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3o3m

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<StructureSection load='3o3m' size='340' side='right'caption='[[3o3m]], [[Resolution|resolution]] 1.82&Aring;' scene=''>
<StructureSection load='3o3m' size='340' side='right'caption='[[3o3m]], [[Resolution|resolution]] 1.82&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3o3m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_difficilis"_hall_and_o'toole_1935 "bacillus difficilis" hall and o'toole 1935]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O3M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O3M FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3o3m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridioides_difficile Clostridioides difficile]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O3M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O3M 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=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.82&#8491;</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;'>[[3o3n|3o3n]], [[3o3o|3o3o]]</div></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=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hadB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1496 "Bacillus difficilis" Hall and O'Toole 1935]), hadC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1496 "Bacillus difficilis" Hall and O'Toole 1935])</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=3o3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o3m OCA], [https://pdbe.org/3o3m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o3m RCSB], [https://www.ebi.ac.uk/pdbsum/3o3m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o3m 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=3o3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o3m OCA], [https://pdbe.org/3o3m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o3m RCSB], [https://www.ebi.ac.uk/pdbsum/3o3m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o3m 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/HADB_CLODI HADB_CLODI] Involved in the reductive branch of L-leucine fermentation. Catalyzes the irreversible beta/alpha-elimination of water from (R)-2-hydroxyisocaproyl-CoA to yield isocaprenoyl-CoA. This beta/alpha-dehydration depends on the reductive formation of ketyl radicals on the substrate generated by injection of a single electron from the ATP-dependent activator protein HadI. The enzyme is specific for the R-isomer.<ref>PMID:15654892</ref> <ref>PMID:21366233</ref>
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The radical enzyme (R)-2-hydroxyisocaproyl-CoA dehydratase catalyzes the dehydration of (R)-2-hydroxyisocaproyl-CoA in the fermentation of l-leucine by the human pathogenic bacterium Clostridium difficile. In contrast to other radical enzymes, such as bacterial class II ribonucleotide reductase or biotin synthase, the Fe/S cluster containing (R)-2-hydroxyisocaproyl-CoA dehydratase requires no special cofactors such as coenzyme B(12) or S-adenosylmethionine for radical generation. Instead it uses a single high-energy electron that is recycled after each turnover. The catalyzed reaction, an atypical alpha/beta-dehydration, depends on the reductive formation of ketyl radicals on the substrate generated by injection of a single electron from the ATP-dependent activator protein. So far, it is unknown how the active electron is recycled and how unwanted side reactions are prevented, allowing for up to 10 000 turnovers. The crystal structure reveals that the heterodimeric protein contains two [4Fe-4S] clusters at a distance of 12 A, each coordinated by three cysteines and one terminal ligand. The cluster in the alpha-subunit is part of the active site. In the absence of substrate, a water/hydroxide ion acts as the fourth ligand. The substrate replaces this ligand and coordinates the cluster via the carbonyl-oxygen of the thioester group. The cluster in the beta-subunit has a terminal sulfhydryl/sulfido ligand and can act as a reservoir to protect the electron from unwanted side reactions via a recycling mechanism. The crystal structure of (R)-2-hydroxyisocaproyl-CoA dehydratase serves as a model for the reductively radical-generating metalloenzymes of the (R)-2-hydroxyacyl-CoA dehydratase and benzoyl-CoA reductase families.
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Structural Basis for Reductive Radical Formation and Electron Recycling in (R)-2-Hydroxyisocaproyl-CoA Dehydratase.,Knauer SH, Buckel W, Dobbek H J Am Chem Soc. 2011 Mar 2. PMID:21366233<ref>PMID:21366233</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 3o3m" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bacillus difficilis hall and o'toole 1935]]
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[[Category: Clostridioides difficile]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Buckel, W]]
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[[Category: Buckel W]]
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[[Category: Dobbek, H]]
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[[Category: Dobbek H]]
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[[Category: Knauer, S H]]
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[[Category: Knauer SH]]
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[[Category: Atypical dehydratase]]
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[[Category: Lyase]]
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Current revision

(R)-2-Hydroxyisocaproyl-CoA Dehydratase

PDB ID 3o3m

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