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3oum

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Current revision (11:18, 21 February 2024) (edit) (undo)
 
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<StructureSection load='3oum' size='340' side='right'caption='[[3oum]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='3oum' size='340' side='right'caption='[[3oum]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3oum]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"aerobacillus_polymyxa"_(prazmowski_1880)_donker_1926 "aerobacillus polymyxa" (prazmowski 1880) donker 1926]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OUM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OUM FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3oum]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenibacillus_polymyxa Paenibacillus polymyxa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OUM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OUM FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TOF:1,6-DIMETHYLPYRIMIDO[5,4-E][1,2,4]TRIAZINE-5,7(1H,6H)-DIONE'>TOF</scene></td></tr>
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</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&#8491;</td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=TOF:1,6-DIMETHYLPYRIMIDO[5,4-E][1,2,4]TRIAZINE-5,7(1H,6H)-DIONE'>TOF</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3oul|3oul]]</div></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3oum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oum OCA], [https://pdbe.org/3oum PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3oum RCSB], [https://www.ebi.ac.uk/pdbsum/3oum PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3oum ProSAT]</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=3oum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oum OCA], [https://pdbe.org/3oum PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3oum RCSB], [https://www.ebi.ac.uk/pdbsum/3oum PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3oum ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/E3SET7_PAEPO E3SET7_PAEPO]
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Pathogenic bacteria synthesize and secrete toxic low molecular weight compounds as virulence factors. These microbial toxins play essential roles in the pathogenicity of bacteria in various hosts, and are emerging as targets for antivirulence strategies. Toxoflavin, a phytotoxin produced by Burkholderia glumae BGR1, has been known to be the key factor in rice grain rot and wilt in many field crops. Recently, toxoflavin-degrading enzyme (TxDE) was identified from Paenibacillus polymyxa JH2, thereby providing a possible antivirulence strategy for toxoflavin-mediated plant diseases. Here, we report the crystal structure of TxDE in the substrate-free form and in complex with toxoflavin, along with the results of a functional analysis. The overall structure of TxDE is similar to those of the vicinal oxygen chelate superfamily of metalloenzymes, despite the lack of apparent sequence identity. The active site is located at the end of the hydrophobic channel, 9 A in length, and contains a Mn(II) ion interacting with one histidine residue, two glutamate residues, and three water molecules in an octahedral coordination. In the complex, toxoflavin binds in the hydrophobic active site, specifically the Mn(II)-coordination shell by replacing a ligating water molecule. A functional analysis indicated that TxDE catalyzes the degradation of toxoflavin in a manner dependent on oxygen, Mn(II), and the reducing agent dithiothreitol. These results provide the structural features of TxDE and the early events in catalysis.
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Structural and functional analysis of phytotoxin toxoflavin-degrading enzyme.,Jung WS, Lee J, Kim MI, Ma J, Nagamatsu T, Goo E, Kim H, Hwang I, Han J, Rhee S PLoS One. 2011;6(7):e22443. Epub 2011 Jul 25. PMID:21799856<ref>PMID:21799856</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3oum" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Kim, M I]]
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[[Category: Paenibacillus polymyxa]]
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[[Category: Rhee, S]]
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[[Category: Kim MI]]
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[[Category: Paenibacillus polymyxa jh2]]
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[[Category: Rhee S]]
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[[Category: Phytotoxin-degrading enzyme]]
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[[Category: Toxoflavin]]
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[[Category: Toxoflavin binding protein]]
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[[Category: Toxoflavin-degrading enzyme]]
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Current revision

Crystal Structure of toxoflavin-degrading enzyme in complex with toxoflavin

PDB ID 3oum

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