4OPB

AA13 Lytic polysaccharide monooxygenase from Aspergillus oryzae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.121 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1038/ncomms6961
  • Primary Citation of Related Structures:  
    4OPB

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Predicted protein233Aspergillus oryzae RIB40Mutation(s): 0 
Gene Names: AO090701000246
UniProt
Find proteins for Q2U8Y3 (Aspergillus oryzae (strain ATCC 42149 / RIB 40))
Explore Q2U8Y3 
Go to UniProtKB:  Q2U8Y3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2U8Y3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
L [auth A]
M [auth A]
O [auth A]
I [auth A],
J [auth A],
L [auth A],
M [auth A],
O [auth A],
P [auth A],
Q [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU

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B [auth A]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
IPA
Query on IPA

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H [auth A],
K [auth A]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
N [auth A],
R [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC
A
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.121 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.56α = 90
b = 61.6β = 90
c = 73.16γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHENIXmodel building
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2015-03-04
    Changes: Database references, Experimental preparation
  • Version 1.2: 2017-11-22
    Changes: Data collection, Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary