3I6D

Crystal structure of PPO from bacillus subtilis with AF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.272 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1016/j.jsb.2009.11.012

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protoporphyrinogen oxidase
A, B
470Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: hemY (hemG)
EC: 1.3.3.4
Find proteins for P32397 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P32397
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
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
ACJ
Query on ACJ

Download SDF File 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.272 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 96.175α = 90.00
b = 96.175β = 90.00
c = 299.823γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SHELXSphasing
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-07-06 
  • Released Date: 2009-12-08 
  • Deposition Author(s): Shen, Y.

Revision History 

  • Version 1.0: 2009-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-02-19
    Type: Database references