4OPB

AA13 Lytic polysaccharide monooxygenase from Aspergillus oryzae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.119 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and boosting activity of a starch-degrading lytic polysaccharide monooxygenase.

Lo Leggio, L.Simmons, T.J.Poulsen, J.C.Frandsen, K.E.Hemsworth, G.R.Stringer, M.A.von Freiesleben, P.Tovborg, M.Johansen, K.S.De Maria, L.Harris, P.V.Soong, C.L.Dupree, P.Tryfona, T.Lenfant, N.Henrissat, B.Davies, G.J.Walton, P.H.

(2015) Nat Commun 6: 5961-5961

  • DOI: 10.1038/ncomms6961

  • PubMed Abstract: 
  • Lytic polysaccharide monooxygenases (LPMOs) are recently discovered enzymes that oxidatively deconstruct polysaccharides. LPMOs are fundamental in the effective utilization of these substrates by bacteria and fungi; moreover, the enzymes have signifi ...

    Lytic polysaccharide monooxygenases (LPMOs) are recently discovered enzymes that oxidatively deconstruct polysaccharides. LPMOs are fundamental in the effective utilization of these substrates by bacteria and fungi; moreover, the enzymes have significant industrial importance. We report here the activity, spectroscopy and three-dimensional structure of a starch-active LPMO, a representative of the new CAZy AA13 family. We demonstrate that these enzymes generate aldonic acid-terminated malto-oligosaccharides from retrograded starch and boost significantly the conversion of this recalcitrant substrate to maltose by β-amylase. The detailed structure of the enzyme's active site yields insights into the mechanism of action of this important class of enzymes.


    Organizational Affiliation

    Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Predicted protein
A
233Aspergillus oryzae (strain ATCC 42149 / RIB 40)Mutation(s): 0 
Find proteins for Q2U8Y3 (Aspergillus oryzae (strain ATCC 42149 / RIB 40))
Go to UniProtKB:  Q2U8Y3
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

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Download CCD File 
A
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HIC
Query on HIC
A
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.119 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.560α = 90.00
b = 61.600β = 90.00
c = 73.160γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
REFMACrefinement
PHENIXphasing
PHENIXmodel building
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2015-03-04
    Type: Database references, Experimental preparation
  • Version 1.2: 2017-11-22
    Type: Data collection, Refinement description