2ivd
From Proteopedia
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|PDB= 2ivd |SIZE=350|CAPTION= <scene name='initialview01'>2ivd</scene>, resolution 2.30Å | |PDB= 2ivd |SIZE=350|CAPTION= <scene name='initialview01'>2ivd</scene>, resolution 2.30Å | ||
|SITE= <scene name='pdbsite=AC1:Twn+Binding+Site+For+Chain+B'>AC1</scene> | |SITE= <scene name='pdbsite=AC1:Twn+Binding+Site+For+Chain+B'>AC1</scene> | ||
| - | |LIGAND= <scene name='pdbligand=ACJ:5-[2-CHLORO-4-(TRIFLUOROMETHYL)PHENOXY]-2-NITROBENZOIC+ACID'>ACJ</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=TWN:(3S)-3-[(2S,3S,4R)-3,4-DIMETHYLTETRAHYDROFURAN-2-YL]BUTYL+LAURATE'>TWN</scene> | + | |LIGAND= <scene name='pdbligand=ACJ:5-[2-CHLORO-4-(TRIFLUOROMETHYL)PHENOXY]-2-NITROBENZOIC+ACID'>ACJ</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TWN:(3S)-3-[(2S,3S,4R)-3,4-DIMETHYLTETRAHYDROFURAN-2-YL]BUTYL+LAURATE'>TWN</scene> |
| - | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Protoporphyrinogen_oxidase Protoporphyrinogen oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.3.4 1.3.3.4] </span> | |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ivd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ivd OCA], [http://www.ebi.ac.uk/pdbsum/2ivd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2ivd RCSB]</span> | ||
}} | }} | ||
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[[Category: Mohan, C G.]] | [[Category: Mohan, C G.]] | ||
[[Category: Sturrock, E D.]] | [[Category: Sturrock, E D.]] | ||
| - | [[Category: ACJ]] | ||
| - | [[Category: FAD]] | ||
| - | [[Category: GOL]] | ||
| - | [[Category: TWN]] | ||
[[Category: acifluorfen]] | [[Category: acifluorfen]] | ||
[[Category: chlorophyll biosynthesis]] | [[Category: chlorophyll biosynthesis]] | ||
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[[Category: protoporphyrinogen oxidase]] | [[Category: protoporphyrinogen oxidase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:49:10 2008'' |
Revision as of 00:49, 31 March 2008
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| , resolution 2.30Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | |||||||
| Ligands: | , , , | ||||||
| Activity: | Protoporphyrinogen oxidase, with EC number 1.3.3.4 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
STRUCTURE OF PROTOPORPHYRINOGEN OXIDASE FROM MYXOCOCCUS XANTHUS WITH ACIFLUORFEN
Overview
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.
About this Structure
2IVD is a Single protein structure of sequence from Myxococcus xanthus. Full crystallographic information is available from OCA.
Reference
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
Page seeded by OCA on Mon Mar 31 03:49:10 2008
Categories: Myxococcus xanthus | Protoporphyrinogen oxidase | Single protein | Acharya, K R. | Boix, E. | Corradi, H R. | Corrigall, A V. | Meissner, P N. | Mohan, C G. | Sturrock, E D. | Acifluorfen | Chlorophyll biosynthesis | Fad | Flavoprotein | Haem biosynthesis | Heme biosynthesis | Oxidoreductase | Porphyria | Porphyrin biosynthesis
