2IVD

Structure of protoporphyrinogen oxidase from Myxococcus xanthus with acifluorfen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Protoporphyrinogen Oxidase from Myxococcus Xanthus and its Complex with the Inhibitor Acifluorfen.

Corradi, H.R.Corrigall, A.V.Boix, E.Mohan, C.G.Sturrock, E.D.Meissner, P.N.Acharya, K.R.

(2006) J.Biol.Chem. 281: 38625

  • DOI: 10.1074/jbc.M606640200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Protoporphyrinogen IX oxidase, a monotopic membrane protein, which catalyzes the oxidation of protoporphyrinogen IX to protoporphyrin IX in the heme/chlorophyll biosynthetic pathway, is distributed widely throughout nature. Here we present the struct ...

    Protoporphyrinogen IX oxidase, a monotopic membrane protein, which catalyzes the oxidation of protoporphyrinogen IX to protoporphyrin IX in the heme/chlorophyll biosynthetic pathway, is distributed widely throughout nature. Here we present the structure of protoporphyrinogen IX oxidase from Myxococcus xanthus, an enzyme with similar catalytic properties to human protoporphyrinogen IX oxidase that also binds the common plant herbicide, acifluorfen. In the native structure, the planar porphyrinogen substrate is mimicked by a Tween 20 molecule, tracing three sides of the macrocycle. In contrast, acifluorfen does not mimic the planarity of the substrate but is accommodated by the shape of the binding pocket and held in place by electrostatic and aromatic interactions. A hydrophobic patch surrounded by positively charged residues suggests the position of the membrane anchor, differing from the one proposed for the tobacco mitochondrial protoporphyrinogen oxidase. Interestingly, there is a discrepancy between the dimerization state of the protein in solution and in the crystal. Conserved structural features are discussed in relation to a number of South African variegate porphyria-causing mutations in the human enzyme.


    Organizational Affiliation

    Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTOPORPHYRINOGEN OXIDASE
A, B
478Myxococcus xanthusMutation(s): 0 
Gene Names: hemY
EC: 1.3.3.4
Find proteins for P56601 (Myxococcus xanthus)
Go to UniProtKB:  P56601
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

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

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACJ
Query on ACJ

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Download CCD File 
A, B
5-[2-CHLORO-4-(TRIFLUOROMETHYL)PHENOXY]-2-NITROBENZOIC ACID
C14 H7 Cl F3 N O5
NUFNQYOELLVIPL-UHFFFAOYSA-N
 Ligand Interaction
TWN
Query on TWN

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Download CCD File 
B
(3S)-3-[(2S,3S,4R)-3,4-DIMETHYLTETRAHYDROFURAN-2-YL]BUTYL LAURATE
C22 H42 O3
TWHGDIVTXKNMOZ-XWUOBKMESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.234 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 148.918α = 90.00
b = 148.918β = 90.00
c = 131.924γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance