3OUM

Crystal Structure of toxoflavin-degrading enzyme in complex with toxoflavin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.219 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Structural and functional analysis of phytotoxin toxoflavin-degrading enzyme

Jung, W.S.Lee, J.Kim, M.I.Ma, J.Nagamatsu, T.Goo, E.Kim, H.Hwang, I.Han, J.Rhee, S.

(2011) PLoS One 6: e22443-e22443

  • DOI: https://doi.org/10.1371/journal.pone.0022443
  • Primary Citation of Related Structures:  
    3OUL, 3OUM

  • PubMed Abstract: 

    Pathogenic bacteria synthesize and secrete toxic low molecular weight compounds as virulence factors. These microbial toxins play essential roles in the pathogenicity of bacteria in various hosts, and are emerging as targets for antivirulence strategies. Toxoflavin, a phytotoxin produced by Burkholderia glumae BGR1, has been known to be the key factor in rice grain rot and wilt in many field crops. Recently, toxoflavin-degrading enzyme (TxDE) was identified from Paenibacillus polymyxa JH2, thereby providing a possible antivirulence strategy for toxoflavin-mediated plant diseases. Here, we report the crystal structure of TxDE in the substrate-free form and in complex with toxoflavin, along with the results of a functional analysis. The overall structure of TxDE is similar to those of the vicinal oxygen chelate superfamily of metalloenzymes, despite the lack of apparent sequence identity. The active site is located at the end of the hydrophobic channel, 9 Å in length, and contains a Mn(II) ion interacting with one histidine residue, two glutamate residues, and three water molecules in an octahedral coordination. In the complex, toxoflavin binds in the hydrophobic active site, specifically the Mn(II)-coordination shell by replacing a ligating water molecule. A functional analysis indicated that TxDE catalyzes the degradation of toxoflavin in a manner dependent on oxygen, Mn(II), and the reducing agent dithiothreitol. These results provide the structural features of TxDE and the early events in catalysis.


  • Organizational Affiliation

    Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
toxoflavin-degrading enzyme232Paenibacillus polymyxaMutation(s): 0 
UniProt
Find proteins for E3SET7 (Paenibacillus polymyxa)
Explore E3SET7 
Go to UniProtKB:  E3SET7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE3SET7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TOF
Query on TOF

Download Ideal Coordinates CCD File 
C [auth A]1,6-dimethylpyrimido[5,4-e][1,2,4]triazine-5,7(1H,6H)-dione
C7 H7 N5 O2
SLGRAIAQIAUZAQ-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.219 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.008α = 90
b = 111.008β = 90
c = 57.438γ = 120
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-10
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description