5IJU

Structure of an AA10 Lytic Polysaccharide Monooxygenase from Bacillus amyloliquefaciens with Cu(II) bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Activity, stability and 3-D structure of the Cu(ii) form of a chitin-active lytic polysaccharide monooxygenase from Bacillus amyloliquefaciens.

Gregory, R.C.Hemsworth, G.R.Turkenburg, J.P.Hart, S.J.Walton, P.H.Davies, G.J.

(2016) Dalton Trans 45: 16904-16912

  • DOI: 10.1039/c6dt02793h

  • PubMed Abstract: 
  • The enzymatic deconstruction of recalcitrant polysaccharide biomass is central to the conversion of these substrates for societal benefit, such as in biofuels. Traditional models for enzyme-catalysed polysaccharide degradation involved the synergisti ...

    The enzymatic deconstruction of recalcitrant polysaccharide biomass is central to the conversion of these substrates for societal benefit, such as in biofuels. Traditional models for enzyme-catalysed polysaccharide degradation involved the synergistic action of endo-, exo- and processive glycoside hydrolases working in concert to hydrolyse the substrate. More recently this model has been succeeded by one featuring a newly discovered class of mononuclear copper enzymes: lytic polysaccharide monooxygenases (LPMOs; classified as Auxiliary Activity (AA) enzymes in the CAZy classification). In 2013, the structure of an LPMO from Bacillus amyloliquefaciens, BaAA10, was solved with the Cu centre photoreduced to Cu(i) in the X-ray beam. Here we present the catalytic activity of BaAA10. We show that it is a chitin-active LPMO, active on both α and β chitin, with the Cu(ii) binding with low nM K D , and the substrate greatly increasing the thermal stability of the enzyme. A spiral data collection strategy has been used to facilitate access to the previously unobservable Cu(ii) state of the active centre, revealing a coordination geometry around the copper which is distorted from axial symmetry, consistent with the previous findings from EPR spectroscopy.


    Related Citations: 
    • The copper active site of CBM33 polysaccharide oxygenases.
      Hemsworth, G.R.,Taylor, E.J.,Kim, R.Q.,Gregory, R.C.,Lewis, S.J.,Turkenburg, J.P.,Parkin, A.,Davies, G.J.,Walton, P.H.
      (2013) J. Am. Chem. Soc. 135: 6069


    Organizational Affiliation

    Structural Biology Laboratory, University of York, Heslington, York, YO10 5DD, UK. gideon.davies@york.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BaAA10 Lytic Polysaccharide Monooxygenase
A, B
179N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-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
CU
Query on CU

Download SDF File 
Download CCD File 
A, B
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 34.779α = 90.00
b = 73.482β = 100.40
c = 75.457γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling

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/I014802/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/L000423
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/L021633/1

Revision History 

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-10-19
    Type: Database references
  • Version 1.2: 2016-11-02
    Type: Database references
  • Version 2.0: 2017-08-30
    Type: Atomic model, Author supporting evidence