3I6D

Crystal structure of PPO from bacillus subtilis with AF

Summary for 3I6D

• Entry DOI: 10.2210/pdb3i6d/pdb
• Related: 1SEZ
• Descriptor: Protoporphyrinogen oxidase, FLAVIN-ADENINE DINUCLEOTIDE, 5-[2-CHLORO-4-(TRIFLUOROMETHYL)PHENOXY]-2-NITROBENZOIC ACID, ... (5 entities in total)
• Functional Keywords: protein-inhibitor complex, fad, flavoprotein, oxidoreductase, porphyrin biosynthesis
• Biological source: Bacillus subtilis
• Cellular location: Cytoplasm: P32397
• Total number of polymer chains: 2
• Total formula weight: 105023.91

Authors

Shen, Y. (deposition date: 2009-07-06, release date: 2009-12-08, Last modification date: 2024-03-20)

Primary citation

Qin, X.,Sun, L.,Wen, X.,Yang, X.,Tan, Y.,Jin, H.,Cao, Q.,Zhou, W.,Xi, Z.,Shen, Y.
Structural insight into unique properties of protoporphyrinogen oxidase from Bacillus subtilis
J.Struct.Biol., 170:76-82, 2010

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.

PubMed: 19944166
DOI: 10.1016/j.jsb.2009.11.012

Experimental method

X-RAY DIFFRACTION (2.9 Å)