This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

5k3i

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of Acyl-CoA oxidase-1 in Caenorhabditis elegans complexed with FAD and ATP

Structural highlights

5k3i is a 8 chain structure with sequence from Caenorhabditis elegans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.683Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ACX11_CAEEL Involved in the first step of peroxisomal beta-oxidation by catalyzing the desaturation of fatty acid-derived side chains (PubMed:25775534, PubMed:29537254, PubMed:27551084). Specifically, catalyzes the desaturation of fatty acids heptanoyl-CoA (C7), nonanoyl-CoA (C9), dodecanoyl-CoA (C12) and to a lesser extent pentanoyl-CoA (C5) and hexadecanoyl-CoA (C16), and hydroxylated fatty acid hydroxynonanoyl-CoA (PubMed:25775534, PubMed:29537254, PubMed:27551084). Also, catalyzes the desaturation fatty acid-derived side chains of ascaroside pheromones, which regulates development and behavior (PubMed:20610393, PubMed:25775534, PubMed:29537254, PubMed:29863473, PubMed:27551084). Specifically, shortens ascaroside with 5-carbon omega side chain (asc-omega-C5), 7-carbon side chain (asc-C7), 9-carbon side chain (asc-C9), 11-carbon side chain (asc-C11), 13-carbon side chain (asc-C13), 15-carbon side chain (asc-C15) and to a lesser extent ascarosides with 7-omega-carbon side chain (asc-omega-C7) (PubMed:25775534, PubMed:29537254, PubMed:27551084). Also shortens indol-3-carbonyl(IC)-ascarosides with 7-carbon side chain (IC-asc-C7) and to a lesser extent (IC)-ascarosides with 9-carbon side chain (IC-asc-C9) (PubMed:29863473). May associate and regulate the folding and/or the catalytic activity of other acyl-coenzyme A oxidases including acox-1.2, acox-1.3, acox-1.4 and acox-3 modulating the type of ascarosides produced (PubMed:25775534, PubMed:29537254, PubMed:29863473). In association with acox-1.3, catalyzes the desaturation of asc-C7-CoA but not of fatty acids or hydroxylated fatty acids (PubMed:25775534). Involved in the biosynthesis of asc-C6-MK (daumone 2) and asc-delta-C9 (daumone 3) but not asc-C7 (daumone 1); daumones are pheromones produced during unfavourable growth conditions which promote entry into the dauer stage (PubMed:20610393).^[1] ^[2] ^[3] ^[4] ^[5]

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^[6]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Joo HJ, Kim KY, Yim YH, Jin YX, Kim H, Kim MY, Paik YK. Contribution of the peroxisomal acox gene to the dynamic balance of daumone production in Caenorhabditis elegans. J Biol Chem. 2010 Sep 17;285(38):29319-25. PMID:20610393 doi:10.1074/jbc.M110.122663
↑ 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
↑ Zhang X, Wang Y, Perez DH, Jones Lipinski RA, Butcher RA. Acyl-CoA Oxidases Fine-Tune the Production of Ascaroside Pheromones with Specific Side Chain Lengths. ACS Chem Biol. 2018 Apr 20;13(4):1048-1056. PMID:29537254 doi:10.1021/acschembio.7b01021
↑ 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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5k3i"

@@ Line 3: / Line 3: @@
 <StructureSection load='5k3i' size='340' side='right'caption='[[5k3i]], [[Resolution|resolution]] 2.68&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5k3i]] is a 8 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=5K3I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K3I FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5k3i]] is a 8 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=5K3I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K3I FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 2.683&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5k3g|5k3g]], [[5k3h|5k3h]], [[5k3j|5k3j]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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-1, CELE_F08A8.1, F08A8.1 ([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=5k3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3i OCA], [https://pdbe.org/5k3i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k3i RCSB], [https://www.ebi.ac.uk/pdbsum/5k3i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3i 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=5k3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3i OCA], [http://pdbe.org/5k3i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k3i RCSB], [http://www.ebi.ac.uk/pdbsum/5k3i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3i ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/ACX11_CAEEL ACX11_CAEEL] Involved in the first step of peroxisomal beta-oxidation by catalyzing the desaturation of fatty acid-derived side chains (PubMed:25775534, PubMed:29537254, PubMed:27551084). Specifically, catalyzes the desaturation of fatty acids heptanoyl-CoA (C7), nonanoyl-CoA (C9), dodecanoyl-CoA (C12) and to a lesser extent pentanoyl-CoA (C5) and hexadecanoyl-CoA (C16), and hydroxylated fatty acid hydroxynonanoyl-CoA (PubMed:25775534, PubMed:29537254, PubMed:27551084). Also, catalyzes the desaturation fatty acid-derived side chains of ascaroside pheromones, which regulates development and behavior (PubMed:20610393, PubMed:25775534, PubMed:29537254, PubMed:29863473, PubMed:27551084). Specifically, shortens ascaroside with 5-carbon omega side chain (asc-omega-C5), 7-carbon side chain (asc-C7), 9-carbon side chain (asc-C9), 11-carbon side chain (asc-C11), 13-carbon side chain (asc-C13), 15-carbon side chain (asc-C15) and to a lesser extent ascarosides with 7-omega-carbon side chain (asc-omega-C7) (PubMed:25775534, PubMed:29537254, PubMed:27551084). Also shortens indol-3-carbonyl(IC)-ascarosides with 7-carbon side chain (IC-asc-C7) and to a lesser extent (IC)-ascarosides with 9-carbon side chain (IC-asc-C9) (PubMed:29863473). May associate and regulate the folding and/or the catalytic activity of other acyl-coenzyme A oxidases including acox-1.2, acox-1.3, acox-1.4 and acox-3 modulating the type of ascarosides produced (PubMed:25775534, PubMed:29537254, PubMed:29863473). In association with acox-1.3, catalyzes the desaturation of asc-C7-CoA but not of fatty acids or hydroxylated fatty acids (PubMed:25775534). Involved in the biosynthesis of asc-C6-MK (daumone 2) and asc-delta-C9 (daumone 3) but not asc-C7 (daumone 1); daumones are pheromones produced during unfavourable growth conditions which promote entry into the dauer stage (PubMed:20610393).<ref>PMID:20610393</ref> <ref>PMID:25775534</ref> <ref>PMID:27551084</ref> <ref>PMID:29537254</ref> <ref>PMID:29863473</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Caeel]]
+[[Category: Caenorhabditis elegans]]
 [[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: Dauer pheromone]]
-[[Category: Oxidoreductase]]

5k3i

From Proteopedia

Current revision

Crystal structure of Acyl-CoA oxidase-1 in Caenorhabditis elegans complexed with FAD and ATP

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox