6Q7J

GH3 exo-beta-xylosidase (XlnD) in complex with xylobiose aziridine activity based probe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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:  

  • 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 ...

    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

    Biodiversité et Biotechnologie Fongiques (BBF), UMR1163, INRA, Aix Marseille University, F-13009 Marseille, France.,Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands.,Departament de Quımica Inorgànica i Orgànica (Secció de Química Orgànica) & Institut de Quimica Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08020 Barcelona, Spain.,York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, U.K.,Novozymes Inc., 1445 Drew Avenue, Davis, California 95618, United States.,Novozymes A/S, Krogshøjvej 36, 2880 Bagsværd, Denmark.,Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Exo-1,4-beta-xylosidase xlnD
B, A
785Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139)Mutation(s): 0 
Gene Names: xlnD (xylA)
EC: 3.2.1.37
Find proteins for Q5BAS1 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Go to UniProtKB:  Q5BAS1
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

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

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

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
HLB
Query on HLB

Download SDF File 
Download CCD File 
A, B
5-[3,3-dimethyl-2-[5-(1,3,3-trimethylindol-2-ylidene)penta-1,3-dienyl]indol-1-ium-1-yl]-~{N}-[8-[[(1~{R},2~{S},3~{S},4~{S},5~{R})-2,3,4,5-tetrakis(oxidanyl)cyclohexyl]amino]octyl]pentanamide
C45 H65 N4 O5
QVZIJCUKVKFUJR-XDYJFVOXSA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A, B
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.398α = 90.00
b = 91.579β = 90.00
c = 245.059γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
Aimlessdata scaling
xia2data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M011151/1

Revision History 

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