Structural insight into unique properties of protoporphyrinogen oxidase from Bacillus subtilis.
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.
Qin
Xiaohong
X
Tianjin Key Laboratory of Protein Science, College of Life Science, Nankai University, Tianjin 300071, China.
Sun
Lu
L
Wen
Xin
X
Yang
Xue
X
Tan
Ying
Y
Jin
Hao
H
Cao
Qiongyao
Q
Zhou
Weihong
W
Xi
Zhen
Z
Shen
Yuequan
Y
D001412:Bacillus subtilis / Q000201:enzymology*; D003460:Crystallization; D007700:Kinetics; D008958:Models, Molecular; D015394:Molecular Structure; D016296:Mutagenesis; D009579:Nitrobenzoates / Q000378:metabolism; D011485:Protein Binding; D050768:Protoporphyrinogen Oxidase / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000235:genetics*; D017422:Sequence Analysis, DNA
D009579:Nitrobenzoates; D050768:Protoporphyrinogen Oxidase; C018425:acifluorfen