5NMX

Crystal Structure of the pyrrolizidine alkaloid N-oxygenase from Zonocerus variegatus in complex with FAD and NADP+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of pyrrolizidine alkaloid N-oxygenase from the grasshopper Zonocerus variegatus.

Kubitza, C.Faust, A.Gutt, M.Gath, L.Ober, D.Scheidig, A.J.

(2018) Acta Crystallogr D Struct Biol 74: 422-432

  • DOI: 10.1107/S2059798318003510
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The high-resolution crystal structure of the flavin-dependent monooxygenase (FMO) from the African locust Zonocerus variegatus is presented and the kinetics of structure-based protein variants are discussed. Z. variegatus expresses three flavin-depen ...

    The high-resolution crystal structure of the flavin-dependent monooxygenase (FMO) from the African locust Zonocerus variegatus is presented and the kinetics of structure-based protein variants are discussed. Z. variegatus expresses three flavin-dependent monooxygenase (ZvFMO) isoforms which contribute to a counterstrategy against pyrrolizidine alkaloids (PAs). PAs are protoxic compounds produced by some angiosperm lineages as a chemical defence against herbivores. N-Oxygenation of PAs and the accumulation of PA N-oxides within their haemolymph result in two evolutionary advantages for these insects: (i) they circumvent the defence mechanism of their food plants and (ii) they can use PA N-oxides to protect themselves against predators, which cannot cope with the toxic PAs. Despite a high degree of sequence identity and a similar substrate spectrum, the three ZvFMO isoforms differ greatly in enzyme activity. Here, the crystal structure of the Z. variegatus PA N-oxygenase (ZvPNO), the most active ZvFMO isoform, is reported at 1.6 Å resolution together with kinetic studies of a second isoform, ZvFMOa. This is the first available crystal structure of an FMO from class B (of six different FMO subclasses, A-F) within the family of flavin-dependent monooxygenases that originates from a more highly developed organism than yeast. Despite the differences in sequence between family members, their overall structure is very similar. This indicates the need for high conservation of the three-dimensional structure for this type of reaction throughout all kingdoms of life. Nevertheless, this structure provides the closest relative to the human enzyme that is currently available for modelling studies. Of note, the crystal structure of ZvPNO reveals a unique dimeric arrangement as well as small conformational changes within the active site that have not been observed before. A newly observed kink within helix α8 close to the substrate-binding path might indicate a potential mechanism for product release. The data show that even single amino-acid exchanges in the substrate-entry path, rather than the binding site, have a significant impact on the specific enzyme activity of the isoforms.


    Organizational Affiliation

    Structural Biology, Zoological Institute, Kiel University, Am Botanischen Garten 1-9, 24118 Kiel, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Flavin-containing monooxygenase
A, B, C, D
425Zonocerus variegatusMutation(s): 0 
Gene Names: pno
EC: 1.-.-.-
Find proteins for L0N8S9 (Zonocerus variegatus)
Go to UniProtKB:  L0N8S9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B, C, D
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B, C, D
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.174 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 74.076α = 71.81
b = 76.082β = 81.64
c = 81.669γ = 82.04
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
MOLREPphasing
REFMACrefinement
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-03-28
    Type: Derived calculations
  • Version 1.2: 2018-05-09
    Type: Data collection, Database references