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2ive

From Proteopedia

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Current revision

Structure of protoporphyrinogen oxidase from Myxococcus xanthus

Structural highlights

2ive 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 2.7Å
Ligands:	, ,
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).^[1] ^[2]

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^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Dailey HA, Dailey TA. Protoporphyrinogen oxidase of Myxococcus xanthus. Expression, purification, and characterization of the cloned enzyme. J Biol Chem. 1996 Apr 12;271(15):8714-8. PMID:8621504 doi:10.1074/jbc.271.15.8714
↑ Dailey HA, Dailey TA, Gerdes S, Jahn D, Jahn M, O'Brian MR, Warren MJ. Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product. Microbiol Mol Biol Rev. 2017 Jan 25;81(1):e00048-16. PMID:28123057 doi:10.1128/MMBR.00048-16
↑ Corradi HR, Corrigall AV, Boix E, Mohan CG, Sturrock ED, Meissner PN, Acharya KR. Crystal structure of protoporphyrinogen oxidase from Myxococcus xanthus and its complex with the inhibitor acifluorfen. J Biol Chem. 2006 Dec 15;281(50):38625-33. Epub 2006 Oct 17. PMID:17046834 doi:http://dx.doi.org/10.1074/jbc.M606640200

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2ive"

@@ Line 1: / Line 1: @@
-==STRUCTURE OF PROTOPORPHYRINOGEN OXIDASE FROM MYXOCOCCUS XANTHUS==
-<StructureSection load='2ive' size='340' side='right' caption='[[2ive]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+==Structure of protoporphyrinogen oxidase from Myxococcus xanthus==
+<StructureSection load='2ive' size='340' side='right'caption='[[2ive]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2ive]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25232 Atcc 25232]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IVE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IVE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2ive]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Myxococcus_xanthus Myxococcus xanthus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IVE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IVE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2ivd|2ivd]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ive FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ive OCA], [http://pdbe.org/2ive PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ive RCSB], [http://www.ebi.ac.uk/pdbsum/2ive PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ive FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ive OCA], [https://pdbe.org/2ive PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ive RCSB], [https://www.ebi.ac.uk/pdbsum/2ive PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ive ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PGOX_MYXXA 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).<ref>PMID:8621504</ref> <ref>PMID:28123057</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iv/2ive_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iv/2ive_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ive ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 30: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 25232]]
+[[Category: Large Structures]]
-[[Category: Acharya, K R]]
+[[Category: Myxococcus xanthus]]
-[[Category: Boix, E]]
+[[Category: Acharya KR]]
-[[Category: Corradi, H R]]
+[[Category: Boix E]]
-[[Category: Corrigall, A V]]
+[[Category: Corradi HR]]
-[[Category: Meissner, P N]]
+[[Category: Corrigall AV]]
-[[Category: Mohan, C G]]
+[[Category: Meissner PN]]
-[[Category: Sturrock, E D]]
+[[Category: Mohan CG]]
-[[Category: Chlorophyll biosynthesis]]
+[[Category: Sturrock ED]]
-[[Category: Fad]]
-[[Category: Flavoprotein]]
-[[Category: Haem biosynthesis]]
-[[Category: Heme biosynthesis]]
-[[Category: Oxidoreductase]]
-[[Category: Porphyria]]
-[[Category: Porphyrin biosynthesis]]
-[[Category: Protoporphyrinogen oxidase]]

2ive

From Proteopedia

Current revision

Structure of protoporphyrinogen oxidase from Myxococcus xanthus

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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