6QE8

Crystal structure of Aspergillus niger GH11 endoxylanase XynA in complex with xylobiose epoxide activity based probe

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

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Literature

Dynamic and Functional Profiling of Xylan-Degrading Enzymes inAspergillusSecretomes Using Activity-Based Probes.

Schroder, S.P., de Boer, C., McGregor, N.G.S., Rowland, R.J., Moroz, O., Blagova, E., Reijngoud, J., Arentshorst, M., Osborn, D., Morant, M.D., Abbate, E., Stringer, M.A., Krogh, K.B.R.M., Raich, L., Rovira, C., Berrin, J.G., van Wezel, G.P., Ram, A.F.J., Florea, B.I., van der Marel, G.A., Codee, J.D.C., Wilson, K.S., Wu, L., Davies, G.J., Overkleeft, H.S.

(2019) ACS Cent Sci 5: 1067-1078

  • DOI: 10.1021/acscentsci.9b00221
  • Primary Citation of Related Structures:  
    6Q7I, 6Q7J, 6Q8M, 6Q8N, 6QE8

  • PubMed Abstract: 

    • Plant polysaccharides represent a virtually unlimited feedstock for the generation of biofuels and other commodities. However, the extraordinary recalcitrance of plant polysaccharides toward breakdown necessitates a continued search for enzymes that degrade these materials efficiently under defined conditions ...

    Plant polysaccharides represent a virtually unlimited feedstock for the generation of biofuels and other commodities. However, the extraordinary recalcitrance of plant polysaccharides toward breakdown necessitates a continued search for enzymes that degrade these materials efficiently under defined conditions. Activity-based protein profiling provides a route for the functional discovery of such enzymes in complex mixtures and under industrially relevant conditions. Here, we show the detection and identification of β-xylosidases and endo -β-1,4-xylanases in the secretomes of Aspergillus niger , by the use of chemical probes inspired by the β-glucosidase inhibitor cyclophellitol. Furthermore, we demonstrate the use of these activity-based probes (ABPs) to assess enzyme-substrate specificities, thermal stabilities, and other biotechnologically relevant parameters. Our experiments highlight the utility of ABPs as promising tools for the discovery of relevant enzymes useful for biomass breakdown.

    Organizational Affiliation: 

    Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endo-1,4-beta-xylanase AA211Aspergillus nigerMutation(s): 0 
Gene Names: xynA
EC: 3.2.1.8
UniProt
Find proteins for P55329 (Aspergillus niger)
Explore P55329 
Go to UniProtKB:  P55329
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55329
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HZB (Subject of Investigation/LOI)
Query on HZB
Download Ideal Coordinates CCD File 
K [auth A](1~{R},3~{S},4~{R},5~{R})-5-[(2~{S},3~{R},4~{S},5~{R})-3,4,5-tris(oxidanyl)oxan-2-yl]oxycyclohexane-1,2,3,4-tetrol
C11 H20 O9
SGBDCDJBWZGHGQ-VBGDNJFTSA-N		 Ligand Interaction
MES
Query on MES
Download Ideal Coordinates CCD File 
B [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.508α = 90
b = 67.508β = 90
c = 165.752γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
REFMACphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research CouncilUnited KingdomERC-2012-AdG-32294

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Database references