This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1sez

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:31, 1 May 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1sez.jpg|left|200px]]
 
-
{{Structure
+
==Crystal Structure of Protoporphyrinogen IX Oxidase==
-
|PDB= 1sez |SIZE=350|CAPTION= <scene name='initialview01'>1sez</scene>, resolution 2.90&Aring;
+
<StructureSection load='1sez' size='340' side='right'caption='[[1sez]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=OMN:4-BROMO-3-(5'-CARBOXY-4'-CHLORO-2'-FLUOROPHENYL)-1-METHYL-5-TRIFLUOROMETHYL-PYRAZOL'>OMN</scene> and <scene name='pdbligand=TON:2-{2-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENOXY]ETHOXY}ETHANOL'>TON</scene>
+
<table><tr><td colspan='2'>[[1sez]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Nicotiana_tabacum Nicotiana tabacum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SEZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SEZ FirstGlance]. <br>
-
|ACTIVITY= [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]
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
-
|GENE= PPXII, PPOX2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4097 Nicotiana tabacum])
+
<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=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=OMN:4-BROMO-3-(5-CARBOXY-4-CHLORO-2-FLUOROPHENYL)-1-METHYL-5-TRIFLUOROMETHYL-PYRAZOL'>OMN</scene>, <scene name='pdbligand=TON:2-{2-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENOXY]ETHOXY}ETHANOL'>TON</scene></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=1sez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sez OCA], [https://pdbe.org/1sez PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sez RCSB], [https://www.ebi.ac.uk/pdbsum/1sez PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sez ProSAT]</span></td></tr>
-
 
+
</table>
-
'''Crystal Structure of Protoporphyrinogen IX Oxidase'''
+
== Function ==
-
 
+
[https://www.uniprot.org/uniprot/PPOM_TOBAC PPOM_TOBAC] Catalyzes the 6-electron oxidation of protoporphyrinogen-IX to form protoporphyrin-IX.<ref>PMID:9238074</ref> Provides precursor for the mitochondrial and plastidic heme synthesis and the predominant chlorophyll synthesis in plastids.<ref>PMID:9238074</ref>
-
 
+
== Evolutionary Conservation ==
-
==Overview==
+
[[Image:Consurf_key_small.gif|200px|right]]
-
Protoporphyrinogen IX oxidase (PPO), the last common enzyme of haem and chlorophyll biosynthesis, catalyses the oxidation of protoporphyrinogen IX to protoporphyrin IX. The membrane-embedded flavoprotein is the target of a large class of herbicides. In humans, a defect in PPO is responsible for the dominantly inherited disease variegate porphyria. Here we present the crystal structure of mitochondrial PPO from tobacco complexed with a phenyl-pyrazol inhibitor. PPO forms a loosely associated dimer and folds into an FAD-binding domain of the p-hydroxybenzoate-hydrolase fold and a substrate-binding domain that enclose a narrow active site cavity beneath the FAD and an alpha-helical membrane-binding domain. The active site architecture suggests a specific substrate-binding mode compatible with the unusual six-electron oxidation. The membrane-binding domains can be docked onto the dimeric structure of human ferrochelatase, the next enzyme in haem biosynthesis, embedded in the opposite side of the membrane. This modelled transmembrane complex provides a structural explanation for the uncoupling of haem biosynthesis observed in variegate porphyria patients and in plants after inhibiting PPO.
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==About this Structure==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/se/1sez_consurf.spt"</scriptWhenChecked>
-
1SEZ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Nicotiana_tabacum Nicotiana tabacum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SEZ OCA].
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==Reference==
+
</jmolCheckbox>
-
Crystal structure of protoporphyrinogen IX oxidase: a key enzyme in haem and chlorophyll biosynthesis., Koch M, Breithaupt C, Kiefersauer R, Freigang J, Huber R, Messerschmidt A, EMBO J. 2004 Apr 21;23(8):1720-8. Epub 2004 Apr 1. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15057273 15057273]
+
</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=1sez ConSurf].
 +
<div style="clear:both"></div>
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Nicotiana tabacum]]
[[Category: Nicotiana tabacum]]
-
[[Category: Protoporphyrinogen oxidase]]
+
[[Category: Breithaupt C]]
-
[[Category: Single protein]]
+
[[Category: Freigang J]]
-
[[Category: Breithaupt, C.]]
+
[[Category: Huber R]]
-
[[Category: Freigang, J.]]
+
[[Category: Kiefersauer R]]
-
[[Category: Huber, R.]]
+
[[Category: Koch M]]
-
[[Category: Kiefersauer, R.]]
+
[[Category: Messerschmidt A]]
-
[[Category: Koch, M.]]
+
-
[[Category: Messerschmidt, A.]]
+
-
[[Category: FAD]]
+
-
[[Category: OMN]]
+
-
[[Category: TON]]
+
-
[[Category: fad-binding]]
+
-
[[Category: monotopic membrane-binding domain]]
+
-
[[Category: para-hydroxy-benzoate-hydroxylase fold (phbh-fold)]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:04:04 2008''
+

Current revision

Crystal Structure of Protoporphyrinogen IX Oxidase

PDB ID 1sez

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1sez"
Personal tools