7NIN

X-ray crystal structure of LsAA9A - CinnamtanninB1 soak


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Inhibition of lytic polysaccharide monooxygenase by natural plant extracts.

Tokin, R.Frandsen, K.E.H.Ipsen, J.O.Lo Leggio, L.Poojary, M.M.Berrin, J.G.Grisel, S.Brander, S.Jensen, P.E.Johansen, K.S.

(2021) New Phytol 232: 1337-1349

  • DOI: https://doi.org/10.1111/nph.17676
  • Primary Citation of Related Structures:  
    7NIM, 7NIN

  • PubMed Abstract: 

    Lytic polysaccharide monooxygenases (LPMOs) are monocopper enzymes of industrial and biological importance. In particular, LPMOs play important roles in fungal lifestyle. No inhibitors of LPMOs have yet been reported. In this study, a diverse library of 100 plant extracts was screened for LPMO activity-modulating effects. By employing protein crystallography and LC-MS, we successfully identified a natural LPMO inhibitor. Extract screening revealed a significant LPMO inhibition by methanolic extract of Cinnamomum cassia (cinnamon), which inhibited LsAA9A LPMO from Lentinus similis in a concentration-dependent manner. With a notable exception, other microbial LPMOs from families AA9 and AA10 were also inhibited by this cinnamon extract. The polyphenol cinnamtannin B1 was identified as the inhibitory component by crystallography. Cinnamtannin B1 was bound to the surface of LsAA9A at two distinct binding sites: one close to the active site and another at a pocket on the opposite side of the protein. Independent characterization of cinnamon extract by LC-MS and subsequent activity measurements confirmed that the compound inhibiting LsAA9A was cinnamtannin B1. The results of this study show that specific natural LPMO inhibitors of plant origin exist in nature, providing the opportunity for future exploitation of such compounds within various biotechnological contexts.


  • Organizational Affiliation

    Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, 1871, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Auxiliary activity 9235Panus similisMutation(s): 0 
EC: 1.14.99.56
UniProt
Find proteins for A0A0S2GKZ1 (Panus similis)
Explore A0A0S2GKZ1 
Go to UniProtKB:  A0A0S2GKZ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0S2GKZ1
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UFK (Subject of Investigation/LOI)
Query on UFK

Download Ideal Coordinates CCD File 
J [auth A]Cinnamtannin B1
C45 H36 O18
BYSRPHRKESMCPO-LQNPQWRQSA-N
NAG
Query on NAG

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C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CU
Query on CU

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

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K [auth A]
L [auth A]
M [auth A]
N [auth A]
O [auth A]
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-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: 1.40 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.04α = 90
b = 125.04β = 90
c = 125.04γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF17SA0027704

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-18
    Type: Initial release
  • Version 1.1: 2022-03-02
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description