Crystal structure of PPO from bacillus subtilis with AF

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.272 
  • R-Value Observed: 0.272 

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Structural insight into unique properties of protoporphyrinogen oxidase from Bacillus subtilis

Qin, X.Sun, L.Wen, X.Yang, X.Tan, Y.Jin, H.Cao, Q.Zhou, W.Xi, Z.Shen, Y.

(2010) J Struct Biol 170: 76-82

  • DOI: https://doi.org/10.1016/j.jsb.2009.11.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Protoporphyrinogen IX oxidase (PPO) converts protoporphyrinogen IX to protoporphyrin IX, playing an important part in the heme/chlorophyll biosynthetic pathway. Bacillus subtilis PPO (bsPPO) is unique among PPO family members in that it is a soluble monomer, is inefficiently inhibited by the herbicide acifluorfen (AF) and has broader substrate specificity than other PPO enzymes. Here, we present the crystal structure of bsPPO bound to AF. Our structure shows that the AF molecule binds to a new site outside the previously identified inhibitor binding pocket. Most importantly, the benzene ring of the 2-nitrobenzoic acid moiety of AF lies parallel to the isoalloxazine ring of FAD at a distance of less than 3.5A, providing a framework for the interaction of FAD with the substrate protoporphyrinogen IX. Furthermore, our structure reveals that the larger substrate binding chamber and predominantly positively charged chamber surface of bsPPO are more favorable for the binding of coproporphyrinogen-III. These crystallographic findings uncover biochemically unique properties of bsPPO, providing important information for further understanding the enzymatic mechanism.

  • Organizational Affiliation

    Tianjin Key Laboratory of Protein Science, College of Life Science, Nankai University, Tianjin 300071, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protoporphyrinogen oxidase
A, B
470Bacillus subtilisMutation(s): 0 
Find proteins for P32397 (Bacillus subtilis (strain 168))
Explore P32397 
Go to UniProtKB:  P32397
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32397
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.272 
  • R-Value Observed: 0.272 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.175α = 90
b = 96.175β = 90
c = 299.823γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2009-12-08 
  • Deposition Author(s): Shen, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-02-19
    Changes: Database references
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Derived calculations