3i6d
From Proteopedia
(Difference between revisions)
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<StructureSection load='3i6d' size='340' side='right'caption='[[3i6d]], [[Resolution|resolution]] 2.90Å' scene=''> | <StructureSection load='3i6d' size='340' side='right'caption='[[3i6d]], [[Resolution|resolution]] 2.90Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[3i6d]] is a 2 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[3i6d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I6D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I6D FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=PO4:PHOSPHATE+ION'>PO4</scene | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9Å</td></tr> |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=PO4:PHOSPHATE+ION'>PO4</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=3i6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i6d OCA], [https://pdbe.org/3i6d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i6d RCSB], [https://www.ebi.ac.uk/pdbsum/3i6d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i6d ProSAT]</span></td></tr> | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | |
</table> | </table> | ||
== Function == | == Function == | ||
| - | [ | + | [https://www.uniprot.org/uniprot/CGOX_BACSU CGOX_BACSU] Involved in coproporphyrin-dependent heme b biosynthesis (PubMed:7928957, PubMed:9217019). Catalyzes the oxidation of coproporphyrinogen III to coproporphyrin III (PubMed:8288631, PubMed:7928957, PubMed:9217019, PubMed:9784236). Can also oxidize protoporphyrinogen IX to protoporphyrin-IX (PubMed:8288631, PubMed:7928957, PubMed:9217019, PubMed:9784236, PubMed:19944166). The specific activity for the oxidation of coproporphyrinogen III is much higher than that for the oxidation of protoporphyrinogen IX (PubMed:7928957, PubMed:9217019). Can also oxidize mesoporphyrinogen IX, but not uroporphyrinogen III (PubMed:8288631, PubMed:9784236, PubMed:7928957).<ref>PMID:19944166</ref> <ref>PMID:7928957</ref> <ref>PMID:8288631</ref> <ref>PMID:9217019</ref> <ref>PMID:9784236</ref> |
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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</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=3i6d 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=3i6d ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | Protoporphyrinogen IX oxidase (PPO) converts protoporphyrinogen IX to protoporphyrin IX, playing an important part in the heme/chlorophyll biosynthetic pathway. Bacillus subtilis PPO (bsPPO) is unique among PPO family members in that it is a soluble monomer, is inefficiently inhibited by the herbicide acifluorfen (AF) and has broader substrate specificity than other PPO enzymes. Here, we present the crystal structure of bsPPO bound to AF. Our structure shows that the AF molecule binds to a new site outside the previously identified inhibitor binding pocket. Most importantly, the benzene ring of the 2-nitrobenzoic acid moiety of AF lies parallel to the isoalloxazine ring of FAD at a distance of less than 3.5A, providing a framework for the interaction of FAD with the substrate protoporphyrinogen IX. Furthermore, our structure reveals that the larger substrate binding chamber and predominantly positively charged chamber surface of bsPPO are more favorable for the binding of coproporphyrinogen-III. These crystallographic findings uncover biochemically unique properties of bsPPO, providing important information for further understanding the enzymatic mechanism. | ||
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| - | Structural insight into unique properties of protoporphyrinogen oxidase from Bacillus subtilis.,Qin X, Sun L, Wen X, Yang X, Tan Y, Jin H, Cao Q, Zhou W, Xi Z, Shen Y J Struct Biol. 2010 Apr;170(1):76-82. Epub 2009 Nov 26. PMID:19944166<ref>PMID:19944166</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 3i6d" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: | + | [[Category: Bacillus subtilis]] |
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | + | [[Category: Shen Y]] | |
| - | [[Category: Shen | + | |
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Current revision
Crystal structure of PPO from bacillus subtilis with AF
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