanase from Fusarium oxysporum (FoXyn10a) was determined at 1.94 Å resolution from crystals belonging to the tetragonal space group P4(1)2(1)2 with five molecules per asymmetric unit. Comparison of the structure of FoXyn10a with previously determined structures of GH10 family members indicated that most of the differences were located in the loop regions between the ordered secondary-structure elements of the barrel, as expected. However, alignment of FoXyn10a with sequence and structural homologues denoted an atypically long loop connecting strand β6b and helix α6 that was only present in one other GH10 xylanase, the structure of which is not known. This structural feature may be of functional importance, with potential implications in the catalytic efficiency of the enzyme.


    Organizational Affiliation

    Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDO-1,4-BETA-XYLANASE
A, B, C, D, E
327Fusarium oxysporum f. sp. lycopersici (strain 4287 / CBS 123668 / FGSC 9935 / NRRL 34936)EC: 3.2.1.8
Find proteins for B3A0S5 (Fusarium oxysporum f. sp. lycopersici (strain 4287 / CBS 123668 / FGSC 9935 / NRRL 34936))
Go to UniProtKB:  B3A0S5
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
B, D, E
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C, D, E
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B, C, D, E
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.213 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 124.220α = 90.00
b = 124.220β = 90.00
c = 284.040γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
DNAdata collection
MOSFLMdata reduction
BALBESphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-18
    Type: Initial release