2IVD

Structure of protoporphyrinogen oxidase from Myxococcus xanthus with acifluorfen

Summary for 2IVD

• Entry DOI: 10.2210/pdb2ivd/pdb
• Related: 2IVE
• Descriptor: PROTOPORPHYRINOGEN OXIDASE, 5-[2-CHLORO-4-(TRIFLUOROMETHYL)PHENOXY]-2-NITROBENZOIC ACID, FLAVIN-ADENINE DINUCLEOTIDE, ... (6 entities in total)
• Functional Keywords: protoporphyrinogen oxidase, porphyrin biosynthesis, chlorophyll biosynthesis, oxidoreductase, haem biosynthesis, heme biosynthesis, fad, porphyria, acifluorfen, flavoprotein
• Biological source: MYXOCOCCUS XANTHUS
• Cellular location: Cytoplasm: P56601
• Total number of polymer chains: 2
• Total formula weight: 103902.58

Authors

Corradi, H.R.,Corrigall, A.V.,Boix, E.,Mohan, C.G.,Sturrock, E.D.,Meissner, P.N.,Acharya, K.R. (deposition date: 2006-06-12, release date: 2006-10-17, Last modification date: 2024-05-08)

Primary citation

Corradi, H.R.,Corrigall, A.V.,Boix, E.,Mohan, C.G.,Sturrock, E.D.,Meissner, P.N.,Acharya, K.R.
Crystal Structure of Protoporphyrinogen Oxidase from Myxococcus Xanthus and its Complex with the Inhibitor Acifluorfen.
J.Biol.Chem., 281:38625-, 2006

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 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.

PubMed: 17046834
DOI: 10.1074/JBC.M606640200

Experimental method

X-RAY DIFFRACTION (2.3 Å)