2ivd

Structure of protoporphyrinogen oxidase from Myxococcus xanthus with acifluorfen

spinqualitylabelsall models 2ivd, resolution 2.30Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2ivd is a 2 chain structure with sequence from Myxococcus xanthus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.3Å Ligands: ACJ, FAD, GOL, TWN Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function PGOX_MYXXA Catalyzes the 6-electron oxidation of protoporphyrinogen-IX to form protoporphyrin-IX (PubMed:8621504). Does not oxidize coproporphyrinogen III (PubMed:8621504). Involved in the classical protoporphyrin-dependent (PPD) heme b biosynthesis (PubMed:28123057). Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed 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. Crystal structure of protoporphyrinogen oxidase from Myxococcus xanthus and its complex with the inhibitor acifluorfen.,Corradi HR, Corrigall AV, Boix E, Mohan CG, Sturrock ED, Meissner PN, Acharya KR J Biol Chem. 2006 Dec 15;281(50):38625-33. Epub 2006 Oct 17. PMID:17046834 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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