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5k3j

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==Crystals structure of Acyl-CoA oxidase-2 in Caenorhabditis elegans bound with FAD, ascaroside-CoA, and ATP==
==Crystals structure of Acyl-CoA oxidase-2 in Caenorhabditis elegans bound with FAD, ascaroside-CoA, and ATP==
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<StructureSection load='5k3j' size='340' side='right' caption='[[5k3j]], [[Resolution|resolution]] 2.68&Aring;' scene=''>
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<StructureSection load='5k3j' size='340' side='right'caption='[[5k3j]], [[Resolution|resolution]] 2.68&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5k3j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K3J FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5k3j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K3J FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6QA:~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL-3-PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]OXY-OXIDANYL-PHOSPHORYL]OXY-3,3-DIMETHYL-2-OXIDANYL-BUTANOYL]AMINO]PROPANOYLAMINO]ETHYL]+5-[(2~{R},3~{R},5~{R},6~{S})-6-METHYL-3,5-BIS(OXIDANYL)OXAN-2-YL]OXYPENTANETHIOATE'>6QA</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.68&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5k3g|5k3g]], [[5k3h|5k3h]], [[5k3i|5k3i]]</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=6QA:~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL-3-PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]OXY-OXIDANYL-PHOSPHORYL]OXY-3,3-DIMETHYL-2-OXIDANYL-BUTANOYL]AMINO]PROPANOYLAMINO]ETHYL]+5-[(2~{R},3~{R},5~{R},6~{S})-6-METHYL-3,5-BIS(OXIDANYL)OXAN-2-YL]OXYPENTANETHIOATE'>6QA</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<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=5k3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3j OCA], [http://pdbe.org/5k3j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k3j RCSB], [http://www.ebi.ac.uk/pdbsum/5k3j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3j ProSAT]</span></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=5k3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3j OCA], [https://pdbe.org/5k3j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k3j RCSB], [https://www.ebi.ac.uk/pdbsum/5k3j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3j 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/ACX12_CAEEL ACX12_CAEEL] Involved in the first step of peroxisomal beta-oxidation by catalyzing the desaturation of fatty acid-derived side chains of ascaroside pheromones, which regulates development and behavior (PubMed:25775534, PubMed:27551084). Specifically, shortens ascarosides with 5-carbon omega side chain (asc-omega-C5) (PubMed:25775534, PubMed:27551084). Does not shorten indol-3-carbonyl(IC)-ascaroside with 7-carbon or 9-carbon side chains (PubMed:29863473). Does not catalyze the desaturation of fatty acids or hydroxylated fatty acids (PubMed:25775534, PubMed:27551084).<ref>PMID:25775534</ref> <ref>PMID:27551084</ref> <ref>PMID:29863473</ref>
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Caenorhabditis elegans secretes ascarosides as pheromones to communicate with other worms and to coordinate the development and behavior of the population. Peroxisomal beta-oxidation cycles shorten the side chains of ascaroside precursors to produce the short-chain ascaroside pheromones. Acyl-CoA oxidases, which catalyze the first step in these beta-oxidation cycles, have different side chain-length specificities and enable C. elegans to regulate the production of specific ascaroside pheromones. Here, we determine the crystal structure of the acyl-CoA oxidase 1 (ACOX-1) homodimer and the ACOX-2 homodimer bound to its substrate. Our results provide a molecular basis for the substrate specificities of the acyl-CoA oxidases and reveal why some of these enzymes have a very broad substrate range, whereas others are quite specific. Our results also enable predictions to be made for the roles of uncharacterized acyl-CoA oxidases in C. elegans and in other nematode species. Remarkably, we show that most of the C. elegans acyl-CoA oxidases that participate in ascaroside biosynthesis contain a conserved ATP-binding pocket that lies at the dimer interface, and we identify key residues in this binding pocket. ATP binding induces a structural change that is associated with tighter binding of the FAD cofactor. Mutations that disrupt ATP binding reduce FAD binding and reduce enzyme activity. Thus, ATP may serve as a regulator of acyl-CoA oxidase activity, thereby directly linking ascaroside biosynthesis to ATP concentration and metabolic state.
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Structural characterization of acyl-CoA oxidases reveals a direct link between pheromone biosynthesis and metabolic state in Caenorhabditis elegans.,Zhang X, Li K, Jones RA, Bruner SD, Butcher RA Proc Natl Acad Sci U S A. 2016 Sep 6;113(36):10055-60. doi:, 10.1073/pnas.1608262113. Epub 2016 Aug 22. PMID:27551084<ref>PMID:27551084</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 5k3j" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bruner, S D]]
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[[Category: Caenorhabditis elegans]]
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[[Category: Butcher, R A]]
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[[Category: Large Structures]]
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[[Category: Jones, R A]]
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[[Category: Bruner SD]]
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[[Category: Li, K]]
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[[Category: Butcher RA]]
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[[Category: Zhang, X]]
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[[Category: Jones RA]]
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[[Category: Ascaroside]]
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[[Category: Li K]]
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[[Category: Atp]]
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[[Category: Zhang X]]
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[[Category: B-oxidation]]
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[[Category: Crystal structure]]
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[[Category: Dauer pheromone]]
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[[Category: Oxidoreductase]]
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Current revision

Crystals structure of Acyl-CoA oxidase-2 in Caenorhabditis elegans bound with FAD, ascaroside-CoA, and ATP

PDB ID 5k3j

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