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| | <StructureSection load='5k3j' size='340' side='right'caption='[[5k3j]], [[Resolution|resolution]] 2.68Å' scene=''> | | <StructureSection load='5k3j' size='340' side='right'caption='[[5k3j]], [[Resolution|resolution]] 2.68Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5k3j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Caeel Caeel]. 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> | + | <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> |
| - | </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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.68Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5k3g|5k3g]], [[5k3h|5k3h]], [[5k3i|5k3i]]</td></tr>
| + | <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> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">acox-2, CELE_F08A8.2, F08A8.2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6239 CAEEL])</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=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> |
| - | <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> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [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> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Caeel]] | + | [[Category: Caenorhabditis elegans]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bruner, S D]] | + | [[Category: Bruner SD]] |
| - | [[Category: Butcher, R A]] | + | [[Category: Butcher RA]] |
| - | [[Category: Jones, R A]] | + | [[Category: Jones RA]] |
| - | [[Category: Li, K]] | + | [[Category: Li K]] |
| - | [[Category: Zhang, X]] | + | [[Category: Zhang X]] |
| - | [[Category: Ascaroside]]
| + | |
| - | [[Category: Atp]]
| + | |
| - | [[Category: B-oxidation]]
| + | |
| - | [[Category: Crystal structure]]
| + | |
| - | [[Category: Dauer pheromone]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
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).[1] [2] [3]
Publication Abstract from PubMed
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.
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[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Zhang X, Feng L, Chinta S, Singh P, Wang Y, Nunnery JK, Butcher RA. Acyl-CoA oxidase complexes control the chemical message produced by Caenorhabditis elegans. Proc Natl Acad Sci U S A. 2015 Mar 31;112(13):3955-60. PMID:25775534 doi:10.1073/pnas.1423951112
- ↑ Zhang X, Li K, Jones RA, Bruner SD, Butcher RA. Structural characterization of acyl-CoA oxidases reveals a direct link between pheromone biosynthesis and metabolic state in Caenorhabditis elegans. 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 doi:http://dx.doi.org/10.1073/pnas.1608262113
- ↑ Zhou Y, Wang Y, Zhang X, Bhar S, Jones Lipinski RA, Han J, Feng L, Butcher RA. Biosynthetic tailoring of existing ascaroside pheromones alters their biological function in C. elegans. Elife. 2018 Jun 4;7:e33286. PMID:29863473 doi:10.7554/eLife.33286
- ↑ Zhang X, Li K, Jones RA, Bruner SD, Butcher RA. Structural characterization of acyl-CoA oxidases reveals a direct link between pheromone biosynthesis and metabolic state in Caenorhabditis elegans. 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 doi:http://dx.doi.org/10.1073/pnas.1608262113
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